Starting phenix.real_space_refine on Fri Feb 6 04:30:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vda_31912/02_2026/7vda_31912.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vda_31912/02_2026/7vda_31912.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7vda_31912/02_2026/7vda_31912.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vda_31912/02_2026/7vda_31912.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vda_31912/02_2026/7vda_31912.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vda_31912/02_2026/7vda_31912.map" } resolution = 2.26 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 114 5.16 5 C 14736 2.51 5 N 4074 2.21 5 O 4368 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 66 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23292 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3882 Classifications: {'peptide': 496} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 474} Restraints were copied for chains: B, C, D, E, F Time building chain proxies: 3.61, per 1000 atoms: 0.15 Number of scatterers: 23292 At special positions: 0 Unit cell: (109.85, 117.65, 156.65, 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 114 16.00 O 4368 8.00 N 4074 7.00 C 14736 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: 2.21 Conformation dependent library (CDL) restraints added in 993.1 milliseconds 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5400 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 9 sheets defined 58.5% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 8 through 31 removed outlier: 4.853A pdb=" N ASP A 26 " --> pdb=" O SER A 22 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N LYS A 27 " --> pdb=" O ILE A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 53 Processing helix chain 'A' and resid 100 through 118 Processing helix chain 'A' and resid 132 through 136 Processing helix chain 'A' and resid 137 through 155 removed outlier: 3.530A pdb=" N LYS A 155 " --> pdb=" O GLU A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 186 Processing helix chain 'A' and resid 193 through 198 removed outlier: 4.115A pdb=" N VAL A 198 " --> pdb=" O HIS A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 206 Processing helix chain 'A' and resid 213 through 228 removed outlier: 3.666A pdb=" N PHE A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 237 removed outlier: 3.979A pdb=" N ILE A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 266 removed outlier: 3.572A pdb=" N PHE A 266 " --> pdb=" O TYR A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 299 Processing helix chain 'A' and resid 313 through 317 removed outlier: 3.946A pdb=" N VAL A 317 " --> pdb=" O ILE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 339 removed outlier: 3.605A pdb=" N VAL A 339 " --> pdb=" O ALA A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 363 Processing helix chain 'A' and resid 369 through 374 Processing helix chain 'A' and resid 375 through 391 Processing helix chain 'A' and resid 398 through 421 Processing helix chain 'A' and resid 433 through 442 Processing helix chain 'A' and resid 444 through 471 removed outlier: 3.739A pdb=" N ILE A 448 " --> pdb=" O SER A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 497 removed outlier: 3.589A pdb=" N ALA A 480 " --> pdb=" O ASP A 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 31 removed outlier: 4.853A pdb=" N ASP B 26 " --> pdb=" O SER B 22 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N LYS B 27 " --> pdb=" O ILE B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 53 Processing helix chain 'B' and resid 100 through 118 Processing helix chain 'B' and resid 132 through 136 Processing helix chain 'B' and resid 137 through 155 removed outlier: 3.529A pdb=" N LYS B 155 " --> pdb=" O GLU B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 186 Processing helix chain 'B' and resid 193 through 198 removed outlier: 4.115A pdb=" N VAL B 198 " --> pdb=" O HIS B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 206 Processing helix chain 'B' and resid 213 through 228 removed outlier: 3.666A pdb=" N PHE B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 237 removed outlier: 3.980A pdb=" N ILE B 235 " --> pdb=" O SER B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 266 removed outlier: 3.572A pdb=" N PHE B 266 " --> pdb=" O TYR B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 299 Processing helix chain 'B' and resid 313 through 317 removed outlier: 3.947A pdb=" N VAL B 317 " --> pdb=" O ILE B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 339 removed outlier: 3.607A pdb=" N VAL B 339 " --> pdb=" O ALA B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 363 Processing helix chain 'B' and resid 369 through 374 Processing helix chain 'B' and resid 375 through 391 Processing helix chain 'B' and resid 398 through 421 Processing helix chain 'B' and resid 433 through 442 Processing helix chain 'B' and resid 444 through 471 removed outlier: 3.739A pdb=" N ILE B 448 " --> pdb=" O SER B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 497 removed outlier: 3.589A pdb=" N ALA B 480 " --> pdb=" O ASP B 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 31 removed outlier: 4.852A pdb=" N ASP C 26 " --> pdb=" O SER C 22 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N LYS C 27 " --> pdb=" O ILE C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 53 Processing helix chain 'C' and resid 100 through 118 Processing helix chain 'C' and resid 132 through 136 Processing helix chain 'C' and resid 137 through 155 removed outlier: 3.530A pdb=" N LYS C 155 " --> pdb=" O GLU C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 186 Processing helix chain 'C' and resid 193 through 198 removed outlier: 4.114A pdb=" N VAL C 198 " --> pdb=" O HIS C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 206 Processing helix chain 'C' and resid 213 through 228 removed outlier: 3.665A pdb=" N PHE C 226 " --> pdb=" O GLY C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 237 removed outlier: 3.980A pdb=" N ILE C 235 " --> pdb=" O SER C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 266 removed outlier: 3.572A pdb=" N PHE C 266 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 299 Processing helix chain 'C' and resid 313 through 317 removed outlier: 3.947A pdb=" N VAL C 317 " --> pdb=" O ILE C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 339 removed outlier: 3.606A pdb=" N VAL C 339 " --> pdb=" O ALA C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 363 Processing helix chain 'C' and resid 369 through 374 Processing helix chain 'C' and resid 375 through 391 Processing helix chain 'C' and resid 398 through 421 Processing helix chain 'C' and resid 433 through 442 Processing helix chain 'C' and resid 444 through 471 removed outlier: 3.740A pdb=" N ILE C 448 " --> pdb=" O SER C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 497 removed outlier: 3.589A pdb=" N ALA C 480 " --> pdb=" O ASP C 476 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 31 removed outlier: 4.853A pdb=" N ASP D 26 " --> pdb=" O SER D 22 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N LYS D 27 " --> pdb=" O ILE D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 53 Processing helix chain 'D' and resid 100 through 118 Processing helix chain 'D' and resid 132 through 136 Processing helix chain 'D' and resid 137 through 155 removed outlier: 3.529A pdb=" N LYS D 155 " --> pdb=" O GLU D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 186 Processing helix chain 'D' and resid 193 through 198 removed outlier: 4.115A pdb=" N VAL D 198 " --> pdb=" O HIS D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 206 Processing helix chain 'D' and resid 213 through 228 removed outlier: 3.665A pdb=" N PHE D 226 " --> pdb=" O GLY D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 237 removed outlier: 3.979A pdb=" N ILE D 235 " --> pdb=" O SER D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 266 removed outlier: 3.573A pdb=" N PHE D 266 " --> pdb=" O TYR D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 299 Processing helix chain 'D' and resid 313 through 317 removed outlier: 3.946A pdb=" N VAL D 317 " --> pdb=" O ILE D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 339 removed outlier: 3.606A pdb=" N VAL D 339 " --> pdb=" O ALA D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 363 Processing helix chain 'D' and resid 369 through 374 Processing helix chain 'D' and resid 375 through 391 Processing helix chain 'D' and resid 398 through 421 Processing helix chain 'D' and resid 433 through 442 Processing helix chain 'D' and resid 444 through 471 removed outlier: 3.739A pdb=" N ILE D 448 " --> pdb=" O SER D 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 497 removed outlier: 3.589A pdb=" N ALA D 480 " --> pdb=" O ASP D 476 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 31 removed outlier: 4.853A pdb=" N ASP E 26 " --> pdb=" O SER E 22 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N LYS E 27 " --> pdb=" O ILE E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 53 Processing helix chain 'E' and resid 100 through 118 Processing helix chain 'E' and resid 132 through 136 Processing helix chain 'E' and resid 137 through 155 removed outlier: 3.530A pdb=" N LYS E 155 " --> pdb=" O GLU E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 186 Processing helix chain 'E' and resid 193 through 198 removed outlier: 4.114A pdb=" N VAL E 198 " --> pdb=" O HIS E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 206 Processing helix chain 'E' and resid 213 through 228 removed outlier: 3.666A pdb=" N PHE E 226 " --> pdb=" O GLY E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 237 removed outlier: 3.979A pdb=" N ILE E 235 " --> pdb=" O SER E 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 266 removed outlier: 3.572A pdb=" N PHE E 266 " --> pdb=" O TYR E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 299 Processing helix chain 'E' and resid 313 through 317 removed outlier: 3.946A pdb=" N VAL E 317 " --> pdb=" O ILE E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 339 removed outlier: 3.606A pdb=" N VAL E 339 " --> pdb=" O ALA E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 353 through 363 Processing helix chain 'E' and resid 369 through 374 Processing helix chain 'E' and resid 375 through 391 Processing helix chain 'E' and resid 398 through 421 Processing helix chain 'E' and resid 433 through 442 Processing helix chain 'E' and resid 444 through 471 removed outlier: 3.739A pdb=" N ILE E 448 " --> pdb=" O SER E 444 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 497 removed outlier: 3.589A pdb=" N ALA E 480 " --> pdb=" O ASP E 476 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 31 removed outlier: 4.853A pdb=" N ASP F 26 " --> pdb=" O SER F 22 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N LYS F 27 " --> pdb=" O ILE F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 53 Processing helix chain 'F' and resid 100 through 118 Processing helix chain 'F' and resid 132 through 136 Processing helix chain 'F' and resid 137 through 155 removed outlier: 3.530A pdb=" N LYS F 155 " --> pdb=" O GLU F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 186 Processing helix chain 'F' and resid 193 through 198 removed outlier: 4.114A pdb=" N VAL F 198 " --> pdb=" O HIS F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 206 Processing helix chain 'F' and resid 213 through 228 removed outlier: 3.665A pdb=" N PHE F 226 " --> pdb=" O GLY F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 237 removed outlier: 3.980A pdb=" N ILE F 235 " --> pdb=" O SER F 231 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 266 removed outlier: 3.573A pdb=" N PHE F 266 " --> pdb=" O TYR F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 299 Processing helix chain 'F' and resid 313 through 317 removed outlier: 3.946A pdb=" N VAL F 317 " --> pdb=" O ILE F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 339 removed outlier: 3.606A pdb=" N VAL F 339 " --> pdb=" O ALA F 336 " (cutoff:3.500A) Processing helix chain 'F' and resid 353 through 363 Processing helix chain 'F' and resid 369 through 374 Processing helix chain 'F' and resid 375 through 391 Processing helix chain 'F' and resid 398 through 421 Processing helix chain 'F' and resid 433 through 442 Processing helix chain 'F' and resid 444 through 471 removed outlier: 3.740A pdb=" N ILE F 448 " --> pdb=" O SER F 444 " (cutoff:3.500A) Processing helix chain 'F' and resid 476 through 497 removed outlier: 3.589A pdb=" N ALA F 480 " --> pdb=" O ASP F 476 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 163 through 166 removed outlier: 6.547A pdb=" N CYS A 89 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N ALA A 166 " --> pdb=" O CYS A 89 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLY A 91 " --> pdb=" O ALA A 166 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLY A 92 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLY E 92 " --> pdb=" O ALA E 125 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N CYS E 89 " --> pdb=" O VAL E 164 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ALA E 166 " --> pdb=" O CYS E 89 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLY E 91 " --> pdb=" O ALA E 166 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 308 through 309 removed outlier: 3.670A pdb=" N GLY A 278 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL A 273 " --> pdb=" O ILE A 280 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N PHE A 247 " --> pdb=" O THR A 272 " (cutoff:3.500A) removed outlier: 8.879A pdb=" N GLY A 274 " --> pdb=" O PHE A 247 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL A 249 " --> pdb=" O GLY A 274 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU A 322 " --> pdb=" O ALA A 345 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ILE A 344 " --> pdb=" O ILE A 368 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 163 through 166 removed outlier: 6.548A pdb=" N CYS B 89 " --> pdb=" O VAL B 164 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ALA B 166 " --> pdb=" O CYS B 89 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLY B 91 " --> pdb=" O ALA B 166 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLY B 92 " --> pdb=" O ALA B 125 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLY D 92 " --> pdb=" O ALA D 125 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N CYS D 89 " --> pdb=" O VAL D 164 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N ALA D 166 " --> pdb=" O CYS D 89 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLY D 91 " --> pdb=" O ALA D 166 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 308 through 309 removed outlier: 3.669A pdb=" N GLY B 278 " --> pdb=" O GLU B 275 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL B 273 " --> pdb=" O ILE B 280 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N PHE B 247 " --> pdb=" O THR B 272 " (cutoff:3.500A) removed outlier: 8.879A pdb=" N GLY B 274 " --> pdb=" O PHE B 247 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL B 249 " --> pdb=" O GLY B 274 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU B 322 " --> pdb=" O ALA B 345 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ILE B 344 " --> pdb=" O ILE B 368 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 163 through 166 removed outlier: 6.548A pdb=" N CYS C 89 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N ALA C 166 " --> pdb=" O CYS C 89 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLY C 91 " --> pdb=" O ALA C 166 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLY C 92 " --> pdb=" O ALA C 125 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLY F 92 " --> pdb=" O ALA F 125 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N CYS F 89 " --> pdb=" O VAL F 164 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ALA F 166 " --> pdb=" O CYS F 89 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLY F 91 " --> pdb=" O ALA F 166 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 308 through 309 removed outlier: 3.669A pdb=" N GLY C 278 " --> pdb=" O GLU C 275 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL C 273 " --> pdb=" O ILE C 280 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N PHE C 247 " --> pdb=" O THR C 272 " (cutoff:3.500A) removed outlier: 8.879A pdb=" N GLY C 274 " --> pdb=" O PHE C 247 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL C 249 " --> pdb=" O GLY C 274 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU C 322 " --> pdb=" O ALA C 345 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ILE C 344 " --> pdb=" O ILE C 368 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 308 through 309 removed outlier: 3.669A pdb=" N GLY D 278 " --> pdb=" O GLU D 275 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL D 273 " --> pdb=" O ILE D 280 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N PHE D 247 " --> pdb=" O THR D 272 " (cutoff:3.500A) removed outlier: 8.880A pdb=" N GLY D 274 " --> pdb=" O PHE D 247 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL D 249 " --> pdb=" O GLY D 274 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU D 322 " --> pdb=" O ALA D 345 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE D 344 " --> pdb=" O ILE D 368 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 308 through 309 removed outlier: 3.669A pdb=" N GLY E 278 " --> pdb=" O GLU E 275 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL E 273 " --> pdb=" O ILE E 280 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N PHE E 247 " --> pdb=" O THR E 272 " (cutoff:3.500A) removed outlier: 8.879A pdb=" N GLY E 274 " --> pdb=" O PHE E 247 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL E 249 " --> pdb=" O GLY E 274 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU E 322 " --> pdb=" O ALA E 345 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ILE E 344 " --> pdb=" O ILE E 368 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 308 through 309 removed outlier: 3.669A pdb=" N GLY F 278 " --> pdb=" O GLU F 275 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL F 273 " --> pdb=" O ILE F 280 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N PHE F 247 " --> pdb=" O THR F 272 " (cutoff:3.500A) removed outlier: 8.880A pdb=" N GLY F 274 " --> pdb=" O PHE F 247 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL F 249 " --> pdb=" O GLY F 274 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU F 322 " --> pdb=" O ALA F 345 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE F 344 " --> pdb=" O ILE F 368 " (cutoff:3.500A) 1374 hydrogen bonds defined for protein. 3924 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: 4.36 Time building geometry restraints manager: 2.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 7746 1.35 - 1.46: 5388 1.46 - 1.58: 10464 1.58 - 1.70: 0 1.70 - 1.82: 192 Bond restraints: 23790 Sorted by residual: bond pdb=" CB LYS A 342 " pdb=" CG LYS A 342 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.25e+00 bond pdb=" CB LYS B 342 " pdb=" CG LYS B 342 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.24e+00 bond pdb=" CB LYS C 342 " pdb=" CG LYS C 342 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.23e+00 bond pdb=" CB LYS D 342 " pdb=" CG LYS D 342 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.23e+00 bond pdb=" CB LYS F 342 " pdb=" CG LYS F 342 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.23e+00 ... (remaining 23785 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 31754 2.01 - 4.02: 325 4.02 - 6.03: 33 6.03 - 8.04: 0 8.04 - 10.05: 6 Bond angle restraints: 32118 Sorted by residual: angle pdb=" CB MET E 233 " pdb=" CG MET E 233 " pdb=" SD MET E 233 " ideal model delta sigma weight residual 112.70 122.75 -10.05 3.00e+00 1.11e-01 1.12e+01 angle pdb=" CB MET A 233 " pdb=" CG MET A 233 " pdb=" SD MET A 233 " ideal model delta sigma weight residual 112.70 122.75 -10.05 3.00e+00 1.11e-01 1.12e+01 angle pdb=" CB MET B 233 " pdb=" CG MET B 233 " pdb=" SD MET B 233 " ideal model delta sigma weight residual 112.70 122.72 -10.02 3.00e+00 1.11e-01 1.12e+01 angle pdb=" CB MET C 233 " pdb=" CG MET C 233 " pdb=" SD MET C 233 " ideal model delta sigma weight residual 112.70 122.72 -10.02 3.00e+00 1.11e-01 1.12e+01 angle pdb=" CB MET F 233 " pdb=" CG MET F 233 " pdb=" SD MET F 233 " ideal model delta sigma weight residual 112.70 122.72 -10.02 3.00e+00 1.11e-01 1.11e+01 ... (remaining 32113 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 12196 17.78 - 35.55: 1460 35.55 - 53.33: 468 53.33 - 71.11: 90 71.11 - 88.88: 48 Dihedral angle restraints: 14262 sinusoidal: 5784 harmonic: 8478 Sorted by residual: dihedral pdb=" CA LYS D 420 " pdb=" C LYS D 420 " pdb=" N PHE D 421 " pdb=" CA PHE D 421 " ideal model delta harmonic sigma weight residual 180.00 157.84 22.16 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA LYS B 420 " pdb=" C LYS B 420 " pdb=" N PHE B 421 " pdb=" CA PHE B 421 " ideal model delta harmonic sigma weight residual 180.00 157.87 22.13 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA LYS E 420 " pdb=" C LYS E 420 " pdb=" N PHE E 421 " pdb=" CA PHE E 421 " ideal model delta harmonic sigma weight residual 180.00 157.87 22.13 0 5.00e+00 4.00e-02 1.96e+01 ... (remaining 14259 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 2138 0.028 - 0.056: 821 0.056 - 0.084: 311 0.084 - 0.111: 157 0.111 - 0.139: 65 Chirality restraints: 3492 Sorted by residual: chirality pdb=" CA ILE D 280 " pdb=" N ILE D 280 " pdb=" C ILE D 280 " pdb=" CB ILE D 280 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.85e-01 chirality pdb=" CA ILE B 280 " pdb=" N ILE B 280 " pdb=" C ILE B 280 " pdb=" CB ILE B 280 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.81e-01 chirality pdb=" CA ILE C 280 " pdb=" N ILE C 280 " pdb=" C ILE C 280 " pdb=" CB ILE C 280 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.70e-01 ... (remaining 3489 not shown) Planarity restraints: 4182 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN D 282 " -0.035 5.00e-02 4.00e+02 5.42e-02 4.71e+00 pdb=" N PRO D 283 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO D 283 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 283 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 282 " 0.035 5.00e-02 4.00e+02 5.41e-02 4.68e+00 pdb=" N PRO A 283 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 283 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 283 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 282 " 0.035 5.00e-02 4.00e+02 5.40e-02 4.66e+00 pdb=" N PRO B 283 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 283 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 283 " 0.030 5.00e-02 4.00e+02 ... (remaining 4179 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 425 2.69 - 3.25: 22597 3.25 - 3.80: 38986 3.80 - 4.35: 51149 4.35 - 4.90: 85292 Nonbonded interactions: 198449 Sorted by model distance: nonbonded pdb=" OG1 THR F 272 " pdb=" O ILE F 280 " model vdw 2.142 3.040 nonbonded pdb=" OG1 THR A 272 " pdb=" O ILE A 280 " model vdw 2.143 3.040 nonbonded pdb=" OG1 THR B 272 " pdb=" O ILE B 280 " model vdw 2.143 3.040 nonbonded pdb=" OG1 THR E 272 " pdb=" O ILE E 280 " model vdw 2.143 3.040 nonbonded pdb=" OG1 THR C 272 " pdb=" O ILE C 280 " model vdw 2.143 3.040 ... (remaining 198444 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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=0.00 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: 6.060 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: 0.470 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 19.480 Find NCS groups from input model: 0.160 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:9.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 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 : 0.003 0.034 23790 Z= 0.122 Angle : 0.531 10.055 32118 Z= 0.296 Chirality : 0.041 0.139 3492 Planarity : 0.004 0.054 4182 Dihedral : 17.671 88.884 8862 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.20 % Allowed : 19.15 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.67 (0.16), residues: 2964 helix: 2.57 (0.13), residues: 1542 sheet: -0.25 (0.28), residues: 396 loop : -0.63 (0.19), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 44 TYR 0.012 0.001 TYR B 407 PHE 0.028 0.001 PHE B 360 TRP 0.010 0.002 TRP F 281 HIS 0.004 0.001 HIS D 258 Details of bonding type rmsd covalent geometry : bond 0.00253 (23790) covalent geometry : angle 0.53150 (32118) hydrogen bonds : bond 0.12546 ( 1374) hydrogen bonds : angle 4.84140 ( 3924) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 323 time to evaluate : 0.999 Fit side-chains REVERT: A 269 LYS cc_start: 0.7252 (OUTLIER) cc_final: 0.6771 (ptmm) REVERT: A 342 LYS cc_start: 0.5378 (mmpt) cc_final: 0.4841 (mppt) REVERT: B 233 MET cc_start: 0.6251 (mmp) cc_final: 0.5806 (mmm) REVERT: C 11 LYS cc_start: 0.7198 (mmmt) cc_final: 0.6939 (mppt) REVERT: D 340 LYS cc_start: 0.5513 (mmtp) cc_final: 0.5149 (pttt) REVERT: D 342 LYS cc_start: 0.5476 (mmpt) cc_final: 0.4933 (mppt) REVERT: F 11 LYS cc_start: 0.7207 (mmmt) cc_final: 0.6941 (mppt) outliers start: 55 outliers final: 48 residues processed: 362 average time/residue: 0.7275 time to fit residues: 295.8470 Evaluate side-chains 341 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 292 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 269 LYS Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 269 LYS Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 168 ASP Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 269 LYS Chi-restraints excluded: chain C residue 313 SER Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 269 LYS Chi-restraints excluded: chain D residue 313 SER Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 168 ASP Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 269 LYS Chi-restraints excluded: chain E residue 313 SER Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 168 ASP Chi-restraints excluded: chain F residue 231 SER Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 269 LYS Chi-restraints excluded: chain F residue 313 SER Chi-restraints excluded: chain F residue 397 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 0.0370 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 10.0000 chunk 111 optimal weight: 0.8980 overall best weight: 0.7462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 ASN C 374 ASN C 463 GLN D 374 ASN F 374 ASN F 463 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.178433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.139694 restraints weight = 24620.696| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 1.32 r_work: 0.3510 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.0870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 23790 Z= 0.103 Angle : 0.476 6.844 32118 Z= 0.255 Chirality : 0.041 0.132 3492 Planarity : 0.004 0.043 4182 Dihedral : 6.199 58.951 3337 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 4.77 % Allowed : 17.75 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.71 (0.16), residues: 2964 helix: 2.71 (0.13), residues: 1548 sheet: -0.38 (0.27), residues: 396 loop : -0.74 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 44 TYR 0.009 0.001 TYR B 407 PHE 0.027 0.001 PHE F 360 TRP 0.008 0.001 TRP D 281 HIS 0.009 0.001 HIS A 264 Details of bonding type rmsd covalent geometry : bond 0.00216 (23790) covalent geometry : angle 0.47566 (32118) hydrogen bonds : bond 0.03760 ( 1374) hydrogen bonds : angle 4.02678 ( 3924) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 320 time to evaluate : 0.774 Fit side-chains REVERT: A 169 MET cc_start: 0.6789 (OUTLIER) cc_final: 0.6560 (ppp) REVERT: A 269 LYS cc_start: 0.7060 (OUTLIER) cc_final: 0.6745 (ptpp) REVERT: A 340 LYS cc_start: 0.5322 (mmtp) cc_final: 0.4767 (ptmt) REVERT: A 342 LYS cc_start: 0.5044 (mmpt) cc_final: 0.4648 (mmtt) REVERT: B 30 GLU cc_start: 0.6522 (mt-10) cc_final: 0.6148 (mm-30) REVERT: B 72 TRP cc_start: 0.7270 (m100) cc_final: 0.6948 (m100) REVERT: B 169 MET cc_start: 0.6712 (OUTLIER) cc_final: 0.6389 (ppp) REVERT: B 269 LYS cc_start: 0.7162 (OUTLIER) cc_final: 0.6775 (ptpp) REVERT: B 340 LYS cc_start: 0.5275 (mmtp) cc_final: 0.4927 (ptmt) REVERT: B 358 LYS cc_start: 0.7341 (ttpt) cc_final: 0.7103 (ttmp) REVERT: C 11 LYS cc_start: 0.7221 (mmmt) cc_final: 0.6761 (mppt) REVERT: C 30 GLU cc_start: 0.6428 (mt-10) cc_final: 0.6210 (mm-30) REVERT: C 169 MET cc_start: 0.6739 (OUTLIER) cc_final: 0.6518 (ppp) REVERT: C 269 LYS cc_start: 0.7140 (OUTLIER) cc_final: 0.6823 (ptpp) REVERT: C 340 LYS cc_start: 0.5249 (mmtp) cc_final: 0.5022 (ptmt) REVERT: D 169 MET cc_start: 0.6781 (OUTLIER) cc_final: 0.6538 (ppp) REVERT: D 269 LYS cc_start: 0.7033 (OUTLIER) cc_final: 0.6711 (ptpp) REVERT: D 340 LYS cc_start: 0.5329 (mmtp) cc_final: 0.5057 (ptmt) REVERT: E 30 GLU cc_start: 0.6474 (mt-10) cc_final: 0.6125 (mm-30) REVERT: E 169 MET cc_start: 0.6655 (OUTLIER) cc_final: 0.6381 (ppp) REVERT: E 269 LYS cc_start: 0.7167 (OUTLIER) cc_final: 0.6768 (ptpp) REVERT: E 340 LYS cc_start: 0.5260 (mmtp) cc_final: 0.4921 (ptmt) REVERT: F 11 LYS cc_start: 0.7220 (mmmt) cc_final: 0.6757 (mppt) REVERT: F 30 GLU cc_start: 0.6398 (mt-10) cc_final: 0.6191 (mm-30) REVERT: F 169 MET cc_start: 0.6745 (OUTLIER) cc_final: 0.6514 (ppp) REVERT: F 224 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7683 (pt0) REVERT: F 233 MET cc_start: 0.6087 (mmp) cc_final: 0.5834 (mmp) REVERT: F 269 LYS cc_start: 0.7175 (OUTLIER) cc_final: 0.6853 (ptpp) outliers start: 119 outliers final: 34 residues processed: 400 average time/residue: 0.6389 time to fit residues: 289.2120 Evaluate side-chains 344 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 297 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 269 LYS Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 269 LYS Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain C residue 169 MET Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 269 LYS Chi-restraints excluded: chain C residue 313 SER Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 169 MET Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 269 LYS Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 313 SER Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 501 THR Chi-restraints excluded: chain E residue 169 MET Chi-restraints excluded: chain E residue 238 MET Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 269 LYS Chi-restraints excluded: chain E residue 313 SER Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain F residue 169 MET Chi-restraints excluded: chain F residue 224 GLU Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 269 LYS Chi-restraints excluded: chain F residue 313 SER Chi-restraints excluded: chain F residue 397 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 16 optimal weight: 0.3980 chunk 110 optimal weight: 5.9990 chunk 251 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 257 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 53 optimal weight: 20.0000 chunk 229 optimal weight: 6.9990 chunk 235 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN B 374 ASN D 374 ASN ** D 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 463 GLN E 374 ASN E 414 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.174789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.136746 restraints weight = 24426.868| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 1.34 r_work: 0.3440 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23790 Z= 0.146 Angle : 0.541 7.264 32118 Z= 0.291 Chirality : 0.044 0.144 3492 Planarity : 0.005 0.055 4182 Dihedral : 5.920 59.694 3306 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 5.21 % Allowed : 17.23 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.30 (0.16), residues: 2964 helix: 2.32 (0.13), residues: 1584 sheet: -0.42 (0.27), residues: 396 loop : -1.03 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 146 TYR 0.012 0.002 TYR C 113 PHE 0.028 0.002 PHE C 360 TRP 0.011 0.002 TRP C 281 HIS 0.011 0.002 HIS C 264 Details of bonding type rmsd covalent geometry : bond 0.00327 (23790) covalent geometry : angle 0.54102 (32118) hydrogen bonds : bond 0.04996 ( 1374) hydrogen bonds : angle 4.23542 ( 3924) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 299 time to evaluate : 0.808 Fit side-chains REVERT: A 269 LYS cc_start: 0.7067 (OUTLIER) cc_final: 0.6798 (ptpp) REVERT: A 342 LYS cc_start: 0.5218 (mmpt) cc_final: 0.4748 (mmtt) REVERT: A 357 ASP cc_start: 0.7252 (OUTLIER) cc_final: 0.7024 (m-30) REVERT: A 358 LYS cc_start: 0.7104 (ttmm) cc_final: 0.6774 (ttmp) REVERT: B 72 TRP cc_start: 0.7520 (m100) cc_final: 0.7232 (m100) REVERT: B 227 ILE cc_start: 0.7732 (OUTLIER) cc_final: 0.7454 (tp) REVERT: B 264 HIS cc_start: 0.7406 (t-170) cc_final: 0.7204 (t70) REVERT: B 269 LYS cc_start: 0.7182 (OUTLIER) cc_final: 0.6857 (ptpp) REVERT: C 11 LYS cc_start: 0.7295 (mmmt) cc_final: 0.6852 (mppt) REVERT: C 25 GLU cc_start: 0.6850 (OUTLIER) cc_final: 0.6544 (tt0) REVERT: C 30 GLU cc_start: 0.6481 (mt-10) cc_final: 0.6188 (mm-30) REVERT: C 269 LYS cc_start: 0.7177 (OUTLIER) cc_final: 0.6879 (ptpp) REVERT: C 342 LYS cc_start: 0.5264 (mmpt) cc_final: 0.4291 (mttp) REVERT: D 25 GLU cc_start: 0.6844 (OUTLIER) cc_final: 0.6560 (tt0) REVERT: D 269 LYS cc_start: 0.7053 (OUTLIER) cc_final: 0.6801 (ptpp) REVERT: D 342 LYS cc_start: 0.5325 (mmpt) cc_final: 0.4728 (mmtt) REVERT: E 224 GLU cc_start: 0.7807 (pp20) cc_final: 0.7606 (tm-30) REVERT: E 269 LYS cc_start: 0.7153 (OUTLIER) cc_final: 0.6834 (ptpp) REVERT: F 11 LYS cc_start: 0.7310 (mmmt) cc_final: 0.6861 (mppt) REVERT: F 25 GLU cc_start: 0.6846 (OUTLIER) cc_final: 0.6540 (tt0) REVERT: F 30 GLU cc_start: 0.6470 (mt-10) cc_final: 0.6207 (mm-30) REVERT: F 224 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7744 (pt0) REVERT: F 269 LYS cc_start: 0.7197 (OUTLIER) cc_final: 0.6897 (ptpp) outliers start: 130 outliers final: 63 residues processed: 375 average time/residue: 0.5589 time to fit residues: 239.4655 Evaluate side-chains 370 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 295 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 269 LYS Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 245 LYS Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 269 LYS Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 168 ASP Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 269 LYS Chi-restraints excluded: chain C residue 313 SER Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 25 GLU Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 238 MET Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 269 LYS Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 313 SER Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 501 THR Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 25 GLU Chi-restraints excluded: chain E residue 168 ASP Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 238 MET Chi-restraints excluded: chain E residue 245 LYS Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 269 LYS Chi-restraints excluded: chain E residue 313 SER Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 168 ASP Chi-restraints excluded: chain F residue 224 GLU Chi-restraints excluded: chain F residue 231 SER Chi-restraints excluded: chain F residue 238 MET Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 269 LYS Chi-restraints excluded: chain F residue 313 SER Chi-restraints excluded: chain F residue 357 ASP Chi-restraints excluded: chain F residue 397 LEU Chi-restraints excluded: chain F residue 430 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 116 optimal weight: 0.4980 chunk 45 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 254 optimal weight: 0.6980 chunk 76 optimal weight: 10.0000 chunk 136 optimal weight: 0.9990 chunk 277 optimal weight: 10.0000 chunk 154 optimal weight: 10.0000 chunk 167 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 268 optimal weight: 20.0000 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN A 374 ASN C 254 ASN C 374 ASN D 254 ASN ** D 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 463 GLN F 254 ASN F 374 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.176361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.138348 restraints weight = 24575.677| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 1.32 r_work: 0.3471 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 23790 Z= 0.108 Angle : 0.480 6.909 32118 Z= 0.259 Chirality : 0.042 0.133 3492 Planarity : 0.004 0.046 4182 Dihedral : 5.529 57.048 3306 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 6.05 % Allowed : 17.39 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.43 (0.16), residues: 2964 helix: 2.48 (0.13), residues: 1584 sheet: -0.46 (0.27), residues: 396 loop : -1.05 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 146 TYR 0.010 0.001 TYR D 407 PHE 0.024 0.001 PHE C 360 TRP 0.009 0.001 TRP A 385 HIS 0.008 0.001 HIS D 264 Details of bonding type rmsd covalent geometry : bond 0.00229 (23790) covalent geometry : angle 0.47963 (32118) hydrogen bonds : bond 0.04041 ( 1374) hydrogen bonds : angle 4.02764 ( 3924) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 303 time to evaluate : 0.958 Fit side-chains REVERT: A 269 LYS cc_start: 0.6975 (OUTLIER) cc_final: 0.6733 (ptpp) REVERT: A 342 LYS cc_start: 0.5134 (mmpt) cc_final: 0.4686 (mppt) REVERT: A 357 ASP cc_start: 0.7228 (OUTLIER) cc_final: 0.7005 (m-30) REVERT: A 358 LYS cc_start: 0.7118 (ttmm) cc_final: 0.6775 (ttmp) REVERT: A 419 ARG cc_start: 0.6458 (ttp-110) cc_final: 0.6099 (ttm110) REVERT: B 72 TRP cc_start: 0.7292 (m100) cc_final: 0.7041 (m100) REVERT: B 227 ILE cc_start: 0.7768 (OUTLIER) cc_final: 0.7469 (tp) REVERT: B 269 LYS cc_start: 0.7111 (OUTLIER) cc_final: 0.6804 (ptpp) REVERT: B 358 LYS cc_start: 0.7345 (ttpt) cc_final: 0.7132 (ttmp) REVERT: B 411 MET cc_start: 0.8091 (tpt) cc_final: 0.7763 (tpp) REVERT: C 11 LYS cc_start: 0.7288 (mmmt) cc_final: 0.6853 (mppt) REVERT: C 25 GLU cc_start: 0.6807 (OUTLIER) cc_final: 0.6476 (tt0) REVERT: C 30 GLU cc_start: 0.6486 (mt-10) cc_final: 0.6196 (mm-30) REVERT: C 110 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8673 (tp) REVERT: C 169 MET cc_start: 0.6769 (OUTLIER) cc_final: 0.6564 (ppp) REVERT: C 269 LYS cc_start: 0.7052 (OUTLIER) cc_final: 0.6776 (ptpp) REVERT: C 292 GLU cc_start: 0.5948 (OUTLIER) cc_final: 0.5732 (tt0) REVERT: D 25 GLU cc_start: 0.6805 (OUTLIER) cc_final: 0.6446 (tt0) REVERT: D 269 LYS cc_start: 0.6968 (OUTLIER) cc_final: 0.6737 (ptpp) REVERT: E 224 GLU cc_start: 0.7786 (pp20) cc_final: 0.7565 (tm-30) REVERT: E 269 LYS cc_start: 0.7081 (OUTLIER) cc_final: 0.6807 (ptpp) REVERT: E 411 MET cc_start: 0.7822 (tpp) cc_final: 0.7330 (tpp) REVERT: E 419 ARG cc_start: 0.6495 (ttp-110) cc_final: 0.6106 (ttm110) REVERT: F 11 LYS cc_start: 0.7298 (mmmt) cc_final: 0.6864 (mppt) REVERT: F 25 GLU cc_start: 0.6818 (OUTLIER) cc_final: 0.6483 (tt0) REVERT: F 30 GLU cc_start: 0.6464 (mt-10) cc_final: 0.6200 (mm-30) REVERT: F 110 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8677 (tp) REVERT: F 169 MET cc_start: 0.6751 (OUTLIER) cc_final: 0.6543 (ppp) REVERT: F 224 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7688 (pt0) REVERT: F 269 LYS cc_start: 0.7070 (OUTLIER) cc_final: 0.6789 (ptpp) REVERT: F 292 GLU cc_start: 0.5940 (OUTLIER) cc_final: 0.5678 (tt0) outliers start: 151 outliers final: 61 residues processed: 392 average time/residue: 0.6082 time to fit residues: 271.2491 Evaluate side-chains 376 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 297 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 269 LYS Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 245 LYS Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 269 LYS Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 168 ASP Chi-restraints excluded: chain C residue 169 MET Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 269 LYS Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 357 ASP Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 25 GLU Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 238 MET Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 269 LYS Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 346 GLU Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 501 THR Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 25 GLU Chi-restraints excluded: chain E residue 168 ASP Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 245 LYS Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 269 LYS Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 168 ASP Chi-restraints excluded: chain F residue 169 MET Chi-restraints excluded: chain F residue 224 GLU Chi-restraints excluded: chain F residue 231 SER Chi-restraints excluded: chain F residue 238 MET Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 254 ASN Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 269 LYS Chi-restraints excluded: chain F residue 292 GLU Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 357 ASP Chi-restraints excluded: chain F residue 397 LEU Chi-restraints excluded: chain F residue 402 GLU Chi-restraints excluded: chain F residue 430 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 39 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 279 optimal weight: 0.9980 chunk 213 optimal weight: 9.9990 chunk 125 optimal weight: 0.0770 chunk 195 optimal weight: 10.0000 chunk 162 optimal weight: 9.9990 chunk 283 optimal weight: 6.9990 chunk 105 optimal weight: 7.9990 chunk 126 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 overall best weight: 3.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 GLN B 374 ASN B 463 GLN ** C 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 ASN ** D 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 463 GLN E 374 ASN F 258 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.173877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.135164 restraints weight = 24262.614| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 1.27 r_work: 0.3432 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 23790 Z= 0.168 Angle : 0.568 7.615 32118 Z= 0.307 Chirality : 0.045 0.150 3492 Planarity : 0.005 0.045 4182 Dihedral : 5.386 51.237 3298 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 5.85 % Allowed : 18.27 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.15 (0.15), residues: 2964 helix: 2.19 (0.13), residues: 1584 sheet: -0.32 (0.27), residues: 396 loop : -1.19 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 79 TYR 0.014 0.002 TYR F 113 PHE 0.028 0.002 PHE F 360 TRP 0.010 0.002 TRP B 281 HIS 0.006 0.002 HIS F 258 Details of bonding type rmsd covalent geometry : bond 0.00381 (23790) covalent geometry : angle 0.56772 (32118) hydrogen bonds : bond 0.05314 ( 1374) hydrogen bonds : angle 4.32632 ( 3924) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 310 time to evaluate : 0.665 Fit side-chains REVERT: A 25 GLU cc_start: 0.6866 (OUTLIER) cc_final: 0.6502 (tt0) REVERT: A 269 LYS cc_start: 0.7052 (OUTLIER) cc_final: 0.6796 (ptpp) REVERT: A 342 LYS cc_start: 0.5286 (mmpt) cc_final: 0.4768 (mppt) REVERT: A 357 ASP cc_start: 0.7264 (OUTLIER) cc_final: 0.7027 (m-30) REVERT: A 358 LYS cc_start: 0.7087 (ttmm) cc_final: 0.6735 (ttmp) REVERT: B 72 TRP cc_start: 0.7517 (m100) cc_final: 0.7280 (m100) REVERT: B 227 ILE cc_start: 0.7780 (OUTLIER) cc_final: 0.7535 (tp) REVERT: B 269 LYS cc_start: 0.7147 (OUTLIER) cc_final: 0.6850 (ptpp) REVERT: B 402 GLU cc_start: 0.7542 (pt0) cc_final: 0.7203 (pt0) REVERT: C 11 LYS cc_start: 0.7326 (mmmt) cc_final: 0.6907 (mppt) REVERT: C 25 GLU cc_start: 0.6813 (OUTLIER) cc_final: 0.6529 (tt0) REVERT: C 224 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7714 (pt0) REVERT: C 269 LYS cc_start: 0.7112 (OUTLIER) cc_final: 0.6841 (ptpp) REVERT: C 342 LYS cc_start: 0.5277 (mmpt) cc_final: 0.4513 (mttp) REVERT: D 25 GLU cc_start: 0.6874 (OUTLIER) cc_final: 0.6495 (tt0) REVERT: D 269 LYS cc_start: 0.7061 (OUTLIER) cc_final: 0.6808 (ptpp) REVERT: D 292 GLU cc_start: 0.5802 (tt0) cc_final: 0.5573 (tt0) REVERT: E 224 GLU cc_start: 0.7842 (pp20) cc_final: 0.7642 (tm-30) REVERT: E 269 LYS cc_start: 0.7152 (OUTLIER) cc_final: 0.6855 (ptpp) REVERT: F 11 LYS cc_start: 0.7327 (mmmt) cc_final: 0.6897 (mppt) REVERT: F 25 GLU cc_start: 0.6816 (OUTLIER) cc_final: 0.6525 (tt0) REVERT: F 224 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7719 (pt0) REVERT: F 269 LYS cc_start: 0.7121 (OUTLIER) cc_final: 0.6848 (ptpp) REVERT: F 342 LYS cc_start: 0.5342 (mmpt) cc_final: 0.4355 (mttp) outliers start: 146 outliers final: 67 residues processed: 395 average time/residue: 0.6349 time to fit residues: 284.0533 Evaluate side-chains 392 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 311 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 269 LYS Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 245 LYS Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 269 LYS Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 357 ASP Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 168 ASP Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 269 LYS Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 357 ASP Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 25 GLU Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 238 MET Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 269 LYS Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 346 GLU Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 25 GLU Chi-restraints excluded: chain E residue 168 ASP Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 238 MET Chi-restraints excluded: chain E residue 245 LYS Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 269 LYS Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain E residue 357 ASP Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 168 ASP Chi-restraints excluded: chain F residue 224 GLU Chi-restraints excluded: chain F residue 231 SER Chi-restraints excluded: chain F residue 238 MET Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 269 LYS Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain F residue 357 ASP Chi-restraints excluded: chain F residue 397 LEU Chi-restraints excluded: chain F residue 430 ILE Chi-restraints excluded: chain F residue 431 VAL Chi-restraints excluded: chain F residue 435 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 57 optimal weight: 6.9990 chunk 116 optimal weight: 4.9990 chunk 224 optimal weight: 0.0060 chunk 273 optimal weight: 3.9990 chunk 38 optimal weight: 9.9990 chunk 172 optimal weight: 10.0000 chunk 247 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 193 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 overall best weight: 3.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 ASN B 297 GLN B 330 GLN ** C 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 ASN C 374 ASN ** D 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 463 GLN ** F 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 374 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.173825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.135511 restraints weight = 24437.062| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 1.26 r_work: 0.3429 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 23790 Z= 0.160 Angle : 0.562 7.621 32118 Z= 0.304 Chirality : 0.045 0.143 3492 Planarity : 0.005 0.042 4182 Dihedral : 5.406 50.595 3298 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 5.53 % Allowed : 18.43 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.03 (0.15), residues: 2964 helix: 2.11 (0.13), residues: 1584 sheet: -0.34 (0.27), residues: 396 loop : -1.29 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 79 TYR 0.012 0.002 TYR F 113 PHE 0.027 0.002 PHE C 360 TRP 0.011 0.002 TRP F 385 HIS 0.008 0.001 HIS A 264 Details of bonding type rmsd covalent geometry : bond 0.00360 (23790) covalent geometry : angle 0.56201 (32118) hydrogen bonds : bond 0.05138 ( 1374) hydrogen bonds : angle 4.30522 ( 3924) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 306 time to evaluate : 0.656 Fit side-chains REVERT: A 25 GLU cc_start: 0.6814 (OUTLIER) cc_final: 0.6435 (tt0) REVERT: A 110 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8737 (tm) REVERT: A 269 LYS cc_start: 0.7089 (OUTLIER) cc_final: 0.6819 (ptpp) REVERT: A 342 LYS cc_start: 0.5309 (mmpt) cc_final: 0.4829 (mppt) REVERT: A 357 ASP cc_start: 0.7248 (OUTLIER) cc_final: 0.7009 (m-30) REVERT: A 358 LYS cc_start: 0.7086 (ttmm) cc_final: 0.6739 (ttmp) REVERT: A 419 ARG cc_start: 0.6635 (ttp-110) cc_final: 0.6279 (ttm110) REVERT: B 72 TRP cc_start: 0.7500 (m100) cc_final: 0.7260 (m100) REVERT: B 227 ILE cc_start: 0.7771 (OUTLIER) cc_final: 0.7538 (tp) REVERT: B 269 LYS cc_start: 0.7182 (OUTLIER) cc_final: 0.6884 (ptpp) REVERT: B 402 GLU cc_start: 0.7573 (pt0) cc_final: 0.7193 (pt0) REVERT: C 11 LYS cc_start: 0.7311 (mmmt) cc_final: 0.6880 (mppt) REVERT: C 224 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7720 (pt0) REVERT: C 269 LYS cc_start: 0.7099 (OUTLIER) cc_final: 0.6824 (ptpp) REVERT: C 328 GLU cc_start: 0.5348 (OUTLIER) cc_final: 0.4665 (pp20) REVERT: C 342 LYS cc_start: 0.5229 (mmpt) cc_final: 0.4452 (mttp) REVERT: D 25 GLU cc_start: 0.6838 (OUTLIER) cc_final: 0.6437 (tt0) REVERT: D 110 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8735 (tm) REVERT: D 269 LYS cc_start: 0.7076 (OUTLIER) cc_final: 0.6819 (ptpp) REVERT: D 292 GLU cc_start: 0.5824 (tt0) cc_final: 0.5590 (tt0) REVERT: E 224 GLU cc_start: 0.7846 (pp20) cc_final: 0.7638 (tm-30) REVERT: E 269 LYS cc_start: 0.7170 (OUTLIER) cc_final: 0.6877 (ptpp) REVERT: E 292 GLU cc_start: 0.5940 (OUTLIER) cc_final: 0.5656 (tt0) REVERT: F 25 GLU cc_start: 0.6802 (OUTLIER) cc_final: 0.6512 (tt0) REVERT: F 224 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7704 (pt0) REVERT: F 269 LYS cc_start: 0.7104 (OUTLIER) cc_final: 0.6825 (ptpp) REVERT: F 328 GLU cc_start: 0.5349 (OUTLIER) cc_final: 0.4614 (pp20) outliers start: 138 outliers final: 80 residues processed: 389 average time/residue: 0.6218 time to fit residues: 274.3221 Evaluate side-chains 401 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 303 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 269 LYS Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 245 LYS Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 254 ASN Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 269 LYS Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 357 ASP Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 168 ASP Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 245 LYS Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 254 ASN Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 269 LYS Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 328 GLU Chi-restraints excluded: chain C residue 357 ASP Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 25 GLU Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 238 MET Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 269 LYS Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 346 GLU Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 501 THR Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 25 GLU Chi-restraints excluded: chain E residue 168 ASP Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 238 MET Chi-restraints excluded: chain E residue 245 LYS Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 269 LYS Chi-restraints excluded: chain E residue 292 GLU Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain E residue 357 ASP Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 168 ASP Chi-restraints excluded: chain F residue 224 GLU Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain F residue 231 SER Chi-restraints excluded: chain F residue 238 MET Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 245 LYS Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 269 LYS Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 328 GLU Chi-restraints excluded: chain F residue 357 ASP Chi-restraints excluded: chain F residue 397 LEU Chi-restraints excluded: chain F residue 402 GLU Chi-restraints excluded: chain F residue 430 ILE Chi-restraints excluded: chain F residue 431 VAL Chi-restraints excluded: chain F residue 435 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 246 optimal weight: 6.9990 chunk 187 optimal weight: 5.9990 chunk 36 optimal weight: 9.9990 chunk 192 optimal weight: 7.9990 chunk 275 optimal weight: 0.9990 chunk 212 optimal weight: 6.9990 chunk 135 optimal weight: 4.9990 chunk 256 optimal weight: 1.9990 chunk 108 optimal weight: 0.6980 chunk 83 optimal weight: 7.9990 chunk 247 optimal weight: 6.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 254 ASN B 330 GLN ** C 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 254 ASN D 374 ASN ** D 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 330 GLN E 374 ASN ** F 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.173372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.135229 restraints weight = 24491.074| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 1.31 r_work: 0.3434 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 23790 Z= 0.159 Angle : 0.562 8.280 32118 Z= 0.304 Chirality : 0.045 0.144 3492 Planarity : 0.005 0.042 4182 Dihedral : 5.416 50.900 3298 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 5.13 % Allowed : 18.91 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.15), residues: 2964 helix: 2.07 (0.13), residues: 1584 sheet: -0.39 (0.27), residues: 396 loop : -1.35 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 79 TYR 0.012 0.002 TYR A 407 PHE 0.030 0.002 PHE C 360 TRP 0.011 0.002 TRP F 385 HIS 0.008 0.001 HIS A 264 Details of bonding type rmsd covalent geometry : bond 0.00359 (23790) covalent geometry : angle 0.56215 (32118) hydrogen bonds : bond 0.05164 ( 1374) hydrogen bonds : angle 4.29237 ( 3924) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 311 time to evaluate : 1.055 Fit side-chains REVERT: A 25 GLU cc_start: 0.6844 (OUTLIER) cc_final: 0.6444 (tt0) REVERT: A 110 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8735 (tm) REVERT: A 269 LYS cc_start: 0.7071 (OUTLIER) cc_final: 0.6806 (ptpp) REVERT: A 342 LYS cc_start: 0.5272 (mmpt) cc_final: 0.4918 (mmtt) REVERT: A 357 ASP cc_start: 0.7237 (OUTLIER) cc_final: 0.6998 (m-30) REVERT: A 358 LYS cc_start: 0.7076 (ttmm) cc_final: 0.6728 (ttmp) REVERT: A 411 MET cc_start: 0.7777 (tpp) cc_final: 0.7407 (tpp) REVERT: A 419 ARG cc_start: 0.6637 (ttp-110) cc_final: 0.6291 (ttm110) REVERT: B 72 TRP cc_start: 0.7494 (m100) cc_final: 0.7266 (m100) REVERT: B 227 ILE cc_start: 0.7771 (OUTLIER) cc_final: 0.7558 (tp) REVERT: B 269 LYS cc_start: 0.7168 (OUTLIER) cc_final: 0.6869 (ptpp) REVERT: B 402 GLU cc_start: 0.7560 (pt0) cc_final: 0.7182 (pt0) REVERT: C 110 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8818 (tp) REVERT: C 224 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7721 (pt0) REVERT: C 269 LYS cc_start: 0.7105 (OUTLIER) cc_final: 0.6828 (ptpp) REVERT: C 328 GLU cc_start: 0.5353 (OUTLIER) cc_final: 0.4662 (pp20) REVERT: C 342 LYS cc_start: 0.5219 (mmpt) cc_final: 0.4486 (mttp) REVERT: D 25 GLU cc_start: 0.6840 (OUTLIER) cc_final: 0.6427 (tt0) REVERT: D 110 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8736 (tm) REVERT: D 269 LYS cc_start: 0.7077 (OUTLIER) cc_final: 0.6819 (ptpp) REVERT: D 292 GLU cc_start: 0.5823 (tt0) cc_final: 0.5583 (tt0) REVERT: E 269 LYS cc_start: 0.7157 (OUTLIER) cc_final: 0.6861 (ptpp) REVERT: E 292 GLU cc_start: 0.5970 (OUTLIER) cc_final: 0.5672 (tt0) REVERT: E 411 MET cc_start: 0.7842 (tpp) cc_final: 0.7409 (tpp) REVERT: F 110 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8815 (tp) REVERT: F 224 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7698 (pt0) REVERT: F 269 LYS cc_start: 0.7103 (OUTLIER) cc_final: 0.6821 (ptpp) REVERT: F 328 GLU cc_start: 0.5347 (OUTLIER) cc_final: 0.4618 (pp20) outliers start: 128 outliers final: 80 residues processed: 382 average time/residue: 0.6507 time to fit residues: 282.2306 Evaluate side-chains 408 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 309 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 269 LYS Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 269 LYS Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 357 ASP Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 168 ASP Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 245 LYS Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 269 LYS Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 328 GLU Chi-restraints excluded: chain C residue 357 ASP Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 25 GLU Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 238 MET Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 269 LYS Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 346 GLU Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 501 THR Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 25 GLU Chi-restraints excluded: chain E residue 168 ASP Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 238 MET Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 245 LYS Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 254 ASN Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 269 LYS Chi-restraints excluded: chain E residue 292 GLU Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain E residue 357 ASP Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 168 ASP Chi-restraints excluded: chain F residue 224 GLU Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain F residue 231 SER Chi-restraints excluded: chain F residue 238 MET Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 245 LYS Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 269 LYS Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 328 GLU Chi-restraints excluded: chain F residue 357 ASP Chi-restraints excluded: chain F residue 397 LEU Chi-restraints excluded: chain F residue 402 GLU Chi-restraints excluded: chain F residue 431 VAL Chi-restraints excluded: chain F residue 435 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 92 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 129 optimal weight: 7.9990 chunk 166 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 206 optimal weight: 1.9990 chunk 136 optimal weight: 0.5980 chunk 239 optimal weight: 6.9990 chunk 143 optimal weight: 5.9990 chunk 145 optimal weight: 7.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 254 ASN A 330 GLN A 374 ASN B 330 GLN ** C 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 ASN C 330 GLN C 374 ASN ** D 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 254 ASN D 330 GLN ** D 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 330 GLN ** F 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.174550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.136138 restraints weight = 24366.334| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 1.34 r_work: 0.3436 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23790 Z= 0.135 Angle : 0.532 8.839 32118 Z= 0.288 Chirality : 0.044 0.137 3492 Planarity : 0.004 0.042 4182 Dihedral : 5.256 51.713 3298 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 4.77 % Allowed : 19.11 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.07 (0.15), residues: 2964 helix: 2.21 (0.13), residues: 1584 sheet: -0.43 (0.27), residues: 396 loop : -1.34 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 419 TYR 0.013 0.001 TYR D 407 PHE 0.030 0.002 PHE C 360 TRP 0.011 0.002 TRP F 385 HIS 0.008 0.001 HIS D 264 Details of bonding type rmsd covalent geometry : bond 0.00297 (23790) covalent geometry : angle 0.53192 (32118) hydrogen bonds : bond 0.04709 ( 1374) hydrogen bonds : angle 4.19333 ( 3924) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 304 time to evaluate : 0.932 Fit side-chains REVERT: A 110 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8718 (tm) REVERT: A 269 LYS cc_start: 0.7116 (OUTLIER) cc_final: 0.6893 (ptpp) REVERT: A 342 LYS cc_start: 0.5251 (mmpt) cc_final: 0.4790 (mppt) REVERT: A 357 ASP cc_start: 0.7242 (OUTLIER) cc_final: 0.7008 (m-30) REVERT: A 358 LYS cc_start: 0.7088 (ttmm) cc_final: 0.6746 (ttmp) REVERT: A 419 ARG cc_start: 0.6603 (ttp-110) cc_final: 0.6309 (ttm110) REVERT: B 72 TRP cc_start: 0.7430 (m100) cc_final: 0.7208 (m100) REVERT: B 227 ILE cc_start: 0.7778 (OUTLIER) cc_final: 0.7572 (tp) REVERT: B 269 LYS cc_start: 0.7192 (OUTLIER) cc_final: 0.6893 (ptpp) REVERT: B 402 GLU cc_start: 0.7581 (pt0) cc_final: 0.7212 (pt0) REVERT: B 411 MET cc_start: 0.8105 (tpt) cc_final: 0.7824 (tpp) REVERT: C 11 LYS cc_start: 0.7293 (mmmt) cc_final: 0.6816 (mppt) REVERT: C 25 GLU cc_start: 0.6775 (OUTLIER) cc_final: 0.6478 (tt0) REVERT: C 224 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7751 (pt0) REVERT: C 269 LYS cc_start: 0.7131 (OUTLIER) cc_final: 0.6861 (ptpp) REVERT: C 328 GLU cc_start: 0.5332 (OUTLIER) cc_final: 0.4696 (pp20) REVERT: C 342 LYS cc_start: 0.5107 (mmpt) cc_final: 0.4457 (mttp) REVERT: D 110 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8718 (tm) REVERT: D 269 LYS cc_start: 0.7134 (OUTLIER) cc_final: 0.6915 (ptpp) REVERT: E 269 LYS cc_start: 0.7198 (OUTLIER) cc_final: 0.6901 (ptpp) REVERT: E 411 MET cc_start: 0.7884 (tpp) cc_final: 0.7439 (tpp) REVERT: F 11 LYS cc_start: 0.7284 (mmmt) cc_final: 0.6794 (mppt) REVERT: F 25 GLU cc_start: 0.6761 (OUTLIER) cc_final: 0.6455 (tt0) REVERT: F 224 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7721 (pt0) REVERT: F 269 LYS cc_start: 0.7135 (OUTLIER) cc_final: 0.6865 (ptpp) REVERT: F 328 GLU cc_start: 0.5315 (OUTLIER) cc_final: 0.4640 (pp20) outliers start: 119 outliers final: 73 residues processed: 375 average time/residue: 0.6942 time to fit residues: 295.3065 Evaluate side-chains 389 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 300 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 269 LYS Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 245 LYS Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 269 LYS Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 357 ASP Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 168 ASP Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 245 LYS Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 269 LYS Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 328 GLU Chi-restraints excluded: chain C residue 357 ASP Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 25 GLU Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 238 MET Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 269 LYS Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 346 GLU Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 501 THR Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 25 GLU Chi-restraints excluded: chain E residue 168 ASP Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 238 MET Chi-restraints excluded: chain E residue 245 LYS Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 254 ASN Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 269 LYS Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain E residue 357 ASP Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 168 ASP Chi-restraints excluded: chain F residue 224 GLU Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain F residue 231 SER Chi-restraints excluded: chain F residue 238 MET Chi-restraints excluded: chain F residue 245 LYS Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 254 ASN Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 269 LYS Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 328 GLU Chi-restraints excluded: chain F residue 357 ASP Chi-restraints excluded: chain F residue 397 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 39 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 260 optimal weight: 2.9990 chunk 51 optimal weight: 8.9990 chunk 78 optimal weight: 6.9990 chunk 68 optimal weight: 0.7980 chunk 80 optimal weight: 20.0000 chunk 38 optimal weight: 5.9990 chunk 134 optimal weight: 0.8980 chunk 200 optimal weight: 3.9990 chunk 191 optimal weight: 8.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 254 ASN B 330 GLN ** C 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 ASN ** D 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 254 ASN D 374 ASN ** D 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 330 GLN ** F 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 374 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.174539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.136341 restraints weight = 24475.191| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 1.26 r_work: 0.3445 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23790 Z= 0.136 Angle : 0.535 9.015 32118 Z= 0.289 Chirality : 0.044 0.140 3492 Planarity : 0.004 0.041 4182 Dihedral : 5.251 51.882 3298 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 4.69 % Allowed : 19.19 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.15), residues: 2964 helix: 2.19 (0.13), residues: 1584 sheet: -0.44 (0.27), residues: 396 loop : -1.35 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 79 TYR 0.013 0.001 TYR D 407 PHE 0.034 0.002 PHE C 360 TRP 0.011 0.002 TRP F 385 HIS 0.008 0.001 HIS D 264 Details of bonding type rmsd covalent geometry : bond 0.00300 (23790) covalent geometry : angle 0.53471 (32118) hydrogen bonds : bond 0.04740 ( 1374) hydrogen bonds : angle 4.20167 ( 3924) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 299 time to evaluate : 0.894 Fit side-chains REVERT: A 110 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8709 (tm) REVERT: A 269 LYS cc_start: 0.7133 (OUTLIER) cc_final: 0.6907 (ptpp) REVERT: A 342 LYS cc_start: 0.5217 (mmpt) cc_final: 0.4790 (mmtt) REVERT: A 357 ASP cc_start: 0.7229 (OUTLIER) cc_final: 0.6994 (m-30) REVERT: A 358 LYS cc_start: 0.7082 (ttmm) cc_final: 0.6742 (ttmp) REVERT: A 419 ARG cc_start: 0.6615 (ttp-110) cc_final: 0.6308 (ttm110) REVERT: B 72 TRP cc_start: 0.7413 (m100) cc_final: 0.7209 (m100) REVERT: B 227 ILE cc_start: 0.7791 (OUTLIER) cc_final: 0.7588 (tp) REVERT: B 269 LYS cc_start: 0.7164 (OUTLIER) cc_final: 0.6864 (ptpp) REVERT: B 402 GLU cc_start: 0.7550 (pt0) cc_final: 0.7192 (pt0) REVERT: B 411 MET cc_start: 0.8072 (tpt) cc_final: 0.7781 (tpp) REVERT: C 11 LYS cc_start: 0.7303 (mmmt) cc_final: 0.6835 (mppt) REVERT: C 25 GLU cc_start: 0.6770 (OUTLIER) cc_final: 0.6455 (tt0) REVERT: C 224 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7705 (pt0) REVERT: C 269 LYS cc_start: 0.7115 (OUTLIER) cc_final: 0.6853 (ptpp) REVERT: C 292 GLU cc_start: 0.6026 (OUTLIER) cc_final: 0.5824 (tt0) REVERT: C 328 GLU cc_start: 0.5326 (OUTLIER) cc_final: 0.4632 (pp20) REVERT: C 342 LYS cc_start: 0.5051 (mmpt) cc_final: 0.4371 (mttp) REVERT: D 110 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8708 (tm) REVERT: D 269 LYS cc_start: 0.7137 (OUTLIER) cc_final: 0.6915 (ptpp) REVERT: E 269 LYS cc_start: 0.7226 (OUTLIER) cc_final: 0.6914 (ptpp) REVERT: E 402 GLU cc_start: 0.7537 (pt0) cc_final: 0.7181 (pt0) REVERT: F 11 LYS cc_start: 0.7280 (mmmt) cc_final: 0.6804 (mppt) REVERT: F 25 GLU cc_start: 0.6759 (OUTLIER) cc_final: 0.6441 (tt0) REVERT: F 224 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7680 (pt0) REVERT: F 269 LYS cc_start: 0.7106 (OUTLIER) cc_final: 0.6842 (ptpp) REVERT: F 328 GLU cc_start: 0.5315 (OUTLIER) cc_final: 0.4643 (pp20) outliers start: 117 outliers final: 78 residues processed: 371 average time/residue: 0.6892 time to fit residues: 289.3358 Evaluate side-chains 393 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 298 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 269 LYS Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 245 LYS Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 254 ASN Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 269 LYS Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 357 ASP Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 168 ASP Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 245 LYS Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 254 ASN Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 269 LYS Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 328 GLU Chi-restraints excluded: chain C residue 357 ASP Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 25 GLU Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 269 LYS Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 501 THR Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 25 GLU Chi-restraints excluded: chain E residue 168 ASP Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 238 MET Chi-restraints excluded: chain E residue 245 LYS Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 269 LYS Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain E residue 357 ASP Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 168 ASP Chi-restraints excluded: chain F residue 224 GLU Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain F residue 231 SER Chi-restraints excluded: chain F residue 238 MET Chi-restraints excluded: chain F residue 245 LYS Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 254 ASN Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 269 LYS Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 328 GLU Chi-restraints excluded: chain F residue 357 ASP Chi-restraints excluded: chain F residue 397 LEU Chi-restraints excluded: chain F residue 402 GLU Chi-restraints excluded: chain F residue 431 VAL Chi-restraints excluded: chain F residue 435 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 137 optimal weight: 0.9990 chunk 279 optimal weight: 0.7980 chunk 289 optimal weight: 1.9990 chunk 113 optimal weight: 0.6980 chunk 120 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 32 optimal weight: 8.9990 chunk 270 optimal weight: 5.9990 chunk 201 optimal weight: 1.9990 chunk 243 optimal weight: 7.9990 chunk 50 optimal weight: 10.0000 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 254 ASN A 374 ASN B 330 GLN ** C 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 254 ASN ** D 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 297 GLN E 330 GLN E 463 GLN ** F 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 254 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.175972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.137361 restraints weight = 24381.690| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 1.36 r_work: 0.3452 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 23790 Z= 0.116 Angle : 0.523 12.409 32118 Z= 0.279 Chirality : 0.043 0.151 3492 Planarity : 0.004 0.041 4182 Dihedral : 5.052 52.388 3298 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.73 % Allowed : 20.11 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.19 (0.16), residues: 2964 helix: 2.33 (0.13), residues: 1584 sheet: -0.44 (0.27), residues: 396 loop : -1.32 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 419 TYR 0.016 0.001 TYR A 407 PHE 0.035 0.001 PHE C 360 TRP 0.015 0.002 TRP C 72 HIS 0.009 0.001 HIS D 264 Details of bonding type rmsd covalent geometry : bond 0.00251 (23790) covalent geometry : angle 0.52289 (32118) hydrogen bonds : bond 0.04203 ( 1374) hydrogen bonds : angle 4.09524 ( 3924) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 293 time to evaluate : 0.611 Fit side-chains REVERT: A 110 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8694 (tm) REVERT: A 269 LYS cc_start: 0.7148 (OUTLIER) cc_final: 0.6921 (ptpp) REVERT: A 342 LYS cc_start: 0.5170 (mmpt) cc_final: 0.4791 (mppt) REVERT: A 357 ASP cc_start: 0.7214 (OUTLIER) cc_final: 0.6976 (m-30) REVERT: A 358 LYS cc_start: 0.7050 (ttmm) cc_final: 0.6707 (ttmp) REVERT: A 411 MET cc_start: 0.7776 (tpp) cc_final: 0.7483 (tpp) REVERT: A 415 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7487 (mt-10) REVERT: A 419 ARG cc_start: 0.6589 (ttp-110) cc_final: 0.6288 (ttm110) REVERT: B 72 TRP cc_start: 0.7315 (m100) cc_final: 0.7069 (m100) REVERT: B 227 ILE cc_start: 0.7781 (OUTLIER) cc_final: 0.7548 (tp) REVERT: B 269 LYS cc_start: 0.7196 (OUTLIER) cc_final: 0.6900 (ptpp) REVERT: B 342 LYS cc_start: 0.5308 (mmpt) cc_final: 0.4614 (mmpt) REVERT: B 402 GLU cc_start: 0.7539 (pt0) cc_final: 0.7175 (pt0) REVERT: B 411 MET cc_start: 0.8086 (tpt) cc_final: 0.7762 (tpp) REVERT: C 11 LYS cc_start: 0.7290 (mmmt) cc_final: 0.6811 (mppt) REVERT: C 25 GLU cc_start: 0.6742 (OUTLIER) cc_final: 0.6420 (tt0) REVERT: C 269 LYS cc_start: 0.7097 (OUTLIER) cc_final: 0.6833 (ptpp) REVERT: C 292 GLU cc_start: 0.6027 (OUTLIER) cc_final: 0.5825 (tt0) REVERT: C 328 GLU cc_start: 0.5260 (OUTLIER) cc_final: 0.4690 (pp20) REVERT: C 342 LYS cc_start: 0.4997 (mmpt) cc_final: 0.4410 (mttp) REVERT: D 110 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8694 (tm) REVERT: D 269 LYS cc_start: 0.7166 (OUTLIER) cc_final: 0.6947 (ptpp) REVERT: D 342 LYS cc_start: 0.5454 (mmpt) cc_final: 0.4723 (mmpt) REVERT: D 411 MET cc_start: 0.7999 (tpt) cc_final: 0.7695 (tpp) REVERT: E 269 LYS cc_start: 0.7207 (OUTLIER) cc_final: 0.6909 (ptpp) REVERT: E 402 GLU cc_start: 0.7524 (pt0) cc_final: 0.7140 (pt0) REVERT: E 411 MET cc_start: 0.7868 (mmm) cc_final: 0.7520 (tpp) REVERT: F 11 LYS cc_start: 0.7263 (mmmt) cc_final: 0.6778 (mppt) REVERT: F 25 GLU cc_start: 0.6711 (OUTLIER) cc_final: 0.6384 (tt0) REVERT: F 269 LYS cc_start: 0.7092 (OUTLIER) cc_final: 0.6827 (ptpp) REVERT: F 328 GLU cc_start: 0.5260 (OUTLIER) cc_final: 0.4648 (pp20) REVERT: F 342 LYS cc_start: 0.5330 (mmpt) cc_final: 0.4280 (mttp) outliers start: 93 outliers final: 57 residues processed: 351 average time/residue: 0.6380 time to fit residues: 254.0695 Evaluate side-chains 363 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 291 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 269 LYS Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 245 LYS Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 269 LYS Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 357 ASP Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 269 LYS Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 328 GLU Chi-restraints excluded: chain C residue 357 ASP Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 269 LYS Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 501 THR Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 25 GLU Chi-restraints excluded: chain E residue 168 ASP Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 245 LYS Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 269 LYS Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain F residue 231 SER Chi-restraints excluded: chain F residue 238 MET Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 269 LYS Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 328 GLU Chi-restraints excluded: chain F residue 357 ASP Chi-restraints excluded: chain F residue 397 LEU Chi-restraints excluded: chain F residue 402 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 22 optimal weight: 10.0000 chunk 92 optimal weight: 0.8980 chunk 207 optimal weight: 10.0000 chunk 278 optimal weight: 3.9990 chunk 280 optimal weight: 0.9990 chunk 100 optimal weight: 7.9990 chunk 49 optimal weight: 20.0000 chunk 281 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 247 optimal weight: 0.0980 chunk 3 optimal weight: 8.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 254 ASN C 374 ASN ** D 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 254 ASN D 374 ASN ** D 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 463 GLN ** F 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 374 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.174035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.136119 restraints weight = 24323.940| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 1.36 r_work: 0.3428 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 23790 Z= 0.157 Angle : 0.576 12.662 32118 Z= 0.308 Chirality : 0.045 0.146 3492 Planarity : 0.005 0.040 4182 Dihedral : 5.332 51.732 3298 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.53 % Allowed : 20.71 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.00 (0.15), residues: 2964 helix: 2.13 (0.13), residues: 1584 sheet: -0.38 (0.27), residues: 396 loop : -1.37 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 79 TYR 0.015 0.002 TYR D 407 PHE 0.038 0.002 PHE C 360 TRP 0.011 0.002 TRP C 385 HIS 0.009 0.001 HIS D 264 Details of bonding type rmsd covalent geometry : bond 0.00354 (23790) covalent geometry : angle 0.57611 (32118) hydrogen bonds : bond 0.05076 ( 1374) hydrogen bonds : angle 4.28343 ( 3924) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10924.14 seconds wall clock time: 186 minutes 25.50 seconds (11185.50 seconds total)