Starting phenix.real_space_refine on Thu Mar 5 03:42:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6m02_30028/03_2026/6m02_30028.cif Found real_map, /net/cci-nas-00/data/ceres_data/6m02_30028/03_2026/6m02_30028.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6m02_30028/03_2026/6m02_30028.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6m02_30028/03_2026/6m02_30028.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6m02_30028/03_2026/6m02_30028.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6m02_30028/03_2026/6m02_30028.map" } resolution = 3.2 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= 0.003 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 77 5.16 5 C 12509 2.51 5 N 2996 2.21 5 O 3353 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18935 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2705 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain breaks: 3 Restraints were copied for chains: B, C, D, E, F, G Time building chain proxies: 2.63, per 1000 atoms: 0.14 Number of scatterers: 18935 At special positions: 0 Unit cell: (109.725, 109.725, 124.355, 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 77 16.00 O 3353 8.00 N 2996 7.00 C 12509 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 265 " distance=2.03 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS A 246 " distance=2.03 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 265 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 265 " distance=2.03 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 265 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 265 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 265 " distance=2.03 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 265 " distance=2.03 Simple disulfide: pdb=" SG CYS B 84 " - pdb=" SG CYS B 246 " distance=2.03 Simple disulfide: pdb=" SG CYS C 84 " - pdb=" SG CYS C 246 " distance=2.03 Simple disulfide: pdb=" SG CYS D 84 " - pdb=" SG CYS D 246 " distance=2.03 Simple disulfide: pdb=" SG CYS E 84 " - pdb=" SG CYS E 246 " distance=2.03 Simple disulfide: pdb=" SG CYS F 84 " - pdb=" SG CYS F 246 " distance=2.03 Simple disulfide: pdb=" SG CYS G 84 " - pdb=" SG CYS G 246 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.60 Conformation dependent library (CDL) restraints added in 806.3 milliseconds 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4564 Finding SS restraints... Secondary structure from input PDB file: 119 helices and 7 sheets defined 60.6% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 12 through 16 Processing helix chain 'A' and resid 32 through 54 removed outlier: 3.692A pdb=" N LYS A 36 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA A 42 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Proline residue: A 46 - end of helix removed outlier: 3.879A pdb=" N LEU A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 87 removed outlier: 3.711A pdb=" N TRP A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.818A pdb=" N LYS A 107 " --> pdb=" O LEU A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 119 removed outlier: 3.948A pdb=" N ALA A 117 " --> pdb=" O LEU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 131 Processing helix chain 'A' and resid 135 through 155 removed outlier: 3.960A pdb=" N PHE A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU A 144 " --> pdb=" O LYS A 140 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 146 " --> pdb=" O ILE A 142 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL A 149 " --> pdb=" O GLU A 145 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR A 150 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA A 153 " --> pdb=" O VAL A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 162 removed outlier: 3.916A pdb=" N ARG A 161 " --> pdb=" O ALA A 157 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP A 162 " --> pdb=" O LYS A 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 157 through 162' Processing helix chain 'A' and resid 194 through 200 removed outlier: 3.506A pdb=" N LEU A 200 " --> pdb=" O VAL A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 237 removed outlier: 4.440A pdb=" N LEU A 219 " --> pdb=" O SER A 215 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE A 229 " --> pdb=" O LEU A 225 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY A 232 " --> pdb=" O CYS A 228 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER A 236 " --> pdb=" O GLY A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 256 removed outlier: 4.041A pdb=" N ASN A 255 " --> pdb=" O ILE A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 283 removed outlier: 3.976A pdb=" N LEU A 275 " --> pdb=" O GLY A 271 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL A 278 " --> pdb=" O GLN A 274 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL A 282 " --> pdb=" O VAL A 278 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL A 283 " --> pdb=" O ILE A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 295 Proline residue: A 289 - end of helix removed outlier: 3.548A pdb=" N VAL A 292 " --> pdb=" O ALA A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 312 removed outlier: 3.938A pdb=" N ILE A 311 " --> pdb=" O VAL A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 339 removed outlier: 4.199A pdb=" N LEU A 333 " --> pdb=" O SER A 329 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU A 336 " --> pdb=" O ASN A 332 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN A 338 " --> pdb=" O PHE A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 353 removed outlier: 4.151A pdb=" N LYS A 346 " --> pdb=" O VAL A 342 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N CYS A 347 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL A 350 " --> pdb=" O LYS A 346 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LEU A 351 " --> pdb=" O CYS A 347 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLU A 352 " --> pdb=" O LEU A 348 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASN A 353 " --> pdb=" O LYS A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 422 removed outlier: 3.569A pdb=" N GLN A 419 " --> pdb=" O LYS A 415 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ARG A 420 " --> pdb=" O ASN A 416 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU A 421 " --> pdb=" O ALA A 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 16 Processing helix chain 'B' and resid 32 through 54 removed outlier: 3.692A pdb=" N LYS B 36 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA B 42 " --> pdb=" O VAL B 38 " (cutoff:3.500A) Proline residue: B 46 - end of helix removed outlier: 3.879A pdb=" N LEU B 52 " --> pdb=" O LEU B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 87 removed outlier: 3.711A pdb=" N TRP B 85 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA B 86 " --> pdb=" O SER B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 108 removed outlier: 3.818A pdb=" N LYS B 107 " --> pdb=" O LEU B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 119 removed outlier: 3.948A pdb=" N ALA B 117 " --> pdb=" O LEU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 131 Processing helix chain 'B' and resid 135 through 155 removed outlier: 3.961A pdb=" N PHE B 141 " --> pdb=" O SER B 137 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU B 144 " --> pdb=" O LYS B 140 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU B 146 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL B 149 " --> pdb=" O GLU B 145 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR B 150 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA B 153 " --> pdb=" O VAL B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 162 removed outlier: 3.916A pdb=" N ARG B 161 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP B 162 " --> pdb=" O LYS B 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 157 through 162' Processing helix chain 'B' and resid 194 through 200 removed outlier: 3.506A pdb=" N LEU B 200 " --> pdb=" O VAL B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 237 removed outlier: 4.440A pdb=" N LEU B 219 " --> pdb=" O SER B 215 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY B 232 " --> pdb=" O CYS B 228 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER B 236 " --> pdb=" O GLY B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 256 removed outlier: 4.042A pdb=" N ASN B 255 " --> pdb=" O ILE B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 283 removed outlier: 3.976A pdb=" N LEU B 275 " --> pdb=" O GLY B 271 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL B 278 " --> pdb=" O GLN B 274 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL B 282 " --> pdb=" O VAL B 278 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL B 283 " --> pdb=" O ILE B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 295 Proline residue: B 289 - end of helix removed outlier: 3.547A pdb=" N VAL B 292 " --> pdb=" O ALA B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 312 removed outlier: 3.938A pdb=" N ILE B 311 " --> pdb=" O VAL B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 339 removed outlier: 4.199A pdb=" N LEU B 333 " --> pdb=" O SER B 329 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU B 336 " --> pdb=" O ASN B 332 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU B 337 " --> pdb=" O LEU B 333 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN B 338 " --> pdb=" O PHE B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 353 removed outlier: 4.151A pdb=" N LYS B 346 " --> pdb=" O VAL B 342 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N CYS B 347 " --> pdb=" O LYS B 343 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL B 350 " --> pdb=" O LYS B 346 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LEU B 351 " --> pdb=" O CYS B 347 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLU B 352 " --> pdb=" O LEU B 348 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASN B 353 " --> pdb=" O LYS B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 422 removed outlier: 3.569A pdb=" N GLN B 419 " --> pdb=" O LYS B 415 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ARG B 420 " --> pdb=" O ASN B 416 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU B 421 " --> pdb=" O ALA B 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 16 Processing helix chain 'C' and resid 32 through 54 removed outlier: 3.692A pdb=" N LYS C 36 " --> pdb=" O LEU C 32 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA C 42 " --> pdb=" O VAL C 38 " (cutoff:3.500A) Proline residue: C 46 - end of helix removed outlier: 3.879A pdb=" N LEU C 52 " --> pdb=" O LEU C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 87 removed outlier: 3.711A pdb=" N TRP C 85 " --> pdb=" O ASP C 81 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA C 86 " --> pdb=" O SER C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 108 removed outlier: 3.818A pdb=" N LYS C 107 " --> pdb=" O LEU C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 119 removed outlier: 3.948A pdb=" N ALA C 117 " --> pdb=" O LEU C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 131 Processing helix chain 'C' and resid 135 through 155 removed outlier: 3.960A pdb=" N PHE C 141 " --> pdb=" O SER C 137 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU C 144 " --> pdb=" O LYS C 140 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU C 146 " --> pdb=" O ILE C 142 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL C 149 " --> pdb=" O GLU C 145 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR C 150 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA C 153 " --> pdb=" O VAL C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 162 removed outlier: 3.916A pdb=" N ARG C 161 " --> pdb=" O ALA C 157 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP C 162 " --> pdb=" O LYS C 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 157 through 162' Processing helix chain 'C' and resid 194 through 200 removed outlier: 3.505A pdb=" N LEU C 200 " --> pdb=" O VAL C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 237 removed outlier: 4.440A pdb=" N LEU C 219 " --> pdb=" O SER C 215 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE C 229 " --> pdb=" O LEU C 225 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY C 232 " --> pdb=" O CYS C 228 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER C 236 " --> pdb=" O GLY C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 256 removed outlier: 4.042A pdb=" N ASN C 255 " --> pdb=" O ILE C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 283 removed outlier: 3.976A pdb=" N LEU C 275 " --> pdb=" O GLY C 271 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL C 278 " --> pdb=" O GLN C 274 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL C 282 " --> pdb=" O VAL C 278 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL C 283 " --> pdb=" O ILE C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 295 Proline residue: C 289 - end of helix removed outlier: 3.548A pdb=" N VAL C 292 " --> pdb=" O ALA C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 312 removed outlier: 3.939A pdb=" N ILE C 311 " --> pdb=" O VAL C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 339 removed outlier: 4.199A pdb=" N LEU C 333 " --> pdb=" O SER C 329 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU C 336 " --> pdb=" O ASN C 332 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU C 337 " --> pdb=" O LEU C 333 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN C 338 " --> pdb=" O PHE C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 353 removed outlier: 4.151A pdb=" N LYS C 346 " --> pdb=" O VAL C 342 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N CYS C 347 " --> pdb=" O LYS C 343 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL C 350 " --> pdb=" O LYS C 346 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LEU C 351 " --> pdb=" O CYS C 347 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLU C 352 " --> pdb=" O LEU C 348 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASN C 353 " --> pdb=" O LYS C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 422 removed outlier: 3.569A pdb=" N GLN C 419 " --> pdb=" O LYS C 415 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ARG C 420 " --> pdb=" O ASN C 416 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU C 421 " --> pdb=" O ALA C 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 16 Processing helix chain 'D' and resid 32 through 54 removed outlier: 3.692A pdb=" N LYS D 36 " --> pdb=" O LEU D 32 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA D 42 " --> pdb=" O VAL D 38 " (cutoff:3.500A) Proline residue: D 46 - end of helix removed outlier: 3.879A pdb=" N LEU D 52 " --> pdb=" O LEU D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 87 removed outlier: 3.711A pdb=" N TRP D 85 " --> pdb=" O ASP D 81 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA D 86 " --> pdb=" O SER D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 108 removed outlier: 3.818A pdb=" N LYS D 107 " --> pdb=" O LEU D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 119 removed outlier: 3.948A pdb=" N ALA D 117 " --> pdb=" O LEU D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 131 Processing helix chain 'D' and resid 135 through 155 removed outlier: 3.961A pdb=" N PHE D 141 " --> pdb=" O SER D 137 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU D 144 " --> pdb=" O LYS D 140 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU D 146 " --> pdb=" O ILE D 142 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL D 149 " --> pdb=" O GLU D 145 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR D 150 " --> pdb=" O LEU D 146 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA D 153 " --> pdb=" O VAL D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 162 removed outlier: 3.916A pdb=" N ARG D 161 " --> pdb=" O ALA D 157 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP D 162 " --> pdb=" O LYS D 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 157 through 162' Processing helix chain 'D' and resid 194 through 200 removed outlier: 3.506A pdb=" N LEU D 200 " --> pdb=" O VAL D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 237 removed outlier: 4.440A pdb=" N LEU D 219 " --> pdb=" O SER D 215 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE D 229 " --> pdb=" O LEU D 225 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY D 232 " --> pdb=" O CYS D 228 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER D 236 " --> pdb=" O GLY D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 256 removed outlier: 4.041A pdb=" N ASN D 255 " --> pdb=" O ILE D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 283 removed outlier: 3.976A pdb=" N LEU D 275 " --> pdb=" O GLY D 271 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL D 278 " --> pdb=" O GLN D 274 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL D 282 " --> pdb=" O VAL D 278 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL D 283 " --> pdb=" O ILE D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 295 Proline residue: D 289 - end of helix removed outlier: 3.548A pdb=" N VAL D 292 " --> pdb=" O ALA D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 312 removed outlier: 3.938A pdb=" N ILE D 311 " --> pdb=" O VAL D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 339 removed outlier: 4.199A pdb=" N LEU D 333 " --> pdb=" O SER D 329 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU D 336 " --> pdb=" O ASN D 332 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU D 337 " --> pdb=" O LEU D 333 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN D 338 " --> pdb=" O PHE D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 353 removed outlier: 4.151A pdb=" N LYS D 346 " --> pdb=" O VAL D 342 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N CYS D 347 " --> pdb=" O LYS D 343 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL D 350 " --> pdb=" O LYS D 346 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LEU D 351 " --> pdb=" O CYS D 347 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLU D 352 " --> pdb=" O LEU D 348 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASN D 353 " --> pdb=" O LYS D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 422 removed outlier: 3.569A pdb=" N GLN D 419 " --> pdb=" O LYS D 415 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ARG D 420 " --> pdb=" O ASN D 416 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU D 421 " --> pdb=" O ALA D 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 16 Processing helix chain 'E' and resid 32 through 54 removed outlier: 3.692A pdb=" N LYS E 36 " --> pdb=" O LEU E 32 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA E 42 " --> pdb=" O VAL E 38 " (cutoff:3.500A) Proline residue: E 46 - end of helix removed outlier: 3.878A pdb=" N LEU E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 87 removed outlier: 3.711A pdb=" N TRP E 85 " --> pdb=" O ASP E 81 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA E 86 " --> pdb=" O SER E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 108 removed outlier: 3.818A pdb=" N LYS E 107 " --> pdb=" O LEU E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 119 removed outlier: 3.948A pdb=" N ALA E 117 " --> pdb=" O LEU E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 131 Processing helix chain 'E' and resid 135 through 155 removed outlier: 3.960A pdb=" N PHE E 141 " --> pdb=" O SER E 137 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU E 144 " --> pdb=" O LYS E 140 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU E 146 " --> pdb=" O ILE E 142 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL E 149 " --> pdb=" O GLU E 145 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR E 150 " --> pdb=" O LEU E 146 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA E 153 " --> pdb=" O VAL E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 162 removed outlier: 3.916A pdb=" N ARG E 161 " --> pdb=" O ALA E 157 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP E 162 " --> pdb=" O LYS E 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 157 through 162' Processing helix chain 'E' and resid 194 through 200 removed outlier: 3.506A pdb=" N LEU E 200 " --> pdb=" O VAL E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 237 removed outlier: 4.440A pdb=" N LEU E 219 " --> pdb=" O SER E 215 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE E 229 " --> pdb=" O LEU E 225 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY E 232 " --> pdb=" O CYS E 228 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER E 236 " --> pdb=" O GLY E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 256 removed outlier: 4.041A pdb=" N ASN E 255 " --> pdb=" O ILE E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 283 removed outlier: 3.976A pdb=" N LEU E 275 " --> pdb=" O GLY E 271 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL E 278 " --> pdb=" O GLN E 274 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL E 282 " --> pdb=" O VAL E 278 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL E 283 " --> pdb=" O ILE E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 295 Proline residue: E 289 - end of helix removed outlier: 3.547A pdb=" N VAL E 292 " --> pdb=" O ALA E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 312 removed outlier: 3.938A pdb=" N ILE E 311 " --> pdb=" O VAL E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 339 removed outlier: 4.199A pdb=" N LEU E 333 " --> pdb=" O SER E 329 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU E 336 " --> pdb=" O ASN E 332 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU E 337 " --> pdb=" O LEU E 333 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN E 338 " --> pdb=" O PHE E 334 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 353 removed outlier: 4.151A pdb=" N LYS E 346 " --> pdb=" O VAL E 342 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N CYS E 347 " --> pdb=" O LYS E 343 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL E 350 " --> pdb=" O LYS E 346 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LEU E 351 " --> pdb=" O CYS E 347 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLU E 352 " --> pdb=" O LEU E 348 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASN E 353 " --> pdb=" O LYS E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 422 removed outlier: 3.570A pdb=" N GLN E 419 " --> pdb=" O LYS E 415 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ARG E 420 " --> pdb=" O ASN E 416 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU E 421 " --> pdb=" O ALA E 417 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 16 Processing helix chain 'F' and resid 32 through 54 removed outlier: 3.692A pdb=" N LYS F 36 " --> pdb=" O LEU F 32 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA F 42 " --> pdb=" O VAL F 38 " (cutoff:3.500A) Proline residue: F 46 - end of helix removed outlier: 3.879A pdb=" N LEU F 52 " --> pdb=" O LEU F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 87 removed outlier: 3.711A pdb=" N TRP F 85 " --> pdb=" O ASP F 81 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA F 86 " --> pdb=" O SER F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 108 removed outlier: 3.818A pdb=" N LYS F 107 " --> pdb=" O LEU F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 119 removed outlier: 3.948A pdb=" N ALA F 117 " --> pdb=" O LEU F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 131 Processing helix chain 'F' and resid 135 through 155 removed outlier: 3.960A pdb=" N PHE F 141 " --> pdb=" O SER F 137 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU F 144 " --> pdb=" O LYS F 140 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU F 146 " --> pdb=" O ILE F 142 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL F 149 " --> pdb=" O GLU F 145 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR F 150 " --> pdb=" O LEU F 146 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA F 153 " --> pdb=" O VAL F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 162 removed outlier: 3.916A pdb=" N ARG F 161 " --> pdb=" O ALA F 157 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP F 162 " --> pdb=" O LYS F 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 157 through 162' Processing helix chain 'F' and resid 194 through 200 removed outlier: 3.506A pdb=" N LEU F 200 " --> pdb=" O VAL F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 237 removed outlier: 4.441A pdb=" N LEU F 219 " --> pdb=" O SER F 215 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE F 229 " --> pdb=" O LEU F 225 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY F 232 " --> pdb=" O CYS F 228 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER F 236 " --> pdb=" O GLY F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 256 removed outlier: 4.040A pdb=" N ASN F 255 " --> pdb=" O ILE F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 283 removed outlier: 3.976A pdb=" N LEU F 275 " --> pdb=" O GLY F 271 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL F 278 " --> pdb=" O GLN F 274 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL F 282 " --> pdb=" O VAL F 278 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL F 283 " --> pdb=" O ILE F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 283 through 295 Proline residue: F 289 - end of helix removed outlier: 3.547A pdb=" N VAL F 292 " --> pdb=" O ALA F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 312 removed outlier: 3.938A pdb=" N ILE F 311 " --> pdb=" O VAL F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 339 removed outlier: 4.199A pdb=" N LEU F 333 " --> pdb=" O SER F 329 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU F 336 " --> pdb=" O ASN F 332 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU F 337 " --> pdb=" O LEU F 333 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN F 338 " --> pdb=" O PHE F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 353 removed outlier: 4.151A pdb=" N LYS F 346 " --> pdb=" O VAL F 342 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N CYS F 347 " --> pdb=" O LYS F 343 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL F 350 " --> pdb=" O LYS F 346 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LEU F 351 " --> pdb=" O CYS F 347 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLU F 352 " --> pdb=" O LEU F 348 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASN F 353 " --> pdb=" O LYS F 349 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 422 removed outlier: 3.569A pdb=" N GLN F 419 " --> pdb=" O LYS F 415 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ARG F 420 " --> pdb=" O ASN F 416 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU F 421 " --> pdb=" O ALA F 417 " (cutoff:3.500A) Processing helix chain 'G' and resid 12 through 16 Processing helix chain 'G' and resid 32 through 54 removed outlier: 3.692A pdb=" N LYS G 36 " --> pdb=" O LEU G 32 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA G 42 " --> pdb=" O VAL G 38 " (cutoff:3.500A) Proline residue: G 46 - end of helix removed outlier: 3.879A pdb=" N LEU G 52 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 76 through 87 removed outlier: 3.710A pdb=" N TRP G 85 " --> pdb=" O ASP G 81 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA G 86 " --> pdb=" O SER G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 103 through 108 removed outlier: 3.819A pdb=" N LYS G 107 " --> pdb=" O LEU G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 119 removed outlier: 3.948A pdb=" N ALA G 117 " --> pdb=" O LEU G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 131 Processing helix chain 'G' and resid 135 through 155 removed outlier: 3.961A pdb=" N PHE G 141 " --> pdb=" O SER G 137 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU G 144 " --> pdb=" O LYS G 140 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU G 146 " --> pdb=" O ILE G 142 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL G 149 " --> pdb=" O GLU G 145 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR G 150 " --> pdb=" O LEU G 146 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA G 153 " --> pdb=" O VAL G 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 157 through 162 removed outlier: 3.916A pdb=" N ARG G 161 " --> pdb=" O ALA G 157 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP G 162 " --> pdb=" O LYS G 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 157 through 162' Processing helix chain 'G' and resid 194 through 200 removed outlier: 3.506A pdb=" N LEU G 200 " --> pdb=" O VAL G 196 " (cutoff:3.500A) Processing helix chain 'G' and resid 213 through 237 removed outlier: 4.440A pdb=" N LEU G 219 " --> pdb=" O SER G 215 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE G 229 " --> pdb=" O LEU G 225 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY G 232 " --> pdb=" O CYS G 228 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER G 236 " --> pdb=" O GLY G 232 " (cutoff:3.500A) Processing helix chain 'G' and resid 252 through 256 removed outlier: 4.041A pdb=" N ASN G 255 " --> pdb=" O ILE G 252 " (cutoff:3.500A) Processing helix chain 'G' and resid 269 through 283 removed outlier: 3.976A pdb=" N LEU G 275 " --> pdb=" O GLY G 271 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL G 278 " --> pdb=" O GLN G 274 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL G 282 " --> pdb=" O VAL G 278 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL G 283 " --> pdb=" O ILE G 279 " (cutoff:3.500A) Processing helix chain 'G' and resid 283 through 295 Proline residue: G 289 - end of helix removed outlier: 3.548A pdb=" N VAL G 292 " --> pdb=" O ALA G 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 306 through 312 removed outlier: 3.938A pdb=" N ILE G 311 " --> pdb=" O VAL G 308 " (cutoff:3.500A) Processing helix chain 'G' and resid 326 through 339 removed outlier: 4.199A pdb=" N LEU G 333 " --> pdb=" O SER G 329 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU G 336 " --> pdb=" O ASN G 332 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU G 337 " --> pdb=" O LEU G 333 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN G 338 " --> pdb=" O PHE G 334 " (cutoff:3.500A) Processing helix chain 'G' and resid 342 through 353 removed outlier: 4.150A pdb=" N LYS G 346 " --> pdb=" O VAL G 342 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N CYS G 347 " --> pdb=" O LYS G 343 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL G 350 " --> pdb=" O LYS G 346 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LEU G 351 " --> pdb=" O CYS G 347 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLU G 352 " --> pdb=" O LEU G 348 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASN G 353 " --> pdb=" O LYS G 349 " (cutoff:3.500A) Processing helix chain 'G' and resid 414 through 422 removed outlier: 3.569A pdb=" N GLN G 419 " --> pdb=" O LYS G 415 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ARG G 420 " --> pdb=" O ASN G 416 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU G 421 " --> pdb=" O ALA G 417 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 66 removed outlier: 3.609A pdb=" N PHE A 244 " --> pdb=" O CYS A 265 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 64 through 66 removed outlier: 3.609A pdb=" N PHE B 244 " --> pdb=" O CYS B 265 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 64 through 66 removed outlier: 3.609A pdb=" N PHE C 244 " --> pdb=" O CYS C 265 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 64 through 66 removed outlier: 3.608A pdb=" N PHE D 244 " --> pdb=" O CYS D 265 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 64 through 66 removed outlier: 3.608A pdb=" N PHE E 244 " --> pdb=" O CYS E 265 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 64 through 66 removed outlier: 3.609A pdb=" N PHE F 244 " --> pdb=" O CYS F 265 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 64 through 66 removed outlier: 3.609A pdb=" N PHE G 244 " --> pdb=" O CYS G 265 " (cutoff:3.500A) 679 hydrogen bonds defined for protein. 1890 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.76 Time building geometry restraints manager: 2.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5660 1.34 - 1.46: 4040 1.46 - 1.57: 9564 1.57 - 1.69: 0 1.69 - 1.81: 91 Bond restraints: 19355 Sorted by residual: bond pdb=" C PRO G 123 " pdb=" N PRO G 124 " ideal model delta sigma weight residual 1.337 1.356 -0.020 1.06e-02 8.90e+03 3.56e+00 bond pdb=" C PRO F 123 " pdb=" N PRO F 124 " ideal model delta sigma weight residual 1.337 1.356 -0.020 1.06e-02 8.90e+03 3.51e+00 bond pdb=" C PRO A 123 " pdb=" N PRO A 124 " ideal model delta sigma weight residual 1.337 1.356 -0.020 1.06e-02 8.90e+03 3.39e+00 bond pdb=" C PRO E 123 " pdb=" N PRO E 124 " ideal model delta sigma weight residual 1.337 1.356 -0.019 1.06e-02 8.90e+03 3.37e+00 bond pdb=" C PRO C 123 " pdb=" N PRO C 124 " ideal model delta sigma weight residual 1.337 1.356 -0.019 1.06e-02 8.90e+03 3.34e+00 ... (remaining 19350 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 25113 2.10 - 4.20: 953 4.20 - 6.31: 79 6.31 - 8.41: 56 8.41 - 10.51: 14 Bond angle restraints: 26215 Sorted by residual: angle pdb=" CA PRO E 123 " pdb=" C PRO E 123 " pdb=" N PRO E 124 " ideal model delta sigma weight residual 117.93 122.19 -4.26 1.20e+00 6.94e-01 1.26e+01 angle pdb=" CA PRO F 123 " pdb=" C PRO F 123 " pdb=" N PRO F 124 " ideal model delta sigma weight residual 117.93 122.19 -4.26 1.20e+00 6.94e-01 1.26e+01 angle pdb=" CA PRO A 123 " pdb=" C PRO A 123 " pdb=" N PRO A 124 " ideal model delta sigma weight residual 117.93 122.19 -4.26 1.20e+00 6.94e-01 1.26e+01 angle pdb=" CA PRO B 123 " pdb=" C PRO B 123 " pdb=" N PRO B 124 " ideal model delta sigma weight residual 117.93 122.18 -4.25 1.20e+00 6.94e-01 1.26e+01 angle pdb=" CA PRO C 123 " pdb=" C PRO C 123 " pdb=" N PRO C 124 " ideal model delta sigma weight residual 117.93 122.18 -4.25 1.20e+00 6.94e-01 1.25e+01 ... (remaining 26210 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 10023 17.97 - 35.93: 1292 35.93 - 53.90: 284 53.90 - 71.86: 7 71.86 - 89.83: 28 Dihedral angle restraints: 11634 sinusoidal: 4634 harmonic: 7000 Sorted by residual: dihedral pdb=" CA ARG A 75 " pdb=" C ARG A 75 " pdb=" N GLN A 76 " pdb=" CA GLN A 76 " ideal model delta harmonic sigma weight residual 180.00 156.98 23.02 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA ARG D 75 " pdb=" C ARG D 75 " pdb=" N GLN D 76 " pdb=" CA GLN D 76 " ideal model delta harmonic sigma weight residual 180.00 156.98 23.02 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA ARG G 75 " pdb=" C ARG G 75 " pdb=" N GLN G 76 " pdb=" CA GLN G 76 " ideal model delta harmonic sigma weight residual 180.00 156.99 23.01 0 5.00e+00 4.00e-02 2.12e+01 ... (remaining 11631 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 2086 0.045 - 0.089: 687 0.089 - 0.134: 205 0.134 - 0.179: 61 0.179 - 0.223: 20 Chirality restraints: 3059 Sorted by residual: chirality pdb=" CB VAL E 278 " pdb=" CA VAL E 278 " pdb=" CG1 VAL E 278 " pdb=" CG2 VAL E 278 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CB VAL F 278 " pdb=" CA VAL F 278 " pdb=" CG1 VAL F 278 " pdb=" CG2 VAL F 278 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CB VAL C 278 " pdb=" CA VAL C 278 " pdb=" CG1 VAL C 278 " pdb=" CG2 VAL C 278 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 3056 not shown) Planarity restraints: 3206 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 122 " -0.047 5.00e-02 4.00e+02 7.01e-02 7.87e+00 pdb=" N PRO A 123 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO A 123 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 123 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 122 " -0.047 5.00e-02 4.00e+02 7.01e-02 7.85e+00 pdb=" N PRO C 123 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO C 123 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 123 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 122 " 0.047 5.00e-02 4.00e+02 7.01e-02 7.85e+00 pdb=" N PRO E 123 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO E 123 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO E 123 " 0.039 5.00e-02 4.00e+02 ... (remaining 3203 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 5282 2.79 - 3.32: 16628 3.32 - 3.85: 30005 3.85 - 4.37: 35740 4.37 - 4.90: 58553 Nonbonded interactions: 146208 Sorted by model distance: nonbonded pdb=" OH TYR G 83 " pdb=" OG SER G 250 " model vdw 2.263 3.040 nonbonded pdb=" OH TYR A 83 " pdb=" OG SER A 250 " model vdw 2.263 3.040 nonbonded pdb=" OH TYR C 83 " pdb=" OG SER C 250 " model vdw 2.263 3.040 nonbonded pdb=" OH TYR F 83 " pdb=" OG SER F 250 " model vdw 2.263 3.040 nonbonded pdb=" OH TYR D 83 " pdb=" OG SER D 250 " model vdw 2.264 3.040 ... (remaining 146203 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 15.250 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6825 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 19369 Z= 0.248 Angle : 0.955 10.512 26243 Z= 0.526 Chirality : 0.052 0.223 3059 Planarity : 0.007 0.070 3206 Dihedral : 16.354 89.826 7028 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 1.64 % Allowed : 12.83 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.29 (0.12), residues: 2289 helix: -4.88 (0.05), residues: 1365 sheet: -4.13 (0.33), residues: 126 loop : -2.27 (0.20), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 29 TYR 0.014 0.002 TYR B 193 PHE 0.018 0.002 PHE E 15 TRP 0.010 0.002 TRP C 74 HIS 0.003 0.001 HIS D 106 Details of bonding type rmsd covalent geometry : bond 0.00555 (19355) covalent geometry : angle 0.95502 (26215) SS BOND : bond 0.00321 ( 14) SS BOND : angle 1.11410 ( 28) hydrogen bonds : bond 0.32655 ( 679) hydrogen bonds : angle 11.06293 ( 1890) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 323 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ILE cc_start: 0.7723 (mm) cc_final: 0.7503 (mm) REVERT: A 212 LYS cc_start: 0.8057 (mmtt) cc_final: 0.7802 (mtmm) REVERT: A 295 LEU cc_start: 0.8040 (mt) cc_final: 0.7549 (mt) REVERT: A 339 ILE cc_start: 0.8466 (mm) cc_final: 0.8240 (mm) REVERT: A 422 LEU cc_start: 0.7115 (OUTLIER) cc_final: 0.6652 (mm) REVERT: B 63 GLN cc_start: 0.7704 (mm110) cc_final: 0.7395 (mm110) REVERT: B 212 LYS cc_start: 0.7855 (mmtt) cc_final: 0.7574 (mtmm) REVERT: B 295 LEU cc_start: 0.7931 (mt) cc_final: 0.7560 (mt) REVERT: B 422 LEU cc_start: 0.6908 (OUTLIER) cc_final: 0.6520 (mm) REVERT: C 50 ILE cc_start: 0.7788 (mm) cc_final: 0.7573 (mm) REVERT: C 212 LYS cc_start: 0.8109 (mmtt) cc_final: 0.7795 (mtmm) REVERT: C 339 ILE cc_start: 0.8528 (mm) cc_final: 0.8156 (mm) REVERT: C 422 LEU cc_start: 0.7168 (OUTLIER) cc_final: 0.6869 (mm) REVERT: D 295 LEU cc_start: 0.8162 (mt) cc_final: 0.7809 (mt) REVERT: D 310 GLU cc_start: 0.7856 (tm-30) cc_final: 0.7538 (tm-30) REVERT: D 339 ILE cc_start: 0.8446 (mm) cc_final: 0.8194 (mm) REVERT: D 422 LEU cc_start: 0.7073 (OUTLIER) cc_final: 0.6671 (mm) REVERT: E 48 LEU cc_start: 0.9015 (mm) cc_final: 0.8800 (mm) REVERT: E 50 ILE cc_start: 0.7608 (mm) cc_final: 0.7398 (mm) REVERT: E 212 LYS cc_start: 0.8016 (mmtt) cc_final: 0.7649 (mtmm) REVERT: E 295 LEU cc_start: 0.7866 (mt) cc_final: 0.7435 (mt) REVERT: E 339 ILE cc_start: 0.8443 (mm) cc_final: 0.8096 (mm) REVERT: E 418 ARG cc_start: 0.6420 (tpm170) cc_final: 0.6118 (tpp-160) REVERT: E 419 GLN cc_start: 0.5070 (pt0) cc_final: 0.4342 (tt0) REVERT: E 422 LEU cc_start: 0.7178 (OUTLIER) cc_final: 0.6264 (mm) REVERT: F 212 LYS cc_start: 0.8032 (mmtt) cc_final: 0.7767 (mtmm) REVERT: F 295 LEU cc_start: 0.7731 (mt) cc_final: 0.7359 (mt) REVERT: F 339 ILE cc_start: 0.8387 (mm) cc_final: 0.8044 (mm) REVERT: F 422 LEU cc_start: 0.7399 (OUTLIER) cc_final: 0.7081 (mm) REVERT: G 212 LYS cc_start: 0.8031 (mmtt) cc_final: 0.7643 (mtmm) REVERT: G 295 LEU cc_start: 0.8079 (mt) cc_final: 0.7631 (mt) REVERT: G 310 GLU cc_start: 0.7874 (tm-30) cc_final: 0.7566 (tm-30) REVERT: G 339 ILE cc_start: 0.8370 (mm) cc_final: 0.8132 (mm) REVERT: G 422 LEU cc_start: 0.6995 (OUTLIER) cc_final: 0.6686 (mm) outliers start: 35 outliers final: 0 residues processed: 344 average time/residue: 0.1789 time to fit residues: 86.4329 Evaluate side-chains 207 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 200 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain E residue 422 LEU Chi-restraints excluded: chain F residue 422 LEU Chi-restraints excluded: chain G residue 422 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 216 optimal weight: 0.6980 chunk 98 optimal weight: 0.0020 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 2.9990 overall best weight: 1.1394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 95 GLN A 134 HIS A 198 GLN A 207 ASN ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 GLN B 95 GLN B 134 HIS B 198 GLN B 207 ASN B 264 GLN ** B 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 GLN C 95 GLN C 134 HIS C 207 ASN ** C 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 411 ASN D 89 GLN D 95 GLN D 134 HIS D 198 GLN D 207 ASN ** D 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 GLN E 95 GLN E 134 HIS E 198 GLN E 207 ASN ** E 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 89 GLN F 95 GLN F 134 HIS F 207 ASN ** F 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 GLN G 95 GLN G 134 HIS G 198 GLN G 207 ASN ** G 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.131665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.111146 restraints weight = 41313.061| |-----------------------------------------------------------------------------| r_work (start): 0.3918 rms_B_bonded: 3.27 r_work: 0.3809 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19369 Z= 0.139 Angle : 0.671 11.085 26243 Z= 0.346 Chirality : 0.039 0.138 3059 Planarity : 0.005 0.047 3206 Dihedral : 6.190 59.365 2520 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.99 % Allowed : 16.45 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.89 (0.15), residues: 2289 helix: -3.69 (0.10), residues: 1428 sheet: -2.96 (0.37), residues: 126 loop : -1.73 (0.24), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 152 TYR 0.017 0.002 TYR E 345 PHE 0.012 0.001 PHE G 108 TRP 0.008 0.001 TRP A 74 HIS 0.001 0.000 HIS E 134 Details of bonding type rmsd covalent geometry : bond 0.00298 (19355) covalent geometry : angle 0.67071 (26215) SS BOND : bond 0.00138 ( 14) SS BOND : angle 0.73427 ( 28) hydrogen bonds : bond 0.05402 ( 679) hydrogen bonds : angle 5.49883 ( 1890) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 187 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LEU cc_start: 0.8784 (mt) cc_final: 0.8317 (pp) REVERT: A 212 LYS cc_start: 0.8169 (mmtt) cc_final: 0.7670 (mtmm) REVERT: A 336 GLU cc_start: 0.7778 (tp30) cc_final: 0.7501 (pt0) REVERT: B 74 TRP cc_start: 0.7481 (OUTLIER) cc_final: 0.6655 (t60) REVERT: B 339 ILE cc_start: 0.8752 (tp) cc_final: 0.8387 (tp) REVERT: C 209 LEU cc_start: 0.6561 (tp) cc_final: 0.6318 (tt) REVERT: C 212 LYS cc_start: 0.8250 (mmtt) cc_final: 0.7825 (mtmm) REVERT: D 128 ARG cc_start: 0.8086 (ttm170) cc_final: 0.7574 (tmm-80) REVERT: D 209 LEU cc_start: 0.6660 (tp) cc_final: 0.6284 (tt) REVERT: D 310 GLU cc_start: 0.8404 (tm-30) cc_final: 0.8113 (tm-30) REVERT: D 336 GLU cc_start: 0.7723 (tp30) cc_final: 0.7303 (pt0) REVERT: E 49 LEU cc_start: 0.8756 (mt) cc_final: 0.8135 (pp) REVERT: E 212 LYS cc_start: 0.8219 (mmtt) cc_final: 0.7710 (mtmm) REVERT: E 254 ARG cc_start: 0.8368 (mtp85) cc_final: 0.7938 (mmm160) REVERT: E 295 LEU cc_start: 0.7915 (mt) cc_final: 0.7491 (mt) REVERT: E 339 ILE cc_start: 0.8307 (mm) cc_final: 0.8075 (tp) REVERT: E 345 TYR cc_start: 0.7493 (t80) cc_final: 0.7258 (t80) REVERT: E 419 GLN cc_start: 0.5153 (pt0) cc_final: 0.4946 (tt0) REVERT: E 422 LEU cc_start: 0.7406 (OUTLIER) cc_final: 0.7133 (mm) REVERT: F 49 LEU cc_start: 0.8624 (mt) cc_final: 0.8072 (pp) REVERT: F 128 ARG cc_start: 0.8197 (ttm170) cc_final: 0.7677 (tmm-80) REVERT: F 212 LYS cc_start: 0.8160 (mmtt) cc_final: 0.7757 (mtmm) REVERT: G 212 LYS cc_start: 0.8186 (mmtt) cc_final: 0.7695 (mtmt) REVERT: G 234 TYR cc_start: 0.8082 (t80) cc_final: 0.7610 (t80) REVERT: G 310 GLU cc_start: 0.8315 (tm-30) cc_final: 0.7948 (tm-30) REVERT: G 336 GLU cc_start: 0.7749 (tp30) cc_final: 0.7458 (pt0) outliers start: 85 outliers final: 46 residues processed: 248 average time/residue: 0.1583 time to fit residues: 57.4378 Evaluate side-chains 220 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 172 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 CYS Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 74 TRP Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain C residue 40 CYS Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 74 TRP Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 299 PHE Chi-restraints excluded: chain E residue 422 LEU Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 214 ILE Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 420 ARG Chi-restraints excluded: chain F residue 422 LEU Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 214 ILE Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 422 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 160 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 chunk 185 optimal weight: 7.9990 chunk 21 optimal weight: 9.9990 chunk 76 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 200 optimal weight: 7.9990 chunk 22 optimal weight: 0.7980 chunk 85 optimal weight: 5.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 HIS ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 ASN B 319 HIS ** B 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 198 GLN C 207 ASN C 319 HIS D 207 ASN D 319 HIS ** D 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 207 ASN E 319 HIS ** E 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 207 ASN F 319 HIS ** F 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 207 ASN G 319 HIS ** G 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.127698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.107480 restraints weight = 41976.702| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 3.23 r_work: 0.3764 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 19369 Z= 0.189 Angle : 0.683 9.462 26243 Z= 0.344 Chirality : 0.041 0.125 3059 Planarity : 0.004 0.045 3206 Dihedral : 5.935 54.205 2518 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 4.61 % Allowed : 18.37 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.94 (0.16), residues: 2289 helix: -2.94 (0.12), residues: 1414 sheet: -2.47 (0.36), residues: 126 loop : -1.40 (0.25), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 152 TYR 0.021 0.002 TYR B 234 PHE 0.020 0.002 PHE A 108 TRP 0.016 0.002 TRP A 74 HIS 0.002 0.001 HIS D 106 Details of bonding type rmsd covalent geometry : bond 0.00439 (19355) covalent geometry : angle 0.68250 (26215) SS BOND : bond 0.00245 ( 14) SS BOND : angle 0.80579 ( 28) hydrogen bonds : bond 0.04667 ( 679) hydrogen bonds : angle 4.98219 ( 1890) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 178 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LEU cc_start: 0.8835 (mt) cc_final: 0.8393 (pp) REVERT: A 212 LYS cc_start: 0.8303 (mmtt) cc_final: 0.7616 (mtmm) REVERT: A 310 GLU cc_start: 0.8368 (tm-30) cc_final: 0.8120 (tm-30) REVERT: B 74 TRP cc_start: 0.7651 (OUTLIER) cc_final: 0.6699 (t60) REVERT: C 37 MET cc_start: 0.8128 (tpp) cc_final: 0.7650 (tpp) REVERT: C 209 LEU cc_start: 0.6871 (tp) cc_final: 0.6566 (tt) REVERT: D 49 LEU cc_start: 0.8632 (mt) cc_final: 0.8277 (pp) REVERT: D 209 LEU cc_start: 0.6711 (tp) cc_final: 0.6256 (tt) REVERT: D 310 GLU cc_start: 0.8384 (tm-30) cc_final: 0.8097 (tm-30) REVERT: E 37 MET cc_start: 0.8085 (tpp) cc_final: 0.7862 (tpp) REVERT: E 49 LEU cc_start: 0.8849 (mt) cc_final: 0.8321 (pp) REVERT: E 212 LYS cc_start: 0.8194 (mmtt) cc_final: 0.7537 (mtmm) REVERT: E 254 ARG cc_start: 0.8489 (mtp85) cc_final: 0.8238 (mmm-85) REVERT: E 295 LEU cc_start: 0.7871 (mt) cc_final: 0.7406 (mt) REVERT: E 299 PHE cc_start: 0.7786 (OUTLIER) cc_final: 0.6862 (t80) REVERT: F 37 MET cc_start: 0.7916 (tpp) cc_final: 0.7674 (tpp) REVERT: F 49 LEU cc_start: 0.8625 (mt) cc_final: 0.8093 (pp) REVERT: F 128 ARG cc_start: 0.8301 (ttm170) cc_final: 0.7799 (tmm-80) REVERT: G 37 MET cc_start: 0.7812 (tpp) cc_final: 0.7600 (tpp) REVERT: G 233 TYR cc_start: 0.7800 (t80) cc_final: 0.7545 (t80) REVERT: G 310 GLU cc_start: 0.8386 (tm-30) cc_final: 0.8091 (tm-30) REVERT: G 351 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7707 (mt) outliers start: 98 outliers final: 80 residues processed: 249 average time/residue: 0.1332 time to fit residues: 50.5481 Evaluate side-chains 241 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 158 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 40 CYS Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 207 ASN Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 74 TRP Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 40 CYS Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 74 TRP Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 207 ASN Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 74 TRP Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 207 ASN Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 299 PHE Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 422 LEU Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 74 TRP Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 207 ASN Chi-restraints excluded: chain F residue 214 ILE Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 299 PHE Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 420 ARG Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 207 ASN Chi-restraints excluded: chain G residue 214 ILE Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 351 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 61 optimal weight: 8.9990 chunk 133 optimal weight: 10.0000 chunk 81 optimal weight: 6.9990 chunk 122 optimal weight: 0.9980 chunk 123 optimal weight: 0.6980 chunk 217 optimal weight: 2.9990 chunk 136 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 chunk 223 optimal weight: 0.0980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 GLN ** B 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 56 GLN C 280 ASN D 56 GLN ** D 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 ASN ** E 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 198 GLN ** F 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 56 GLN ** G 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.130466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.110536 restraints weight = 41178.231| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 3.21 r_work: 0.3805 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 19369 Z= 0.108 Angle : 0.591 10.891 26243 Z= 0.296 Chirality : 0.037 0.131 3059 Planarity : 0.004 0.041 3206 Dihedral : 5.131 32.655 2508 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.95 % Allowed : 21.48 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.30 (0.17), residues: 2289 helix: -2.42 (0.13), residues: 1407 sheet: -2.03 (0.38), residues: 126 loop : -1.25 (0.25), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 29 TYR 0.016 0.001 TYR B 234 PHE 0.012 0.001 PHE C 108 TRP 0.008 0.001 TRP B 74 HIS 0.001 0.000 HIS D 106 Details of bonding type rmsd covalent geometry : bond 0.00234 (19355) covalent geometry : angle 0.59161 (26215) SS BOND : bond 0.00062 ( 14) SS BOND : angle 0.36085 ( 28) hydrogen bonds : bond 0.03731 ( 679) hydrogen bonds : angle 4.64142 ( 1890) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 173 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LEU cc_start: 0.8804 (mt) cc_final: 0.8322 (pp) REVERT: A 212 LYS cc_start: 0.8236 (mmtt) cc_final: 0.7510 (mtmm) REVERT: A 310 GLU cc_start: 0.8390 (tm-30) cc_final: 0.8093 (tm-30) REVERT: B 74 TRP cc_start: 0.7590 (OUTLIER) cc_final: 0.6602 (t60) REVERT: B 243 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7567 (tm-30) REVERT: B 310 GLU cc_start: 0.8440 (tm-30) cc_final: 0.8043 (tm-30) REVERT: C 37 MET cc_start: 0.8039 (tpp) cc_final: 0.7624 (tpp) REVERT: C 49 LEU cc_start: 0.8693 (mt) cc_final: 0.8136 (pp) REVERT: C 209 LEU cc_start: 0.6751 (tp) cc_final: 0.6440 (tt) REVERT: C 243 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7634 (tm-30) REVERT: C 418 ARG cc_start: 0.7209 (tpp-160) cc_final: 0.6200 (tpp-160) REVERT: D 49 LEU cc_start: 0.8592 (mt) cc_final: 0.8258 (pp) REVERT: D 128 ARG cc_start: 0.8320 (ttm170) cc_final: 0.7759 (tmm-80) REVERT: D 209 LEU cc_start: 0.6680 (tp) cc_final: 0.6455 (tt) REVERT: D 243 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7459 (tm-30) REVERT: D 310 GLU cc_start: 0.8442 (tm-30) cc_final: 0.8143 (tm-30) REVERT: D 336 GLU cc_start: 0.7821 (tp30) cc_final: 0.7511 (pt0) REVERT: E 37 MET cc_start: 0.8117 (tpp) cc_final: 0.7895 (tpp) REVERT: E 49 LEU cc_start: 0.8814 (mt) cc_final: 0.8328 (pp) REVERT: E 212 LYS cc_start: 0.8149 (mmtt) cc_final: 0.7471 (mtmm) REVERT: E 243 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7873 (pp20) REVERT: E 280 ASN cc_start: 0.8255 (OUTLIER) cc_final: 0.7322 (t0) REVERT: E 299 PHE cc_start: 0.7777 (OUTLIER) cc_final: 0.6902 (t80) REVERT: F 37 MET cc_start: 0.7981 (tpp) cc_final: 0.7775 (tpp) REVERT: F 49 LEU cc_start: 0.8589 (mt) cc_final: 0.8098 (pp) REVERT: F 128 ARG cc_start: 0.8258 (ttm170) cc_final: 0.7816 (tmm-80) REVERT: F 243 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7390 (tm-30) REVERT: G 234 TYR cc_start: 0.8183 (t80) cc_final: 0.7593 (t80) REVERT: G 310 GLU cc_start: 0.8407 (tm-30) cc_final: 0.8089 (tm-30) REVERT: G 351 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7621 (mt) outliers start: 84 outliers final: 61 residues processed: 240 average time/residue: 0.1415 time to fit residues: 51.2693 Evaluate side-chains 225 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 155 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 40 CYS Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 74 TRP Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 207 ASN Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 74 TRP Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 40 CYS Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 74 TRP Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 243 GLU Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 299 PHE Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 74 TRP Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 243 GLU Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 280 ASN Chi-restraints excluded: chain E residue 299 PHE Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 74 TRP Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 214 ILE Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 243 GLU Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 299 PHE Chi-restraints excluded: chain F residue 420 ARG Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 214 ILE Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 351 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 14 optimal weight: 7.9990 chunk 118 optimal weight: 0.9990 chunk 140 optimal weight: 0.9980 chunk 186 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 chunk 155 optimal weight: 3.9990 chunk 194 optimal weight: 1.9990 chunk 161 optimal weight: 0.6980 chunk 101 optimal weight: 4.9990 chunk 181 optimal weight: 6.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 264 GLN ** G 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.129835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.109838 restraints weight = 41302.187| |-----------------------------------------------------------------------------| r_work (start): 0.3904 rms_B_bonded: 3.19 r_work: 0.3800 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.3818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 19369 Z= 0.124 Angle : 0.620 13.041 26243 Z= 0.300 Chirality : 0.038 0.129 3059 Planarity : 0.003 0.042 3206 Dihedral : 4.998 16.805 2506 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 4.56 % Allowed : 21.66 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.93 (0.17), residues: 2289 helix: -2.10 (0.13), residues: 1407 sheet: -1.87 (0.38), residues: 126 loop : -1.18 (0.25), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 420 TYR 0.017 0.001 TYR F 234 PHE 0.013 0.001 PHE E 108 TRP 0.009 0.001 TRP B 74 HIS 0.001 0.001 HIS D 319 Details of bonding type rmsd covalent geometry : bond 0.00283 (19355) covalent geometry : angle 0.62034 (26215) SS BOND : bond 0.00124 ( 14) SS BOND : angle 0.43486 ( 28) hydrogen bonds : bond 0.03606 ( 679) hydrogen bonds : angle 4.49236 ( 1890) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 154 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LEU cc_start: 0.8800 (mt) cc_final: 0.8316 (pp) REVERT: A 212 LYS cc_start: 0.8267 (mmtt) cc_final: 0.7575 (mtmm) REVERT: A 310 GLU cc_start: 0.8356 (tm-30) cc_final: 0.8096 (tm-30) REVERT: B 49 LEU cc_start: 0.8675 (mt) cc_final: 0.8274 (pp) REVERT: B 74 TRP cc_start: 0.7605 (OUTLIER) cc_final: 0.6634 (t60) REVERT: B 243 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7617 (tm-30) REVERT: B 310 GLU cc_start: 0.8420 (tm-30) cc_final: 0.8027 (tm-30) REVERT: C 37 MET cc_start: 0.8015 (tpp) cc_final: 0.7587 (tpp) REVERT: C 49 LEU cc_start: 0.8664 (mt) cc_final: 0.8169 (pp) REVERT: C 128 ARG cc_start: 0.8257 (ttm170) cc_final: 0.7766 (tmm-80) REVERT: C 209 LEU cc_start: 0.6596 (tp) cc_final: 0.6272 (tt) REVERT: C 243 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7779 (tm-30) REVERT: D 49 LEU cc_start: 0.8597 (mt) cc_final: 0.8288 (pp) REVERT: D 128 ARG cc_start: 0.8349 (ttm170) cc_final: 0.7796 (tmm-80) REVERT: D 209 LEU cc_start: 0.6803 (tp) cc_final: 0.6587 (tt) REVERT: D 243 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7561 (tm-30) REVERT: D 293 TYR cc_start: 0.6074 (t80) cc_final: 0.5862 (t80) REVERT: D 310 GLU cc_start: 0.8427 (tm-30) cc_final: 0.8148 (tm-30) REVERT: E 37 MET cc_start: 0.8111 (tpp) cc_final: 0.7851 (tpp) REVERT: E 49 LEU cc_start: 0.8742 (mt) cc_final: 0.8302 (pp) REVERT: E 212 LYS cc_start: 0.8100 (mmtt) cc_final: 0.7375 (mtmm) REVERT: E 243 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7943 (pp20) REVERT: E 295 LEU cc_start: 0.7811 (mt) cc_final: 0.7378 (mt) REVERT: E 299 PHE cc_start: 0.7785 (OUTLIER) cc_final: 0.7007 (t80) REVERT: F 49 LEU cc_start: 0.8544 (mt) cc_final: 0.8091 (pp) REVERT: F 128 ARG cc_start: 0.8271 (ttm170) cc_final: 0.7806 (tmm-80) REVERT: F 243 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7382 (tm-30) REVERT: G 49 LEU cc_start: 0.8787 (mt) cc_final: 0.8264 (pp) REVERT: G 212 LYS cc_start: 0.8353 (mmtt) cc_final: 0.7626 (mtmm) REVERT: G 310 GLU cc_start: 0.8411 (tm-30) cc_final: 0.8104 (tm-30) outliers start: 97 outliers final: 78 residues processed: 229 average time/residue: 0.1372 time to fit residues: 47.8988 Evaluate side-chains 230 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 145 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 74 TRP Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 207 ASN Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 74 TRP Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 74 TRP Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 243 GLU Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 299 PHE Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 74 TRP Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 243 GLU Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 299 PHE Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 74 TRP Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 214 ILE Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 243 GLU Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 272 ILE Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 299 PHE Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 420 ARG Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 214 ILE Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 272 ILE Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 299 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 204 optimal weight: 0.9990 chunk 147 optimal weight: 3.9990 chunk 48 optimal weight: 8.9990 chunk 139 optimal weight: 4.9990 chunk 50 optimal weight: 0.6980 chunk 123 optimal weight: 3.9990 chunk 209 optimal weight: 0.7980 chunk 181 optimal weight: 0.7980 chunk 41 optimal weight: 0.0270 chunk 30 optimal weight: 0.0770 chunk 161 optimal weight: 2.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN ** D 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.132710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.112899 restraints weight = 40915.941| |-----------------------------------------------------------------------------| r_work (start): 0.3941 rms_B_bonded: 3.14 r_work: 0.3838 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6943 moved from start: 0.4094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 19369 Z= 0.091 Angle : 0.567 9.790 26243 Z= 0.276 Chirality : 0.036 0.122 3059 Planarity : 0.003 0.042 3206 Dihedral : 4.515 15.625 2506 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.05 % Allowed : 23.03 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.58 (0.18), residues: 2289 helix: -1.74 (0.14), residues: 1421 sheet: -1.86 (0.37), residues: 126 loop : -1.18 (0.25), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 152 TYR 0.017 0.001 TYR F 193 PHE 0.013 0.001 PHE F 79 TRP 0.004 0.000 TRP B 74 HIS 0.001 0.000 HIS D 106 Details of bonding type rmsd covalent geometry : bond 0.00193 (19355) covalent geometry : angle 0.56684 (26215) SS BOND : bond 0.00059 ( 14) SS BOND : angle 0.20689 ( 28) hydrogen bonds : bond 0.03187 ( 679) hydrogen bonds : angle 4.25912 ( 1890) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 160 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 LYS cc_start: 0.8209 (mmtt) cc_final: 0.7475 (mtmm) REVERT: A 234 TYR cc_start: 0.8091 (t80) cc_final: 0.7783 (t80) REVERT: A 310 GLU cc_start: 0.8392 (tm-30) cc_final: 0.8091 (tm-30) REVERT: B 49 LEU cc_start: 0.8552 (mt) cc_final: 0.8155 (pp) REVERT: B 74 TRP cc_start: 0.7618 (OUTLIER) cc_final: 0.6587 (t60) REVERT: B 128 ARG cc_start: 0.8300 (ttm170) cc_final: 0.7866 (tmm-80) REVERT: B 212 LYS cc_start: 0.8147 (mmtt) cc_final: 0.7420 (mtmm) REVERT: B 243 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7443 (tm-30) REVERT: B 310 GLU cc_start: 0.8428 (tm-30) cc_final: 0.8030 (tm-30) REVERT: C 37 MET cc_start: 0.7998 (tpp) cc_final: 0.7640 (tpp) REVERT: C 49 LEU cc_start: 0.8724 (mt) cc_final: 0.8249 (pp) REVERT: C 128 ARG cc_start: 0.8239 (ttm170) cc_final: 0.7750 (tmm-80) REVERT: C 209 LEU cc_start: 0.6385 (tp) cc_final: 0.6106 (tt) REVERT: C 243 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7677 (tm-30) REVERT: D 49 LEU cc_start: 0.8544 (mt) cc_final: 0.8235 (pp) REVERT: D 128 ARG cc_start: 0.8255 (ttm170) cc_final: 0.7818 (tmm-80) REVERT: D 209 LEU cc_start: 0.6434 (tp) cc_final: 0.6114 (tt) REVERT: D 243 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7514 (tm-30) REVERT: D 310 GLU cc_start: 0.8424 (tm-30) cc_final: 0.8144 (tm-30) REVERT: E 37 MET cc_start: 0.8093 (tpp) cc_final: 0.7877 (tpp) REVERT: E 49 LEU cc_start: 0.8732 (mt) cc_final: 0.8287 (pp) REVERT: E 212 LYS cc_start: 0.8037 (mmtt) cc_final: 0.7264 (mtmm) REVERT: E 243 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7914 (pp20) REVERT: E 299 PHE cc_start: 0.7602 (OUTLIER) cc_final: 0.6896 (t80) REVERT: F 49 LEU cc_start: 0.8515 (mt) cc_final: 0.8107 (pp) REVERT: F 128 ARG cc_start: 0.8228 (ttm170) cc_final: 0.7819 (tmm-80) REVERT: F 243 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7232 (tm-30) REVERT: G 49 LEU cc_start: 0.8704 (mt) cc_final: 0.8210 (pp) REVERT: G 212 LYS cc_start: 0.8266 (mmtt) cc_final: 0.7536 (mtmm) REVERT: G 234 TYR cc_start: 0.8044 (t80) cc_final: 0.7694 (t80) REVERT: G 310 GLU cc_start: 0.8416 (tm-30) cc_final: 0.8083 (tm-30) outliers start: 65 outliers final: 52 residues processed: 209 average time/residue: 0.1401 time to fit residues: 44.2480 Evaluate side-chains 208 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 149 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 74 TRP Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 74 TRP Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 74 TRP Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 243 GLU Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 299 PHE Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 74 TRP Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 243 GLU Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 299 PHE Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 74 TRP Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 243 GLU Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 420 ARG Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 299 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 12 optimal weight: 2.9990 chunk 98 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 chunk 172 optimal weight: 0.7980 chunk 134 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 193 optimal weight: 9.9990 chunk 207 optimal weight: 1.9990 chunk 208 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 212 optimal weight: 10.0000 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.129271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.109313 restraints weight = 41471.253| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 3.18 r_work: 0.3789 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.4195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19369 Z= 0.140 Angle : 0.611 8.503 26243 Z= 0.300 Chirality : 0.039 0.116 3059 Planarity : 0.004 0.044 3206 Dihedral : 4.832 17.386 2506 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.85 % Allowed : 23.12 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.42 (0.18), residues: 2289 helix: -1.63 (0.14), residues: 1407 sheet: -1.68 (0.39), residues: 126 loop : -1.12 (0.24), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 152 TYR 0.015 0.002 TYR C 10 PHE 0.016 0.001 PHE C 15 TRP 0.011 0.001 TRP A 74 HIS 0.002 0.001 HIS D 319 Details of bonding type rmsd covalent geometry : bond 0.00326 (19355) covalent geometry : angle 0.61063 (26215) SS BOND : bond 0.00200 ( 14) SS BOND : angle 0.49065 ( 28) hydrogen bonds : bond 0.03541 ( 679) hydrogen bonds : angle 4.32449 ( 1890) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 144 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 LYS cc_start: 0.8209 (mmtt) cc_final: 0.7415 (mtmm) REVERT: A 310 GLU cc_start: 0.8360 (tm-30) cc_final: 0.8123 (tm-30) REVERT: B 49 LEU cc_start: 0.8590 (mt) cc_final: 0.8235 (pp) REVERT: B 74 TRP cc_start: 0.7638 (OUTLIER) cc_final: 0.6772 (t60) REVERT: B 128 ARG cc_start: 0.8316 (ttm170) cc_final: 0.7872 (tmm-80) REVERT: B 212 LYS cc_start: 0.8201 (mmtt) cc_final: 0.7505 (mtmm) REVERT: B 243 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7513 (tm-30) REVERT: B 310 GLU cc_start: 0.8411 (tm-30) cc_final: 0.8043 (tm-30) REVERT: B 420 ARG cc_start: 0.5919 (OUTLIER) cc_final: 0.5567 (mtt90) REVERT: C 37 MET cc_start: 0.7981 (tpp) cc_final: 0.7590 (tpp) REVERT: C 49 LEU cc_start: 0.8733 (mt) cc_final: 0.8307 (pp) REVERT: C 128 ARG cc_start: 0.8264 (ttm170) cc_final: 0.7791 (tmm-80) REVERT: C 209 LEU cc_start: 0.6603 (tp) cc_final: 0.6362 (tt) REVERT: C 243 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7835 (tm-30) REVERT: D 49 LEU cc_start: 0.8561 (mt) cc_final: 0.8263 (pp) REVERT: D 128 ARG cc_start: 0.8317 (ttm170) cc_final: 0.7827 (tmm-80) REVERT: D 209 LEU cc_start: 0.6711 (tp) cc_final: 0.6441 (tt) REVERT: D 243 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7557 (tm-30) REVERT: D 293 TYR cc_start: 0.6080 (t80) cc_final: 0.5871 (t80) REVERT: D 310 GLU cc_start: 0.8426 (tm-30) cc_final: 0.8149 (tm-30) REVERT: E 37 MET cc_start: 0.8081 (tpp) cc_final: 0.7814 (tpp) REVERT: E 49 LEU cc_start: 0.8705 (mt) cc_final: 0.8296 (pp) REVERT: E 212 LYS cc_start: 0.8044 (mmtt) cc_final: 0.7277 (mtmm) REVERT: F 49 LEU cc_start: 0.8515 (mt) cc_final: 0.8184 (pp) REVERT: F 128 ARG cc_start: 0.8298 (ttm170) cc_final: 0.7862 (tmm-80) REVERT: F 243 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7356 (tm-30) REVERT: G 49 LEU cc_start: 0.8728 (mt) cc_final: 0.8359 (pp) REVERT: G 212 LYS cc_start: 0.8297 (mmtt) cc_final: 0.7533 (mtmm) REVERT: G 310 GLU cc_start: 0.8378 (tm-30) cc_final: 0.8070 (tm-30) outliers start: 82 outliers final: 69 residues processed: 207 average time/residue: 0.1461 time to fit residues: 45.6706 Evaluate side-chains 211 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 136 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 74 TRP Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 74 TRP Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain B residue 420 ARG Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 74 TRP Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 243 GLU Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 299 PHE Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 74 TRP Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 243 GLU Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 299 PHE Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 74 TRP Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 243 GLU Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 272 ILE Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 299 PHE Chi-restraints excluded: chain F residue 420 ARG Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 272 ILE Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 299 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 217 optimal weight: 3.9990 chunk 180 optimal weight: 0.7980 chunk 123 optimal weight: 0.7980 chunk 145 optimal weight: 0.9990 chunk 174 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 162 optimal weight: 0.7980 chunk 224 optimal weight: 4.9990 chunk 219 optimal weight: 7.9990 chunk 176 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.131552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.111729 restraints weight = 41310.374| |-----------------------------------------------------------------------------| r_work (start): 0.3925 rms_B_bonded: 3.16 r_work: 0.3821 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 moved from start: 0.4351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 19369 Z= 0.097 Angle : 0.563 8.145 26243 Z= 0.276 Chirality : 0.037 0.119 3059 Planarity : 0.003 0.043 3206 Dihedral : 4.519 16.161 2506 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.43 % Allowed : 23.87 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.23 (0.18), residues: 2289 helix: -1.41 (0.14), residues: 1421 sheet: -1.75 (0.37), residues: 126 loop : -1.15 (0.24), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 418 TYR 0.017 0.001 TYR B 10 PHE 0.011 0.001 PHE E 79 TRP 0.006 0.001 TRP A 74 HIS 0.001 0.000 HIS D 106 Details of bonding type rmsd covalent geometry : bond 0.00214 (19355) covalent geometry : angle 0.56341 (26215) SS BOND : bond 0.00057 ( 14) SS BOND : angle 0.24404 ( 28) hydrogen bonds : bond 0.03197 ( 679) hydrogen bonds : angle 4.19457 ( 1890) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 154 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 LYS cc_start: 0.8135 (mmtt) cc_final: 0.7338 (mtmm) REVERT: A 310 GLU cc_start: 0.8394 (tm-30) cc_final: 0.8118 (tm-30) REVERT: B 74 TRP cc_start: 0.7542 (OUTLIER) cc_final: 0.6618 (t60) REVERT: B 128 ARG cc_start: 0.8315 (ttm170) cc_final: 0.7886 (tmm-80) REVERT: B 243 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7473 (tm-30) REVERT: B 310 GLU cc_start: 0.8299 (tm-30) cc_final: 0.7991 (tm-30) REVERT: B 420 ARG cc_start: 0.5957 (OUTLIER) cc_final: 0.5608 (mtt90) REVERT: C 37 MET cc_start: 0.7993 (tpp) cc_final: 0.7587 (tpp) REVERT: C 49 LEU cc_start: 0.8700 (mt) cc_final: 0.8285 (pp) REVERT: C 128 ARG cc_start: 0.8267 (ttm170) cc_final: 0.7783 (tmm-80) REVERT: C 209 LEU cc_start: 0.6372 (tp) cc_final: 0.6160 (tt) REVERT: C 243 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7801 (tm-30) REVERT: D 49 LEU cc_start: 0.8525 (mt) cc_final: 0.8275 (pp) REVERT: D 128 ARG cc_start: 0.8279 (ttm170) cc_final: 0.7864 (tmm-80) REVERT: D 243 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7347 (tm-30) REVERT: D 310 GLU cc_start: 0.8413 (tm-30) cc_final: 0.8122 (tm-30) REVERT: E 37 MET cc_start: 0.8069 (tpp) cc_final: 0.7845 (tpp) REVERT: E 49 LEU cc_start: 0.8642 (mt) cc_final: 0.8219 (pp) REVERT: E 299 PHE cc_start: 0.7576 (OUTLIER) cc_final: 0.6906 (t80) REVERT: F 128 ARG cc_start: 0.8269 (ttm170) cc_final: 0.7873 (tmm-80) REVERT: F 243 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7219 (tm-30) REVERT: G 49 LEU cc_start: 0.8738 (mt) cc_final: 0.8357 (pp) REVERT: G 212 LYS cc_start: 0.8218 (mmtt) cc_final: 0.7441 (mtmm) REVERT: G 234 TYR cc_start: 0.8091 (t80) cc_final: 0.7694 (t80) REVERT: G 310 GLU cc_start: 0.8390 (tm-30) cc_final: 0.8071 (tm-30) outliers start: 73 outliers final: 65 residues processed: 211 average time/residue: 0.1410 time to fit residues: 44.5840 Evaluate side-chains 213 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 141 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 40 CYS Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 74 TRP Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 74 TRP Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain B residue 420 ARG Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 74 TRP Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 243 GLU Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 299 PHE Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 74 TRP Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 243 GLU Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 299 PHE Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 74 TRP Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 243 GLU Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 272 ILE Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 299 PHE Chi-restraints excluded: chain F residue 420 ARG Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 299 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 183 optimal weight: 6.9990 chunk 227 optimal weight: 0.9980 chunk 2 optimal weight: 8.9990 chunk 196 optimal weight: 1.9990 chunk 133 optimal weight: 7.9990 chunk 64 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 175 optimal weight: 0.4980 chunk 31 optimal weight: 0.7980 chunk 209 optimal weight: 0.8980 chunk 142 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 411 ASN ** E 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.131073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.111369 restraints weight = 40885.671| |-----------------------------------------------------------------------------| r_work (start): 0.3926 rms_B_bonded: 3.13 r_work: 0.3823 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.4491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 19369 Z= 0.099 Angle : 0.574 13.096 26243 Z= 0.279 Chirality : 0.037 0.140 3059 Planarity : 0.003 0.043 3206 Dihedral : 4.449 16.030 2506 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.52 % Allowed : 24.20 % Favored : 72.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.02 (0.18), residues: 2289 helix: -1.25 (0.14), residues: 1407 sheet: -1.71 (0.37), residues: 126 loop : -1.05 (0.24), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 152 TYR 0.020 0.001 TYR B 10 PHE 0.011 0.001 PHE G 15 TRP 0.007 0.001 TRP A 74 HIS 0.001 0.000 HIS A 319 Details of bonding type rmsd covalent geometry : bond 0.00218 (19355) covalent geometry : angle 0.57408 (26215) SS BOND : bond 0.00065 ( 14) SS BOND : angle 0.25500 ( 28) hydrogen bonds : bond 0.03132 ( 679) hydrogen bonds : angle 4.14231 ( 1890) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 141 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 LYS cc_start: 0.8097 (mmtt) cc_final: 0.7322 (mtmm) REVERT: A 310 GLU cc_start: 0.8349 (tm-30) cc_final: 0.8074 (tm-30) REVERT: B 43 VAL cc_start: 0.8233 (t) cc_final: 0.7874 (m) REVERT: B 74 TRP cc_start: 0.7537 (OUTLIER) cc_final: 0.6607 (t60) REVERT: B 128 ARG cc_start: 0.8303 (ttm170) cc_final: 0.7870 (tmm-80) REVERT: B 243 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7421 (tm-30) REVERT: B 310 GLU cc_start: 0.8289 (tm-30) cc_final: 0.8005 (tm-30) REVERT: B 420 ARG cc_start: 0.5889 (OUTLIER) cc_final: 0.5516 (mtt90) REVERT: C 37 MET cc_start: 0.7984 (tpp) cc_final: 0.7558 (tpp) REVERT: C 49 LEU cc_start: 0.8718 (mt) cc_final: 0.8305 (pp) REVERT: C 128 ARG cc_start: 0.8292 (ttm170) cc_final: 0.7812 (tmm-80) REVERT: C 243 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7807 (tm-30) REVERT: D 49 LEU cc_start: 0.8489 (mt) cc_final: 0.8257 (pp) REVERT: D 128 ARG cc_start: 0.8308 (ttm170) cc_final: 0.7875 (tmm-80) REVERT: D 243 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7380 (tm-30) REVERT: D 310 GLU cc_start: 0.8416 (tm-30) cc_final: 0.8125 (tm-30) REVERT: E 37 MET cc_start: 0.8094 (tpp) cc_final: 0.7848 (tpp) REVERT: E 49 LEU cc_start: 0.8615 (mt) cc_final: 0.8223 (pp) REVERT: E 299 PHE cc_start: 0.7548 (OUTLIER) cc_final: 0.7001 (t80) REVERT: F 128 ARG cc_start: 0.8284 (ttm170) cc_final: 0.7883 (tmm-80) REVERT: F 243 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7211 (tm-30) REVERT: G 49 LEU cc_start: 0.8692 (mt) cc_final: 0.8307 (pp) REVERT: G 212 LYS cc_start: 0.8200 (mmtt) cc_final: 0.7402 (mtmm) REVERT: G 234 TYR cc_start: 0.8143 (t80) cc_final: 0.7645 (t80) REVERT: G 310 GLU cc_start: 0.8367 (tm-30) cc_final: 0.8063 (tm-30) outliers start: 75 outliers final: 65 residues processed: 199 average time/residue: 0.1406 time to fit residues: 42.2306 Evaluate side-chains 209 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 137 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 40 CYS Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 74 TRP Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 74 TRP Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain B residue 420 ARG Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 74 TRP Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 243 GLU Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 299 PHE Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 74 TRP Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 299 PHE Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 74 TRP Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 243 GLU Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 272 ILE Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 299 PHE Chi-restraints excluded: chain F residue 420 ARG Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 299 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 195 optimal weight: 10.0000 chunk 105 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 224 optimal weight: 2.9990 chunk 159 optimal weight: 0.9980 chunk 196 optimal weight: 2.9990 chunk 121 optimal weight: 0.0970 chunk 94 optimal weight: 5.9990 chunk 206 optimal weight: 0.0000 chunk 210 optimal weight: 2.9990 chunk 48 optimal weight: 0.0000 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 411 ASN ** F 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.132252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.112529 restraints weight = 41151.361| |-----------------------------------------------------------------------------| r_work (start): 0.3941 rms_B_bonded: 3.10 r_work: 0.3839 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6943 moved from start: 0.4605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 19369 Z= 0.093 Angle : 0.568 11.884 26243 Z= 0.275 Chirality : 0.037 0.166 3059 Planarity : 0.003 0.045 3206 Dihedral : 4.298 15.660 2506 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.52 % Allowed : 24.34 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.18), residues: 2289 helix: -1.12 (0.14), residues: 1407 sheet: -1.71 (0.37), residues: 126 loop : -1.03 (0.24), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 420 TYR 0.019 0.001 TYR B 10 PHE 0.011 0.001 PHE E 79 TRP 0.005 0.001 TRP A 74 HIS 0.001 0.000 HIS D 106 Details of bonding type rmsd covalent geometry : bond 0.00202 (19355) covalent geometry : angle 0.56808 (26215) SS BOND : bond 0.00055 ( 14) SS BOND : angle 0.18928 ( 28) hydrogen bonds : bond 0.03024 ( 679) hydrogen bonds : angle 4.09877 ( 1890) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 139 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ARG cc_start: 0.8285 (ttm170) cc_final: 0.7869 (tmm-80) REVERT: A 212 LYS cc_start: 0.8122 (mmtt) cc_final: 0.7414 (mtmm) REVERT: A 310 GLU cc_start: 0.8365 (tm-30) cc_final: 0.8087 (tm-30) REVERT: A 418 ARG cc_start: 0.7122 (tpp-160) cc_final: 0.6272 (tpp-160) REVERT: B 43 VAL cc_start: 0.8259 (t) cc_final: 0.7899 (m) REVERT: B 74 TRP cc_start: 0.7545 (OUTLIER) cc_final: 0.6587 (t60) REVERT: B 128 ARG cc_start: 0.8271 (ttm170) cc_final: 0.7844 (tmm-80) REVERT: B 243 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7352 (tm-30) REVERT: B 310 GLU cc_start: 0.8309 (tm-30) cc_final: 0.8036 (tm-30) REVERT: B 420 ARG cc_start: 0.5846 (OUTLIER) cc_final: 0.5622 (mtt90) REVERT: C 37 MET cc_start: 0.8055 (tpp) cc_final: 0.7625 (tpp) REVERT: C 49 LEU cc_start: 0.8695 (mt) cc_final: 0.8257 (pp) REVERT: C 128 ARG cc_start: 0.8275 (ttm170) cc_final: 0.7813 (tmm-80) REVERT: C 243 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7789 (tm-30) REVERT: C 418 ARG cc_start: 0.7251 (tpp-160) cc_final: 0.7004 (tpp-160) REVERT: D 49 LEU cc_start: 0.8518 (mt) cc_final: 0.8280 (pp) REVERT: D 128 ARG cc_start: 0.8257 (ttm170) cc_final: 0.7843 (tmm-80) REVERT: D 243 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7367 (tm-30) REVERT: D 310 GLU cc_start: 0.8411 (tm-30) cc_final: 0.8125 (tm-30) REVERT: E 37 MET cc_start: 0.8073 (tpp) cc_final: 0.7836 (tpp) REVERT: E 49 LEU cc_start: 0.8561 (mt) cc_final: 0.8185 (pp) REVERT: E 243 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7950 (tm-30) REVERT: E 299 PHE cc_start: 0.7526 (OUTLIER) cc_final: 0.7040 (t80) REVERT: F 128 ARG cc_start: 0.8260 (ttm170) cc_final: 0.7874 (tmm-80) REVERT: F 243 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7276 (tm-30) REVERT: G 49 LEU cc_start: 0.8715 (mt) cc_final: 0.8340 (pp) REVERT: G 212 LYS cc_start: 0.8144 (mmtt) cc_final: 0.7343 (mtmm) REVERT: G 234 TYR cc_start: 0.8063 (t80) cc_final: 0.7635 (t80) REVERT: G 310 GLU cc_start: 0.8343 (tm-30) cc_final: 0.8053 (tm-30) outliers start: 75 outliers final: 63 residues processed: 197 average time/residue: 0.1484 time to fit residues: 43.9339 Evaluate side-chains 209 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 138 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 40 CYS Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 74 TRP Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 74 TRP Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain B residue 420 ARG Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 74 TRP Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 243 GLU Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 299 PHE Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 74 TRP Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 243 GLU Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 299 PHE Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 74 TRP Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 243 GLU Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 272 ILE Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 299 PHE Chi-restraints excluded: chain F residue 420 ARG Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 214 ILE Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 299 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 5 optimal weight: 0.6980 chunk 90 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 163 optimal weight: 0.7980 chunk 81 optimal weight: 6.9990 chunk 226 optimal weight: 8.9990 chunk 13 optimal weight: 5.9990 chunk 204 optimal weight: 0.5980 chunk 105 optimal weight: 2.9990 chunk 192 optimal weight: 0.0970 chunk 123 optimal weight: 0.5980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 411 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.132952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.113150 restraints weight = 41563.499| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 3.11 r_work: 0.3843 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6928 moved from start: 0.4720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 19369 Z= 0.090 Angle : 0.560 11.425 26243 Z= 0.272 Chirality : 0.037 0.114 3059 Planarity : 0.003 0.046 3206 Dihedral : 4.199 15.381 2506 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.34 % Allowed : 24.72 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.18), residues: 2289 helix: -0.97 (0.15), residues: 1407 sheet: -1.66 (0.37), residues: 126 loop : -1.02 (0.24), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 420 TYR 0.018 0.001 TYR B 10 PHE 0.011 0.001 PHE E 79 TRP 0.004 0.000 TRP A 74 HIS 0.001 0.000 HIS G 106 Details of bonding type rmsd covalent geometry : bond 0.00195 (19355) covalent geometry : angle 0.56058 (26215) SS BOND : bond 0.00043 ( 14) SS BOND : angle 0.15354 ( 28) hydrogen bonds : bond 0.02937 ( 679) hydrogen bonds : angle 4.04137 ( 1890) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3641.44 seconds wall clock time: 64 minutes 10.95 seconds (3850.95 seconds total)