Starting phenix.real_space_refine on Tue Aug 26 00:52:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fql_29392/08_2025/8fql_29392.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fql_29392/08_2025/8fql_29392.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fql_29392/08_2025/8fql_29392.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fql_29392/08_2025/8fql_29392.map" model { file = "/net/cci-nas-00/data/ceres_data/8fql_29392/08_2025/8fql_29392.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fql_29392/08_2025/8fql_29392.cif" } resolution = 3.6 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= 0.007 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 180 5.16 5 C 20592 2.51 5 N 5736 2.21 5 O 6144 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 286 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32652 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2721 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 15, 'TRANS': 330} Chain: "B" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2721 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 15, 'TRANS': 330} Chain: "C" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2721 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 15, 'TRANS': 330} Chain: "D" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2721 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 15, 'TRANS': 330} Chain: "E" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2721 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 15, 'TRANS': 330} Chain: "F" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2721 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 15, 'TRANS': 330} Chain: "G" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2721 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 15, 'TRANS': 330} Chain: "H" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2721 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 15, 'TRANS': 330} Chain: "I" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2721 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 15, 'TRANS': 330} Chain: "J" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2721 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 15, 'TRANS': 330} Chain: "K" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2721 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 15, 'TRANS': 330} Chain: "L" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2721 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 15, 'TRANS': 330} Time building chain proxies: 7.66, per 1000 atoms: 0.23 Number of scatterers: 32652 At special positions: 0 Unit cell: (152.28, 154.44, 123.12, 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 180 16.00 O 6144 8.00 N 5736 7.00 C 20592 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.93 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 476.8 nanoseconds 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7704 Finding SS restraints... Secondary structure from input PDB file: 171 helices and 48 sheets defined 50.9% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 53 through 59 Processing helix chain 'A' and resid 60 through 77 Processing helix chain 'A' and resid 97 through 105 Processing helix chain 'A' and resid 112 through 128 Processing helix chain 'A' and resid 195 through 220 removed outlier: 3.823A pdb=" N PHE A 199 " --> pdb=" O SER A 195 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N LYS A 202 " --> pdb=" O ALA A 198 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N SER A 203 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE A 218 " --> pdb=" O GLN A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 247 removed outlier: 4.267A pdb=" N GLU A 244 " --> pdb=" O ARG A 240 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLU A 245 " --> pdb=" O SER A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 296 removed outlier: 3.975A pdb=" N SER A 289 " --> pdb=" O LYS A 285 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU A 290 " --> pdb=" O PHE A 286 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE A 294 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N PHE A 295 " --> pdb=" O LEU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 326 Processing helix chain 'A' and resid 327 through 342 removed outlier: 3.666A pdb=" N ILE A 331 " --> pdb=" O LEU A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 348 Processing helix chain 'A' and resid 357 through 362 Processing helix chain 'A' and resid 364 through 377 Processing helix chain 'A' and resid 382 through 390 removed outlier: 3.780A pdb=" N ASP A 390 " --> pdb=" O MET A 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 59 Processing helix chain 'B' and resid 60 through 77 Processing helix chain 'B' and resid 97 through 105 Processing helix chain 'B' and resid 112 through 128 Processing helix chain 'B' and resid 149 through 151 No H-bonds generated for 'chain 'B' and resid 149 through 151' Processing helix chain 'B' and resid 195 through 220 removed outlier: 3.768A pdb=" N PHE B 199 " --> pdb=" O SER B 195 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N LYS B 202 " --> pdb=" O ALA B 198 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N SER B 203 " --> pdb=" O PHE B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 247 removed outlier: 4.482A pdb=" N VAL B 243 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N GLU B 244 " --> pdb=" O ARG B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 296 removed outlier: 5.176A pdb=" N ARG B 284 " --> pdb=" O MET B 280 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL B 288 " --> pdb=" O ARG B 284 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N SER B 289 " --> pdb=" O LYS B 285 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU B 290 " --> pdb=" O PHE B 286 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE B 294 " --> pdb=" O GLU B 290 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N PHE B 295 " --> pdb=" O LEU B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 303 removed outlier: 3.772A pdb=" N VAL B 302 " --> pdb=" O PRO B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 326 Processing helix chain 'B' and resid 327 through 342 removed outlier: 3.859A pdb=" N ILE B 331 " --> pdb=" O LEU B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 348 Processing helix chain 'B' and resid 357 through 362 Processing helix chain 'B' and resid 364 through 377 removed outlier: 4.284A pdb=" N GLU B 377 " --> pdb=" O LYS B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 390 removed outlier: 3.766A pdb=" N ASP B 390 " --> pdb=" O MET B 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 59 Processing helix chain 'C' and resid 60 through 77 Processing helix chain 'C' and resid 97 through 105 Processing helix chain 'C' and resid 112 through 128 Processing helix chain 'C' and resid 195 through 220 removed outlier: 3.823A pdb=" N PHE C 199 " --> pdb=" O SER C 195 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N LYS C 202 " --> pdb=" O ALA C 198 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N SER C 203 " --> pdb=" O PHE C 199 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE C 218 " --> pdb=" O GLN C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 247 removed outlier: 4.156A pdb=" N GLU C 244 " --> pdb=" O ARG C 240 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLU C 245 " --> pdb=" O SER C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 296 removed outlier: 3.613A pdb=" N VAL C 288 " --> pdb=" O ARG C 284 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N SER C 289 " --> pdb=" O LYS C 285 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU C 290 " --> pdb=" O PHE C 286 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE C 294 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N PHE C 295 " --> pdb=" O LEU C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 326 Processing helix chain 'C' and resid 327 through 342 removed outlier: 3.666A pdb=" N ILE C 331 " --> pdb=" O LEU C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 348 Processing helix chain 'C' and resid 357 through 362 Processing helix chain 'C' and resid 364 through 377 Processing helix chain 'C' and resid 382 through 390 removed outlier: 3.780A pdb=" N ASP C 390 " --> pdb=" O MET C 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 59 Processing helix chain 'D' and resid 60 through 77 Processing helix chain 'D' and resid 97 through 105 Processing helix chain 'D' and resid 112 through 128 Processing helix chain 'D' and resid 149 through 151 No H-bonds generated for 'chain 'D' and resid 149 through 151' Processing helix chain 'D' and resid 195 through 220 removed outlier: 3.768A pdb=" N PHE D 199 " --> pdb=" O SER D 195 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N LYS D 202 " --> pdb=" O ALA D 198 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N SER D 203 " --> pdb=" O PHE D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 247 removed outlier: 3.663A pdb=" N GLN D 242 " --> pdb=" O GLN D 238 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N VAL D 243 " --> pdb=" O GLN D 239 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLU D 244 " --> pdb=" O ARG D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 296 removed outlier: 5.279A pdb=" N ARG D 284 " --> pdb=" O MET D 280 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL D 288 " --> pdb=" O ARG D 284 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N SER D 289 " --> pdb=" O LYS D 285 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU D 290 " --> pdb=" O PHE D 286 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE D 294 " --> pdb=" O GLU D 290 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N PHE D 295 " --> pdb=" O LEU D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 303 removed outlier: 3.772A pdb=" N VAL D 302 " --> pdb=" O PRO D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 326 Processing helix chain 'D' and resid 327 through 342 removed outlier: 3.859A pdb=" N ILE D 331 " --> pdb=" O LEU D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 348 Processing helix chain 'D' and resid 357 through 362 Processing helix chain 'D' and resid 364 through 377 removed outlier: 4.284A pdb=" N GLU D 377 " --> pdb=" O LYS D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 382 through 390 removed outlier: 3.766A pdb=" N ASP D 390 " --> pdb=" O MET D 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 59 Processing helix chain 'E' and resid 60 through 77 Processing helix chain 'E' and resid 97 through 105 Processing helix chain 'E' and resid 112 through 128 Processing helix chain 'E' and resid 195 through 220 removed outlier: 3.823A pdb=" N PHE E 199 " --> pdb=" O SER E 195 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N LYS E 202 " --> pdb=" O ALA E 198 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N SER E 203 " --> pdb=" O PHE E 199 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE E 218 " --> pdb=" O GLN E 214 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 247 removed outlier: 3.663A pdb=" N GLU E 244 " --> pdb=" O ARG E 240 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLU E 245 " --> pdb=" O SER E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 252 removed outlier: 4.042A pdb=" N ALA E 251 " --> pdb=" O LYS E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 296 removed outlier: 3.597A pdb=" N ARG E 284 " --> pdb=" O MET E 280 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL E 288 " --> pdb=" O ARG E 284 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N SER E 289 " --> pdb=" O LYS E 285 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU E 290 " --> pdb=" O PHE E 286 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE E 294 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N PHE E 295 " --> pdb=" O LEU E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 326 Processing helix chain 'E' and resid 327 through 342 removed outlier: 3.666A pdb=" N ILE E 331 " --> pdb=" O LEU E 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 344 through 348 Processing helix chain 'E' and resid 357 through 362 Processing helix chain 'E' and resid 364 through 377 Processing helix chain 'E' and resid 382 through 390 removed outlier: 3.780A pdb=" N ASP E 390 " --> pdb=" O MET E 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 59 Processing helix chain 'F' and resid 60 through 77 Processing helix chain 'F' and resid 97 through 105 Processing helix chain 'F' and resid 112 through 128 Processing helix chain 'F' and resid 149 through 151 No H-bonds generated for 'chain 'F' and resid 149 through 151' Processing helix chain 'F' and resid 195 through 220 removed outlier: 3.768A pdb=" N PHE F 199 " --> pdb=" O SER F 195 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N LYS F 202 " --> pdb=" O ALA F 198 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N SER F 203 " --> pdb=" O PHE F 199 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE F 218 " --> pdb=" O GLN F 214 " (cutoff:3.500A) Processing helix chain 'F' and resid 236 through 246 removed outlier: 4.197A pdb=" N VAL F 243 " --> pdb=" O GLN F 239 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N GLU F 244 " --> pdb=" O ARG F 240 " (cutoff:3.500A) Processing helix chain 'F' and resid 278 through 296 removed outlier: 5.176A pdb=" N ARG F 284 " --> pdb=" O MET F 280 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL F 288 " --> pdb=" O ARG F 284 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N SER F 289 " --> pdb=" O LYS F 285 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU F 290 " --> pdb=" O PHE F 286 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE F 294 " --> pdb=" O GLU F 290 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N PHE F 295 " --> pdb=" O LEU F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 303 removed outlier: 3.772A pdb=" N VAL F 302 " --> pdb=" O PRO F 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 326 Processing helix chain 'F' and resid 327 through 342 removed outlier: 3.860A pdb=" N ILE F 331 " --> pdb=" O LEU F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 344 through 348 Processing helix chain 'F' and resid 357 through 362 Processing helix chain 'F' and resid 364 through 377 removed outlier: 4.284A pdb=" N GLU F 377 " --> pdb=" O LYS F 373 " (cutoff:3.500A) Processing helix chain 'F' and resid 382 through 390 removed outlier: 3.766A pdb=" N ASP F 390 " --> pdb=" O MET F 386 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 59 Processing helix chain 'G' and resid 60 through 77 Processing helix chain 'G' and resid 97 through 105 Processing helix chain 'G' and resid 112 through 128 Processing helix chain 'G' and resid 195 through 220 removed outlier: 3.823A pdb=" N PHE G 199 " --> pdb=" O SER G 195 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N LYS G 202 " --> pdb=" O ALA G 198 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N SER G 203 " --> pdb=" O PHE G 199 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N PHE G 218 " --> pdb=" O GLN G 214 " (cutoff:3.500A) Processing helix chain 'G' and resid 236 through 247 removed outlier: 3.823A pdb=" N GLU G 244 " --> pdb=" O ARG G 240 " (cutoff:3.500A) Processing helix chain 'G' and resid 248 through 252 removed outlier: 4.189A pdb=" N ALA G 251 " --> pdb=" O LYS G 248 " (cutoff:3.500A) Processing helix chain 'G' and resid 279 through 296 removed outlier: 3.684A pdb=" N ARG G 284 " --> pdb=" O MET G 280 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS G 285 " --> pdb=" O MET G 281 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL G 288 " --> pdb=" O ARG G 284 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N SER G 289 " --> pdb=" O LYS G 285 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU G 290 " --> pdb=" O PHE G 286 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE G 294 " --> pdb=" O GLU G 290 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N PHE G 295 " --> pdb=" O LEU G 291 " (cutoff:3.500A) Processing helix chain 'G' and resid 314 through 326 Processing helix chain 'G' and resid 327 through 342 removed outlier: 3.666A pdb=" N ILE G 331 " --> pdb=" O LEU G 327 " (cutoff:3.500A) Processing helix chain 'G' and resid 344 through 348 Processing helix chain 'G' and resid 357 through 362 Processing helix chain 'G' and resid 364 through 377 Processing helix chain 'G' and resid 382 through 390 removed outlier: 3.780A pdb=" N ASP G 390 " --> pdb=" O MET G 386 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 59 Processing helix chain 'H' and resid 60 through 77 Processing helix chain 'H' and resid 97 through 105 Processing helix chain 'H' and resid 112 through 128 Processing helix chain 'H' and resid 149 through 151 No H-bonds generated for 'chain 'H' and resid 149 through 151' Processing helix chain 'H' and resid 195 through 220 removed outlier: 3.768A pdb=" N PHE H 199 " --> pdb=" O SER H 195 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N LYS H 202 " --> pdb=" O ALA H 198 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N SER H 203 " --> pdb=" O PHE H 199 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE H 218 " --> pdb=" O GLN H 214 " (cutoff:3.500A) Processing helix chain 'H' and resid 236 through 246 removed outlier: 4.193A pdb=" N GLU H 244 " --> pdb=" O ARG H 240 " (cutoff:3.500A) Processing helix chain 'H' and resid 278 through 296 removed outlier: 5.685A pdb=" N ARG H 284 " --> pdb=" O MET H 280 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL H 288 " --> pdb=" O ARG H 284 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N SER H 289 " --> pdb=" O LYS H 285 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU H 290 " --> pdb=" O PHE H 286 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE H 294 " --> pdb=" O GLU H 290 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N PHE H 295 " --> pdb=" O LEU H 291 " (cutoff:3.500A) Processing helix chain 'H' and resid 298 through 303 removed outlier: 3.772A pdb=" N VAL H 302 " --> pdb=" O PRO H 298 " (cutoff:3.500A) Processing helix chain 'H' and resid 314 through 326 Processing helix chain 'H' and resid 327 through 342 removed outlier: 3.859A pdb=" N ILE H 331 " --> pdb=" O LEU H 327 " (cutoff:3.500A) Processing helix chain 'H' and resid 344 through 348 Processing helix chain 'H' and resid 357 through 362 Processing helix chain 'H' and resid 364 through 377 removed outlier: 4.284A pdb=" N GLU H 377 " --> pdb=" O LYS H 373 " (cutoff:3.500A) Processing helix chain 'H' and resid 382 through 390 removed outlier: 3.766A pdb=" N ASP H 390 " --> pdb=" O MET H 386 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 59 Processing helix chain 'I' and resid 60 through 77 Processing helix chain 'I' and resid 97 through 105 Processing helix chain 'I' and resid 112 through 128 Processing helix chain 'I' and resid 195 through 220 removed outlier: 3.823A pdb=" N PHE I 199 " --> pdb=" O SER I 195 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N LYS I 202 " --> pdb=" O ALA I 198 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N SER I 203 " --> pdb=" O PHE I 199 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE I 218 " --> pdb=" O GLN I 214 " (cutoff:3.500A) Processing helix chain 'I' and resid 236 through 247 Processing helix chain 'I' and resid 248 through 252 Processing helix chain 'I' and resid 279 through 296 removed outlier: 3.743A pdb=" N ARG I 284 " --> pdb=" O MET I 280 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL I 288 " --> pdb=" O ARG I 284 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N SER I 289 " --> pdb=" O LYS I 285 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU I 290 " --> pdb=" O PHE I 286 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE I 294 " --> pdb=" O GLU I 290 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N PHE I 295 " --> pdb=" O LEU I 291 " (cutoff:3.500A) Processing helix chain 'I' and resid 314 through 326 Processing helix chain 'I' and resid 327 through 342 removed outlier: 3.666A pdb=" N ILE I 331 " --> pdb=" O LEU I 327 " (cutoff:3.500A) Processing helix chain 'I' and resid 344 through 348 Processing helix chain 'I' and resid 357 through 362 Processing helix chain 'I' and resid 364 through 377 Processing helix chain 'I' and resid 382 through 390 removed outlier: 3.780A pdb=" N ASP I 390 " --> pdb=" O MET I 386 " (cutoff:3.500A) Processing helix chain 'J' and resid 53 through 59 Processing helix chain 'J' and resid 60 through 77 Processing helix chain 'J' and resid 97 through 105 Processing helix chain 'J' and resid 112 through 128 Processing helix chain 'J' and resid 149 through 151 No H-bonds generated for 'chain 'J' and resid 149 through 151' Processing helix chain 'J' and resid 195 through 220 removed outlier: 3.768A pdb=" N PHE J 199 " --> pdb=" O SER J 195 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N LYS J 202 " --> pdb=" O ALA J 198 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N SER J 203 " --> pdb=" O PHE J 199 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE J 218 " --> pdb=" O GLN J 214 " (cutoff:3.500A) Processing helix chain 'J' and resid 236 through 247 removed outlier: 3.551A pdb=" N GLN J 242 " --> pdb=" O GLN J 238 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N VAL J 243 " --> pdb=" O GLN J 239 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N GLU J 244 " --> pdb=" O ARG J 240 " (cutoff:3.500A) Processing helix chain 'J' and resid 278 through 296 removed outlier: 5.080A pdb=" N ARG J 284 " --> pdb=" O MET J 280 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL J 288 " --> pdb=" O ARG J 284 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N SER J 289 " --> pdb=" O LYS J 285 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU J 290 " --> pdb=" O PHE J 286 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE J 294 " --> pdb=" O GLU J 290 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N PHE J 295 " --> pdb=" O LEU J 291 " (cutoff:3.500A) Processing helix chain 'J' and resid 298 through 303 removed outlier: 3.772A pdb=" N VAL J 302 " --> pdb=" O PRO J 298 " (cutoff:3.500A) Processing helix chain 'J' and resid 314 through 326 Processing helix chain 'J' and resid 327 through 342 removed outlier: 3.859A pdb=" N ILE J 331 " --> pdb=" O LEU J 327 " (cutoff:3.500A) Processing helix chain 'J' and resid 344 through 348 Processing helix chain 'J' and resid 357 through 362 Processing helix chain 'J' and resid 364 through 377 removed outlier: 4.284A pdb=" N GLU J 377 " --> pdb=" O LYS J 373 " (cutoff:3.500A) Processing helix chain 'J' and resid 382 through 390 removed outlier: 3.766A pdb=" N ASP J 390 " --> pdb=" O MET J 386 " (cutoff:3.500A) Processing helix chain 'K' and resid 53 through 59 Processing helix chain 'K' and resid 60 through 77 Processing helix chain 'K' and resid 97 through 105 Processing helix chain 'K' and resid 112 through 128 Processing helix chain 'K' and resid 195 through 220 removed outlier: 3.823A pdb=" N PHE K 199 " --> pdb=" O SER K 195 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LYS K 202 " --> pdb=" O ALA K 198 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N SER K 203 " --> pdb=" O PHE K 199 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N PHE K 218 " --> pdb=" O GLN K 214 " (cutoff:3.500A) Processing helix chain 'K' and resid 236 through 247 removed outlier: 3.965A pdb=" N GLU K 244 " --> pdb=" O ARG K 240 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU K 245 " --> pdb=" O SER K 241 " (cutoff:3.500A) Processing helix chain 'K' and resid 279 through 296 removed outlier: 3.987A pdb=" N SER K 289 " --> pdb=" O LYS K 285 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU K 290 " --> pdb=" O PHE K 286 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE K 294 " --> pdb=" O GLU K 290 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N PHE K 295 " --> pdb=" O LEU K 291 " (cutoff:3.500A) Processing helix chain 'K' and resid 314 through 326 Processing helix chain 'K' and resid 327 through 342 removed outlier: 3.666A pdb=" N ILE K 331 " --> pdb=" O LEU K 327 " (cutoff:3.500A) Processing helix chain 'K' and resid 344 through 348 Processing helix chain 'K' and resid 357 through 362 Processing helix chain 'K' and resid 364 through 377 Processing helix chain 'K' and resid 382 through 390 removed outlier: 3.780A pdb=" N ASP K 390 " --> pdb=" O MET K 386 " (cutoff:3.500A) Processing helix chain 'L' and resid 53 through 59 Processing helix chain 'L' and resid 60 through 77 Processing helix chain 'L' and resid 97 through 105 Processing helix chain 'L' and resid 112 through 128 Processing helix chain 'L' and resid 149 through 151 No H-bonds generated for 'chain 'L' and resid 149 through 151' Processing helix chain 'L' and resid 195 through 220 removed outlier: 3.768A pdb=" N PHE L 199 " --> pdb=" O SER L 195 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N LYS L 202 " --> pdb=" O ALA L 198 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N SER L 203 " --> pdb=" O PHE L 199 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE L 218 " --> pdb=" O GLN L 214 " (cutoff:3.500A) Processing helix chain 'L' and resid 236 through 247 removed outlier: 3.899A pdb=" N VAL L 243 " --> pdb=" O GLN L 239 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU L 244 " --> pdb=" O ARG L 240 " (cutoff:3.500A) Processing helix chain 'L' and resid 278 through 296 removed outlier: 5.212A pdb=" N ARG L 284 " --> pdb=" O MET L 280 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL L 288 " --> pdb=" O ARG L 284 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N SER L 289 " --> pdb=" O LYS L 285 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU L 290 " --> pdb=" O PHE L 286 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE L 294 " --> pdb=" O GLU L 290 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N PHE L 295 " --> pdb=" O LEU L 291 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 303 removed outlier: 3.772A pdb=" N VAL L 302 " --> pdb=" O PRO L 298 " (cutoff:3.500A) Processing helix chain 'L' and resid 314 through 326 Processing helix chain 'L' and resid 327 through 342 removed outlier: 3.860A pdb=" N ILE L 331 " --> pdb=" O LEU L 327 " (cutoff:3.500A) Processing helix chain 'L' and resid 344 through 348 Processing helix chain 'L' and resid 357 through 362 Processing helix chain 'L' and resid 364 through 377 removed outlier: 4.284A pdb=" N GLU L 377 " --> pdb=" O LYS L 373 " (cutoff:3.500A) Processing helix chain 'L' and resid 382 through 390 removed outlier: 3.766A pdb=" N ASP L 390 " --> pdb=" O MET L 386 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA2, first strand: chain 'A' and resid 131 through 136 removed outlier: 7.436A pdb=" N TYR A 131 " --> pdb=" O PRO A 147 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU A 133 " --> pdb=" O LEU A 145 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU A 145 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ASP A 135 " --> pdb=" O ILE A 143 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 153 through 158 Processing sheet with id=AA4, first strand: chain 'A' and resid 226 through 227 removed outlier: 3.528A pdb=" N SER A 269 " --> pdb=" O ILE A 227 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AA6, first strand: chain 'B' and resid 131 through 136 removed outlier: 4.355A pdb=" N TYR B 131 " --> pdb=" O LEU B 148 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 153 through 158 Processing sheet with id=AA8, first strand: chain 'B' and resid 226 through 227 Processing sheet with id=AA9, first strand: chain 'B' and resid 259 through 260 removed outlier: 6.061A pdb=" N LEU B 259 " --> pdb=" O LEU C 228 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 90 through 92 Processing sheet with id=AB2, first strand: chain 'C' and resid 131 through 136 removed outlier: 7.436A pdb=" N TYR C 131 " --> pdb=" O PRO C 147 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU C 133 " --> pdb=" O LEU C 145 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU C 145 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ASP C 135 " --> pdb=" O ILE C 143 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 153 through 158 Processing sheet with id=AB4, first strand: chain 'C' and resid 259 through 260 removed outlier: 6.874A pdb=" N LEU C 259 " --> pdb=" O LEU D 228 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'D' and resid 90 through 92 Processing sheet with id=AB6, first strand: chain 'D' and resid 131 through 136 removed outlier: 4.354A pdb=" N TYR D 131 " --> pdb=" O LEU D 148 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 153 through 158 Processing sheet with id=AB8, first strand: chain 'D' and resid 259 through 261 removed outlier: 5.959A pdb=" N LEU D 259 " --> pdb=" O LEU E 228 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 90 through 92 Processing sheet with id=AC1, first strand: chain 'E' and resid 131 through 136 removed outlier: 7.436A pdb=" N TYR E 131 " --> pdb=" O PRO E 147 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU E 133 " --> pdb=" O LEU E 145 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU E 145 " --> pdb=" O LEU E 133 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ASP E 135 " --> pdb=" O ILE E 143 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 153 through 158 Processing sheet with id=AC3, first strand: chain 'E' and resid 259 through 260 removed outlier: 6.079A pdb=" N LEU E 259 " --> pdb=" O LEU F 228 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 90 through 92 Processing sheet with id=AC5, first strand: chain 'F' and resid 131 through 136 removed outlier: 4.354A pdb=" N TYR F 131 " --> pdb=" O LEU F 148 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 153 through 158 Processing sheet with id=AC7, first strand: chain 'F' and resid 259 through 261 removed outlier: 5.554A pdb=" N LEU F 259 " --> pdb=" O LEU G 228 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 90 through 92 Processing sheet with id=AC9, first strand: chain 'G' and resid 131 through 136 removed outlier: 7.436A pdb=" N TYR G 131 " --> pdb=" O PRO G 147 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU G 133 " --> pdb=" O LEU G 145 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU G 145 " --> pdb=" O LEU G 133 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ASP G 135 " --> pdb=" O ILE G 143 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 153 through 158 Processing sheet with id=AD2, first strand: chain 'G' and resid 259 through 260 removed outlier: 6.157A pdb=" N LEU G 259 " --> pdb=" O LEU H 228 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 90 through 92 Processing sheet with id=AD4, first strand: chain 'H' and resid 131 through 136 removed outlier: 4.355A pdb=" N TYR H 131 " --> pdb=" O LEU H 148 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 153 through 158 Processing sheet with id=AD6, first strand: chain 'H' and resid 259 through 260 removed outlier: 6.036A pdb=" N LEU H 259 " --> pdb=" O LEU I 228 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 90 through 92 Processing sheet with id=AD8, first strand: chain 'I' and resid 131 through 136 removed outlier: 7.436A pdb=" N TYR I 131 " --> pdb=" O PRO I 147 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU I 133 " --> pdb=" O LEU I 145 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU I 145 " --> pdb=" O LEU I 133 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ASP I 135 " --> pdb=" O ILE I 143 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 153 through 158 Processing sheet with id=AE1, first strand: chain 'I' and resid 259 through 260 removed outlier: 6.459A pdb=" N LEU I 259 " --> pdb=" O LEU J 228 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 90 through 92 Processing sheet with id=AE3, first strand: chain 'J' and resid 131 through 136 removed outlier: 4.354A pdb=" N TYR J 131 " --> pdb=" O LEU J 148 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 153 through 158 Processing sheet with id=AE5, first strand: chain 'J' and resid 259 through 260 removed outlier: 6.125A pdb=" N LEU J 259 " --> pdb=" O LEU K 228 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 90 through 92 Processing sheet with id=AE7, first strand: chain 'K' and resid 131 through 136 removed outlier: 7.436A pdb=" N TYR K 131 " --> pdb=" O PRO K 147 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU K 133 " --> pdb=" O LEU K 145 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU K 145 " --> pdb=" O LEU K 133 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ASP K 135 " --> pdb=" O ILE K 143 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 153 through 158 Processing sheet with id=AE9, first strand: chain 'K' and resid 259 through 260 removed outlier: 6.424A pdb=" N LEU K 259 " --> pdb=" O LEU L 228 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 90 through 92 Processing sheet with id=AF2, first strand: chain 'L' and resid 131 through 136 removed outlier: 4.354A pdb=" N TYR L 131 " --> pdb=" O LEU L 148 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 153 through 158 1549 hydrogen bonds defined for protein. 4461 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: 6.22 Time building geometry restraints manager: 3.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9842 1.33 - 1.45: 5439 1.45 - 1.58: 17707 1.58 - 1.70: 0 1.70 - 1.82: 312 Bond restraints: 33300 Sorted by residual: bond pdb=" CZ ARG E 387 " pdb=" NH2 ARG E 387 " ideal model delta sigma weight residual 1.330 1.289 0.041 1.30e-02 5.92e+03 9.81e+00 bond pdb=" CZ ARG K 387 " pdb=" NH2 ARG K 387 " ideal model delta sigma weight residual 1.330 1.289 0.041 1.30e-02 5.92e+03 9.81e+00 bond pdb=" CZ ARG A 387 " pdb=" NH2 ARG A 387 " ideal model delta sigma weight residual 1.330 1.289 0.041 1.30e-02 5.92e+03 9.72e+00 bond pdb=" CZ ARG G 387 " pdb=" NH2 ARG G 387 " ideal model delta sigma weight residual 1.330 1.289 0.041 1.30e-02 5.92e+03 9.72e+00 bond pdb=" CZ ARG C 387 " pdb=" NH2 ARG C 387 " ideal model delta sigma weight residual 1.330 1.290 0.040 1.30e-02 5.92e+03 9.70e+00 ... (remaining 33295 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 36607 2.28 - 4.57: 7618 4.57 - 6.85: 701 6.85 - 9.13: 45 9.13 - 11.41: 5 Bond angle restraints: 44976 Sorted by residual: angle pdb=" CA TRP J 260 " pdb=" CB TRP J 260 " pdb=" CG TRP J 260 " ideal model delta sigma weight residual 113.60 125.01 -11.41 1.90e+00 2.77e-01 3.61e+01 angle pdb=" OE1 GLN A 214 " pdb=" CD GLN A 214 " pdb=" NE2 GLN A 214 " ideal model delta sigma weight residual 122.60 116.79 5.81 1.00e+00 1.00e+00 3.37e+01 angle pdb=" OE1 GLN C 214 " pdb=" CD GLN C 214 " pdb=" NE2 GLN C 214 " ideal model delta sigma weight residual 122.60 116.86 5.74 1.00e+00 1.00e+00 3.30e+01 angle pdb=" OE1 GLN K 214 " pdb=" CD GLN K 214 " pdb=" NE2 GLN K 214 " ideal model delta sigma weight residual 122.60 116.89 5.71 1.00e+00 1.00e+00 3.26e+01 angle pdb=" C SER K 229 " pdb=" N THR K 230 " pdb=" CA THR K 230 " ideal model delta sigma weight residual 121.54 132.20 -10.66 1.91e+00 2.74e-01 3.11e+01 ... (remaining 44971 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.02: 18446 18.02 - 36.03: 1265 36.03 - 54.05: 309 54.05 - 72.06: 110 72.06 - 90.07: 66 Dihedral angle restraints: 20196 sinusoidal: 8244 harmonic: 11952 Sorted by residual: dihedral pdb=" C LYS F 248 " pdb=" N LYS F 248 " pdb=" CA LYS F 248 " pdb=" CB LYS F 248 " ideal model delta harmonic sigma weight residual -122.60 -139.00 16.40 0 2.50e+00 1.60e-01 4.30e+01 dihedral pdb=" C LYS L 248 " pdb=" N LYS L 248 " pdb=" CA LYS L 248 " pdb=" CB LYS L 248 " ideal model delta harmonic sigma weight residual -122.60 -137.88 15.28 0 2.50e+00 1.60e-01 3.74e+01 dihedral pdb=" C LYS B 248 " pdb=" N LYS B 248 " pdb=" CA LYS B 248 " pdb=" CB LYS B 248 " ideal model delta harmonic sigma weight residual -122.60 -137.86 15.26 0 2.50e+00 1.60e-01 3.73e+01 ... (remaining 20193 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 3970 0.118 - 0.236: 844 0.236 - 0.353: 60 0.353 - 0.471: 11 0.471 - 0.589: 11 Chirality restraints: 4896 Sorted by residual: chirality pdb=" CA LYS F 248 " pdb=" N LYS F 248 " pdb=" C LYS F 248 " pdb=" CB LYS F 248 " both_signs ideal model delta sigma weight residual False 2.51 1.92 0.59 2.00e-01 2.50e+01 8.67e+00 chirality pdb=" CA LYS L 248 " pdb=" N LYS L 248 " pdb=" C LYS L 248 " pdb=" CB LYS L 248 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.88e+00 chirality pdb=" CA LYS B 248 " pdb=" N LYS B 248 " pdb=" C LYS B 248 " pdb=" CB LYS B 248 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.39e+00 ... (remaining 4893 not shown) Planarity restraints: 5904 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR I 172 " 0.179 2.00e-02 2.50e+03 9.19e-02 1.69e+02 pdb=" CG TYR I 172 " -0.079 2.00e-02 2.50e+03 pdb=" CD1 TYR I 172 " -0.076 2.00e-02 2.50e+03 pdb=" CD2 TYR I 172 " -0.086 2.00e-02 2.50e+03 pdb=" CE1 TYR I 172 " -0.039 2.00e-02 2.50e+03 pdb=" CE2 TYR I 172 " -0.031 2.00e-02 2.50e+03 pdb=" CZ TYR I 172 " 0.018 2.00e-02 2.50e+03 pdb=" OH TYR I 172 " 0.115 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 172 " -0.179 2.00e-02 2.50e+03 9.19e-02 1.69e+02 pdb=" CG TYR C 172 " 0.079 2.00e-02 2.50e+03 pdb=" CD1 TYR C 172 " 0.076 2.00e-02 2.50e+03 pdb=" CD2 TYR C 172 " 0.086 2.00e-02 2.50e+03 pdb=" CE1 TYR C 172 " 0.039 2.00e-02 2.50e+03 pdb=" CE2 TYR C 172 " 0.031 2.00e-02 2.50e+03 pdb=" CZ TYR C 172 " -0.018 2.00e-02 2.50e+03 pdb=" OH TYR C 172 " -0.115 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR K 172 " 0.179 2.00e-02 2.50e+03 9.17e-02 1.68e+02 pdb=" CG TYR K 172 " -0.079 2.00e-02 2.50e+03 pdb=" CD1 TYR K 172 " -0.076 2.00e-02 2.50e+03 pdb=" CD2 TYR K 172 " -0.086 2.00e-02 2.50e+03 pdb=" CE1 TYR K 172 " -0.039 2.00e-02 2.50e+03 pdb=" CE2 TYR K 172 " -0.031 2.00e-02 2.50e+03 pdb=" CZ TYR K 172 " 0.018 2.00e-02 2.50e+03 pdb=" OH TYR K 172 " 0.115 2.00e-02 2.50e+03 ... (remaining 5901 not shown) Histogram of nonbonded interaction distances: 1.26 - 1.99: 42 1.99 - 2.72: 575 2.72 - 3.44: 51039 3.44 - 4.17: 78344 4.17 - 4.90: 138801 Nonbonded interactions: 268801 Sorted by model distance: nonbonded pdb=" CE LYS H 307 " pdb=" CB SER I 308 " model vdw 1.258 3.840 nonbonded pdb=" CE LYS B 307 " pdb=" CB SER C 308 " model vdw 1.258 3.840 nonbonded pdb=" CE LYS D 307 " pdb=" CB SER E 308 " model vdw 1.259 3.840 nonbonded pdb=" CE LYS J 307 " pdb=" CB SER K 308 " model vdw 1.259 3.840 nonbonded pdb=" CB SER A 308 " pdb=" CE LYS L 307 " model vdw 1.259 3.840 ... (remaining 268796 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: 0.01 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' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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 group one per residue 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: 4.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 30.030 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6765 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 : 0.012 0.041 33300 Z= 0.710 Angle : 1.783 11.414 44976 Z= 1.169 Chirality : 0.095 0.589 4896 Planarity : 0.016 0.150 5904 Dihedral : 15.334 90.075 12492 Min Nonbonded Distance : 1.258 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 2.57 % Allowed : 6.64 % Favored : 90.79 % Rotamer: Outliers : 2.01 % Allowed : 6.94 % Favored : 91.04 % Cbeta Deviations : 0.39 % 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 aren not related in a simple way. whole: -2.43 (0.12), residues: 4128 helix: -1.37 (0.10), residues: 1744 sheet: 0.26 (0.24), residues: 424 loop : -2.27 (0.14), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 258 TYR 0.179 0.022 TYR I 172 PHE 0.069 0.017 PHE K 218 TRP 0.118 0.021 TRP F 260 HIS 0.013 0.004 HIS J 300 Details of bonding type rmsd covalent geometry : bond 0.01186 (33300) covalent geometry : angle 1.78272 (44976) hydrogen bonds : bond 0.16397 ( 1549) hydrogen bonds : angle 8.19612 ( 4461) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1193 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 1122 time to evaluate : 1.143 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 85 ASP cc_start: 0.6114 (OUTLIER) cc_final: 0.5586 (m-30) REVERT: A 89 ASN cc_start: 0.6561 (m-40) cc_final: 0.5740 (m-40) REVERT: A 244 GLU cc_start: 0.5844 (OUTLIER) cc_final: 0.5285 (mm-30) REVERT: B 195 SER cc_start: 0.7796 (t) cc_final: 0.7547 (p) REVERT: B 232 GLU cc_start: 0.3631 (OUTLIER) cc_final: 0.3307 (pm20) REVERT: C 382 THR cc_start: 0.8621 (p) cc_final: 0.8178 (p) REVERT: D 88 ASP cc_start: 0.5990 (t0) cc_final: 0.5634 (t0) REVERT: D 220 ASN cc_start: 0.7524 (m-40) cc_final: 0.6933 (m110) REVERT: D 364 ASP cc_start: 0.4987 (OUTLIER) cc_final: 0.4442 (p0) REVERT: E 248 LYS cc_start: 0.6120 (OUTLIER) cc_final: 0.4968 (ttpp) REVERT: E 320 LEU cc_start: 0.8479 (mt) cc_final: 0.8207 (mt) REVERT: F 118 GLU cc_start: 0.7185 (tt0) cc_final: 0.6903 (tt0) REVERT: G 106 SER cc_start: 0.7910 (t) cc_final: 0.7223 (p) REVERT: H 280 MET cc_start: 0.7069 (tpp) cc_final: 0.6756 (tpp) REVERT: I 279 GLU cc_start: 0.5144 (OUTLIER) cc_final: 0.4716 (tt0) REVERT: J 223 LYS cc_start: 0.8345 (mtmt) cc_final: 0.7975 (mtpp) REVERT: K 333 ARG cc_start: 0.5947 (mtt-85) cc_final: 0.5693 (mtm-85) REVERT: L 341 TRP cc_start: 0.8169 (m100) cc_final: 0.7732 (m100) outliers start: 71 outliers final: 20 residues processed: 1178 average time/residue: 0.2316 time to fit residues: 422.5770 Evaluate side-chains 648 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 622 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 248 LYS Chi-restraints excluded: chain E residue 279 GLU Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain G residue 112 THR Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 327 LEU Chi-restraints excluded: chain I residue 112 THR Chi-restraints excluded: chain I residue 279 GLU Chi-restraints excluded: chain J residue 229 SER Chi-restraints excluded: chain J residue 245 GLU Chi-restraints excluded: chain J residue 327 LEU Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 228 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 7.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.2980 chunk 207 optimal weight: 4.9990 chunk 401 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 4.9990 overall best weight: 3.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN A 220 ASN B 86 GLN B 318 GLN C 86 GLN C 89 ASN C 182 HIS C 246 ASN D 86 GLN D 318 GLN D 352 HIS E 86 GLN E 89 ASN E 324 GLN F 86 GLN F 87 ASN F 300 HIS F 318 GLN G 86 GLN G 214 GLN G 242 GLN G 328 GLN H 86 GLN H 149 GLN I 86 GLN ** I 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 167 GLN ** I 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 220 ASN I 318 GLN I 319 ASN J 86 GLN ** J 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 226 GLN J 324 GLN K 86 GLN K 220 ASN L 86 GLN L 89 ASN L 287 GLN L 318 GLN L 391 ASN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.165991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.137694 restraints weight = 46684.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.141129 restraints weight = 27363.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.143299 restraints weight = 19558.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.144639 restraints weight = 15887.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.145477 restraints weight = 13966.610| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.4067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 33300 Z= 0.212 Angle : 0.814 9.679 44976 Z= 0.432 Chirality : 0.047 0.164 4896 Planarity : 0.005 0.048 5904 Dihedral : 7.451 110.131 4565 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.92 % Allowed : 5.98 % Favored : 93.10 % Rotamer: Outliers : 3.80 % Allowed : 13.89 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.08 % 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 aren not related in a simple way. whole: -0.91 (0.13), residues: 4128 helix: 0.47 (0.12), residues: 1756 sheet: -0.80 (0.20), residues: 648 loop : -1.63 (0.15), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 362 TYR 0.021 0.002 TYR D 172 PHE 0.038 0.003 PHE H 186 TRP 0.035 0.003 TRP H 311 HIS 0.007 0.001 HIS D 352 Details of bonding type rmsd covalent geometry : bond 0.00480 (33300) covalent geometry : angle 0.81449 (44976) hydrogen bonds : bond 0.05597 ( 1549) hydrogen bonds : angle 5.70403 ( 4461) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 826 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 692 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ASN cc_start: 0.7943 (m-40) cc_final: 0.7652 (m-40) REVERT: A 242 GLN cc_start: 0.8049 (mm110) cc_final: 0.7593 (pp30) REVERT: A 350 ARG cc_start: 0.7789 (mmp-170) cc_final: 0.7578 (mmp80) REVERT: B 354 GLU cc_start: 0.7496 (mt-10) cc_final: 0.7217 (mt-10) REVERT: C 85 ASP cc_start: 0.6980 (OUTLIER) cc_final: 0.6585 (p0) REVERT: C 112 THR cc_start: 0.8785 (OUTLIER) cc_final: 0.8462 (p) REVERT: C 168 ARG cc_start: 0.7478 (ttp-170) cc_final: 0.6836 (ptt-90) REVERT: C 347 ASP cc_start: 0.6024 (m-30) cc_final: 0.5653 (m-30) REVERT: D 88 ASP cc_start: 0.8119 (t0) cc_final: 0.7899 (t0) REVERT: D 212 ASP cc_start: 0.7247 (m-30) cc_final: 0.7025 (m-30) REVERT: D 216 ASP cc_start: 0.7475 (m-30) cc_final: 0.6980 (m-30) REVERT: D 220 ASN cc_start: 0.7838 (m-40) cc_final: 0.7559 (m-40) REVERT: D 239 GLN cc_start: 0.3287 (mt0) cc_final: 0.3039 (tp40) REVERT: D 283 SER cc_start: 0.7498 (OUTLIER) cc_final: 0.7198 (p) REVERT: E 58 LEU cc_start: 0.8989 (tp) cc_final: 0.8766 (tt) REVERT: E 248 LYS cc_start: 0.7241 (OUTLIER) cc_final: 0.5696 (ttpp) REVERT: E 279 GLU cc_start: 0.5755 (OUTLIER) cc_final: 0.4438 (tm-30) REVERT: F 111 MET cc_start: 0.7124 (mtt) cc_final: 0.6897 (mtt) REVERT: F 316 GLU cc_start: 0.8033 (tt0) cc_final: 0.7766 (tt0) REVERT: F 335 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7605 (mt-10) REVERT: G 72 THR cc_start: 0.8703 (m) cc_final: 0.8116 (p) REVERT: G 76 CYS cc_start: 0.8327 (m) cc_final: 0.7779 (m) REVERT: G 189 THR cc_start: 0.7162 (p) cc_final: 0.6924 (p) REVERT: G 214 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.8139 (tm130) REVERT: G 392 MET cc_start: 0.6837 (mmm) cc_final: 0.6335 (mmm) REVERT: H 122 MET cc_start: 0.8112 (tpp) cc_final: 0.7861 (tpp) REVERT: H 171 GLU cc_start: 0.5742 (mp0) cc_final: 0.5056 (pp20) REVERT: H 392 MET cc_start: 0.7498 (mmt) cc_final: 0.7103 (mmt) REVERT: I 168 ARG cc_start: 0.6713 (tpt170) cc_final: 0.6481 (tmt170) REVERT: I 215 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.7282 (ttt90) REVERT: I 245 GLU cc_start: 0.7902 (tm-30) cc_final: 0.7632 (tm-30) REVERT: I 261 ILE cc_start: 0.5907 (OUTLIER) cc_final: 0.5447 (pt) REVERT: I 279 GLU cc_start: 0.6329 (OUTLIER) cc_final: 0.5708 (tp30) REVERT: I 318 GLN cc_start: 0.7271 (OUTLIER) cc_final: 0.6778 (mt0) REVERT: J 115 GLU cc_start: 0.6705 (tt0) cc_final: 0.6093 (tt0) REVERT: J 320 LEU cc_start: 0.8969 (mt) cc_final: 0.8724 (mm) REVERT: J 350 ARG cc_start: 0.6779 (mtm110) cc_final: 0.6420 (ttp80) REVERT: K 184 LYS cc_start: 0.7114 (OUTLIER) cc_final: 0.6257 (ttpt) REVERT: K 311 TRP cc_start: 0.3480 (OUTLIER) cc_final: 0.2988 (p90) REVERT: K 318 GLN cc_start: 0.8468 (tm-30) cc_final: 0.7847 (tm-30) REVERT: L 350 ARG cc_start: 0.7394 (mtp85) cc_final: 0.7191 (ttm-80) outliers start: 134 outliers final: 72 residues processed: 792 average time/residue: 0.2152 time to fit residues: 271.9035 Evaluate side-chains 620 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 536 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 283 SER Chi-restraints excluded: chain E residue 53 ASN Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 149 GLN Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 248 LYS Chi-restraints excluded: chain E residue 279 GLU Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain F residue 203 SER Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain F residue 243 VAL Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 389 THR Chi-restraints excluded: chain F residue 390 ASP Chi-restraints excluded: chain G residue 112 THR Chi-restraints excluded: chain G residue 214 GLN Chi-restraints excluded: chain G residue 311 TRP Chi-restraints excluded: chain G residue 338 ILE Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 109 GLN Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 125 CYS Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain H residue 382 THR Chi-restraints excluded: chain I residue 84 THR Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 112 THR Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 215 ARG Chi-restraints excluded: chain I residue 261 ILE Chi-restraints excluded: chain I residue 279 GLU Chi-restraints excluded: chain I residue 318 GLN Chi-restraints excluded: chain I residue 320 LEU Chi-restraints excluded: chain I residue 389 THR Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 122 MET Chi-restraints excluded: chain J residue 144 SER Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain J residue 227 ILE Chi-restraints excluded: chain J residue 360 LEU Chi-restraints excluded: chain J residue 395 LEU Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain K residue 184 LYS Chi-restraints excluded: chain K residue 228 LEU Chi-restraints excluded: chain K residue 268 THR Chi-restraints excluded: chain K residue 302 VAL Chi-restraints excluded: chain K residue 311 TRP Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 110 TYR Chi-restraints excluded: chain L residue 112 THR Chi-restraints excluded: chain L residue 313 SER Chi-restraints excluded: chain L residue 327 LEU Chi-restraints excluded: chain L residue 388 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 388 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 361 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 127 optimal weight: 0.7980 chunk 136 optimal weight: 10.0000 chunk 394 optimal weight: 8.9990 chunk 240 optimal weight: 3.9990 chunk 355 optimal weight: 4.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 GLN B 214 GLN B 226 GLN B 352 HIS C 276 GLN D 276 GLN D 318 GLN E 182 HIS E 214 GLN E 220 ASN F 87 ASN F 214 GLN G 220 ASN G 242 GLN H 152 ASN H 182 HIS H 226 GLN H 242 GLN I 129 ASN I 182 HIS I 214 GLN I 319 ASN I 356 ASN ** J 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 324 GLN K 89 ASN L 87 ASN L 89 ASN L 182 HIS L 220 ASN L 276 GLN L 287 GLN L 352 HIS L 391 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.155674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.127470 restraints weight = 46958.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.130763 restraints weight = 27694.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.132852 restraints weight = 19858.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.133987 restraints weight = 16174.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.134856 restraints weight = 14379.811| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.5714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 33300 Z= 0.207 Angle : 0.733 9.334 44976 Z= 0.389 Chirality : 0.046 0.167 4896 Planarity : 0.005 0.046 5904 Dihedral : 6.650 100.574 4541 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.75 % Allowed : 6.61 % Favored : 92.64 % Rotamer: Outliers : 4.90 % Allowed : 15.70 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: -0.65 (0.13), residues: 4128 helix: 0.63 (0.12), residues: 1752 sheet: -0.55 (0.21), residues: 588 loop : -1.43 (0.15), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 362 TYR 0.019 0.002 TYR E 330 PHE 0.027 0.002 PHE F 186 TRP 0.033 0.002 TRP D 311 HIS 0.007 0.002 HIS I 355 Details of bonding type rmsd covalent geometry : bond 0.00475 (33300) covalent geometry : angle 0.73327 (44976) hydrogen bonds : bond 0.05522 ( 1549) hydrogen bonds : angle 5.37240 ( 4461) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 776 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 603 time to evaluate : 1.158 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: A 242 GLN cc_start: 0.8088 (mm110) cc_final: 0.7873 (pp30) REVERT: C 110 TYR cc_start: 0.8489 (m-80) cc_final: 0.8236 (m-80) REVERT: C 168 ARG cc_start: 0.7375 (ttp-170) cc_final: 0.6916 (ptt-90) REVERT: C 210 MET cc_start: 0.8440 (mtm) cc_final: 0.8056 (mtt) REVERT: C 368 ARG cc_start: 0.7676 (ptm160) cc_final: 0.7327 (ttp-170) REVERT: C 392 MET cc_start: 0.8307 (mmp) cc_final: 0.7716 (mmt) REVERT: D 88 ASP cc_start: 0.8131 (t0) cc_final: 0.7847 (t0) REVERT: D 120 MET cc_start: 0.8420 (tpp) cc_final: 0.8099 (mmm) REVERT: D 122 MET cc_start: 0.8089 (tpp) cc_final: 0.7639 (tpp) REVERT: D 212 ASP cc_start: 0.7317 (m-30) cc_final: 0.6986 (m-30) REVERT: D 213 GLN cc_start: 0.9052 (tm-30) cc_final: 0.8817 (tm-30) REVERT: D 216 ASP cc_start: 0.7195 (m-30) cc_final: 0.6570 (m-30) REVERT: D 220 ASN cc_start: 0.8274 (m-40) cc_final: 0.7816 (m110) REVERT: E 248 LYS cc_start: 0.7051 (OUTLIER) cc_final: 0.5827 (ttpp) REVERT: F 111 MET cc_start: 0.8212 (mtt) cc_final: 0.7976 (mtt) REVERT: F 335 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7888 (mt-10) REVERT: G 72 THR cc_start: 0.9038 (m) cc_final: 0.8264 (p) REVERT: G 73 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8504 (mt) REVERT: G 76 CYS cc_start: 0.8372 (m) cc_final: 0.7716 (m) REVERT: G 153 MET cc_start: 0.7968 (tpp) cc_final: 0.7081 (tpp) REVERT: G 178 LYS cc_start: 0.8107 (tptt) cc_final: 0.7855 (tppt) REVERT: G 356 ASN cc_start: 0.8337 (p0) cc_final: 0.7992 (p0) REVERT: G 392 MET cc_start: 0.7698 (mmm) cc_final: 0.7399 (mmm) REVERT: H 76 CYS cc_start: 0.7892 (m) cc_final: 0.7571 (m) REVERT: H 122 MET cc_start: 0.8274 (OUTLIER) cc_final: 0.8026 (ttp) REVERT: H 171 GLU cc_start: 0.6066 (mp0) cc_final: 0.5315 (pp20) REVERT: H 393 PRO cc_start: 0.8284 (Cg_exo) cc_final: 0.7979 (Cg_endo) REVERT: I 82 PHE cc_start: 0.8144 (m-80) cc_final: 0.7897 (m-10) REVERT: I 136 ARG cc_start: 0.7587 (ptp-170) cc_final: 0.7269 (ptp-110) REVERT: I 168 ARG cc_start: 0.6721 (tpt170) cc_final: 0.6228 (ttp-110) REVERT: I 215 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.7340 (ttt90) REVERT: I 245 GLU cc_start: 0.8065 (tm-30) cc_final: 0.7770 (tm-30) REVERT: J 76 CYS cc_start: 0.7597 (m) cc_final: 0.6968 (p) REVERT: K 122 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.7952 (mtp) REVERT: K 153 MET cc_start: 0.8205 (mmm) cc_final: 0.7905 (tpp) REVERT: K 311 TRP cc_start: 0.3954 (OUTLIER) cc_final: 0.3412 (p-90) REVERT: K 318 GLN cc_start: 0.8538 (tm-30) cc_final: 0.7932 (tm-30) REVERT: K 375 MET cc_start: 0.7879 (mmt) cc_final: 0.7408 (mmt) REVERT: L 350 ARG cc_start: 0.7534 (mtp85) cc_final: 0.7331 (ttm-80) REVERT: L 375 MET cc_start: 0.8846 (mmp) cc_final: 0.8597 (mmt) outliers start: 173 outliers final: 109 residues processed: 734 average time/residue: 0.1966 time to fit residues: 231.5897 Evaluate side-chains 617 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 502 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 311 TRP Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 125 CYS Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 283 SER Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 345 SER Chi-restraints excluded: chain E residue 53 ASN Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 203 SER Chi-restraints excluded: chain E residue 248 LYS Chi-restraints excluded: chain E residue 279 GLU Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 203 SER Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain F residue 243 VAL Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 271 ILE Chi-restraints excluded: chain F residue 389 THR Chi-restraints excluded: chain F residue 390 ASP Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain G residue 112 THR Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 261 ILE Chi-restraints excluded: chain G residue 311 TRP Chi-restraints excluded: chain G residue 316 GLU Chi-restraints excluded: chain G residue 382 THR Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 122 MET Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain H residue 229 SER Chi-restraints excluded: chain H residue 247 PHE Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain H residue 320 LEU Chi-restraints excluded: chain H residue 389 THR Chi-restraints excluded: chain I residue 84 THR Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain I residue 215 ARG Chi-restraints excluded: chain I residue 273 VAL Chi-restraints excluded: chain I residue 279 GLU Chi-restraints excluded: chain I residue 302 VAL Chi-restraints excluded: chain I residue 389 THR Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 122 MET Chi-restraints excluded: chain J residue 142 VAL Chi-restraints excluded: chain J residue 144 SER Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain J residue 180 ILE Chi-restraints excluded: chain J residue 183 LEU Chi-restraints excluded: chain J residue 227 ILE Chi-restraints excluded: chain J residue 302 VAL Chi-restraints excluded: chain J residue 389 THR Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 122 MET Chi-restraints excluded: chain K residue 125 CYS Chi-restraints excluded: chain K residue 163 VAL Chi-restraints excluded: chain K residue 176 SER Chi-restraints excluded: chain K residue 184 LYS Chi-restraints excluded: chain K residue 228 LEU Chi-restraints excluded: chain K residue 255 VAL Chi-restraints excluded: chain K residue 268 THR Chi-restraints excluded: chain K residue 302 VAL Chi-restraints excluded: chain K residue 311 TRP Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 118 GLU Chi-restraints excluded: chain L residue 122 MET Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain L residue 274 THR Chi-restraints excluded: chain L residue 313 SER Chi-restraints excluded: chain L residue 327 LEU Chi-restraints excluded: chain L residue 388 ARG Chi-restraints excluded: chain L residue 389 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 146 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 46 optimal weight: 9.9990 chunk 166 optimal weight: 9.9990 chunk 261 optimal weight: 0.8980 chunk 232 optimal weight: 3.9990 chunk 361 optimal weight: 10.0000 chunk 276 optimal weight: 0.9990 chunk 384 optimal weight: 4.9990 chunk 376 optimal weight: 5.9990 chunk 407 optimal weight: 0.0000 overall best weight: 2.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN ** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 318 GLN D 239 GLN E 214 GLN F 87 ASN F 182 HIS G 242 GLN G 352 HIS I 177 GLN I 220 ASN I 226 GLN I 318 GLN ** J 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 213 GLN J 287 GLN J 391 ASN L 352 HIS L 391 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.157678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.129818 restraints weight = 46200.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.133261 restraints weight = 26152.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.135443 restraints weight = 18366.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.136815 restraints weight = 14801.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.137648 restraints weight = 12927.948| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.6180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 33300 Z= 0.146 Angle : 0.636 9.476 44976 Z= 0.334 Chirality : 0.043 0.157 4896 Planarity : 0.004 0.065 5904 Dihedral : 6.263 107.868 4534 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.73 % Allowed : 5.89 % Favored : 93.39 % Rotamer: Outliers : 4.28 % Allowed : 17.74 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 aren not related in a simple way. whole: -0.41 (0.13), residues: 4128 helix: 0.82 (0.12), residues: 1761 sheet: -0.53 (0.20), residues: 631 loop : -1.28 (0.15), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 165 TYR 0.017 0.001 TYR F 105 PHE 0.019 0.002 PHE G 186 TRP 0.023 0.002 TRP L 311 HIS 0.007 0.001 HIS L 352 Details of bonding type rmsd covalent geometry : bond 0.00328 (33300) covalent geometry : angle 0.63560 (44976) hydrogen bonds : bond 0.04567 ( 1549) hydrogen bonds : angle 5.15334 ( 4461) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 701 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 550 time to evaluate : 1.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ASN cc_start: 0.7530 (m-40) cc_final: 0.7014 (m-40) REVERT: B 280 MET cc_start: 0.8280 (tpt) cc_final: 0.8039 (tpt) REVERT: B 356 ASN cc_start: 0.7942 (OUTLIER) cc_final: 0.7544 (t0) REVERT: C 168 ARG cc_start: 0.7248 (ttp-170) cc_final: 0.7035 (ptt-90) REVERT: C 368 ARG cc_start: 0.7700 (ptm160) cc_final: 0.7349 (ttp-170) REVERT: C 392 MET cc_start: 0.8478 (mmp) cc_final: 0.8053 (mmt) REVERT: D 120 MET cc_start: 0.8381 (tpp) cc_final: 0.8119 (mmm) REVERT: D 212 ASP cc_start: 0.7368 (m-30) cc_final: 0.6901 (m-30) REVERT: D 216 ASP cc_start: 0.7177 (m-30) cc_final: 0.6484 (m-30) REVERT: D 220 ASN cc_start: 0.8259 (m-40) cc_final: 0.7789 (m110) REVERT: E 58 LEU cc_start: 0.9291 (tp) cc_final: 0.8758 (tt) REVERT: E 248 LYS cc_start: 0.6672 (OUTLIER) cc_final: 0.5608 (ttpp) REVERT: E 390 ASP cc_start: 0.6974 (p0) cc_final: 0.6678 (p0) REVERT: E 392 MET cc_start: 0.7988 (mmt) cc_final: 0.7663 (mpp) REVERT: G 72 THR cc_start: 0.9032 (m) cc_final: 0.8156 (p) REVERT: G 73 LEU cc_start: 0.8883 (mm) cc_final: 0.8522 (mt) REVERT: G 76 CYS cc_start: 0.8265 (m) cc_final: 0.7628 (m) REVERT: G 127 TYR cc_start: 0.8984 (m-80) cc_final: 0.8778 (m-80) REVERT: G 153 MET cc_start: 0.8038 (tpp) cc_final: 0.7169 (tpp) REVERT: G 178 LYS cc_start: 0.7921 (tptt) cc_final: 0.7651 (tppt) REVERT: G 279 GLU cc_start: 0.5902 (OUTLIER) cc_final: 0.5215 (tp30) REVERT: G 356 ASN cc_start: 0.8213 (p0) cc_final: 0.7843 (p0) REVERT: G 392 MET cc_start: 0.7710 (mmm) cc_final: 0.7409 (mmm) REVERT: H 76 CYS cc_start: 0.7707 (m) cc_final: 0.7221 (m) REVERT: H 136 ARG cc_start: 0.5004 (ptp-110) cc_final: 0.4510 (ptm160) REVERT: H 171 GLU cc_start: 0.6048 (mp0) cc_final: 0.5589 (pp20) REVERT: H 392 MET cc_start: 0.7720 (mmt) cc_final: 0.7286 (mmt) REVERT: H 393 PRO cc_start: 0.8354 (Cg_exo) cc_final: 0.7820 (Cg_endo) REVERT: I 82 PHE cc_start: 0.8141 (m-80) cc_final: 0.7900 (m-10) REVERT: I 110 TYR cc_start: 0.7848 (m-80) cc_final: 0.7552 (m-80) REVERT: I 122 MET cc_start: 0.8730 (tpp) cc_final: 0.8317 (tpp) REVERT: I 136 ARG cc_start: 0.7710 (ptp-170) cc_final: 0.7284 (mtm110) REVERT: I 168 ARG cc_start: 0.6742 (tpt170) cc_final: 0.6286 (ttp-110) REVERT: I 215 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.7272 (ttt90) REVERT: I 361 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8648 (mp) REVERT: J 76 CYS cc_start: 0.7764 (m) cc_final: 0.7138 (p) REVERT: J 111 MET cc_start: 0.8561 (mtt) cc_final: 0.8069 (mtt) REVERT: J 161 LYS cc_start: 0.8191 (ptpp) cc_final: 0.7431 (ptmt) REVERT: K 304 ASP cc_start: 0.6707 (t0) cc_final: 0.6466 (t0) REVERT: K 311 TRP cc_start: 0.3924 (OUTLIER) cc_final: 0.2990 (p90) REVERT: K 318 GLN cc_start: 0.8530 (tm-30) cc_final: 0.7929 (tm-30) REVERT: K 375 MET cc_start: 0.7812 (mmt) cc_final: 0.7455 (mmt) outliers start: 151 outliers final: 103 residues processed: 661 average time/residue: 0.1722 time to fit residues: 184.3065 Evaluate side-chains 605 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 496 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 311 TRP Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain B residue 111 MET Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 356 ASN Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 283 SER Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 345 SER Chi-restraints excluded: chain D residue 346 LYS Chi-restraints excluded: chain E residue 53 ASN Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 177 GLN Chi-restraints excluded: chain E residue 203 SER Chi-restraints excluded: chain E residue 248 LYS Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 279 GLU Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 203 SER Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 257 LYS Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 389 THR Chi-restraints excluded: chain F residue 390 ASP Chi-restraints excluded: chain G residue 112 THR Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 261 ILE Chi-restraints excluded: chain G residue 279 GLU Chi-restraints excluded: chain G residue 301 LEU Chi-restraints excluded: chain G residue 311 TRP Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 110 TYR Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 125 CYS Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain H residue 229 SER Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 320 LEU Chi-restraints excluded: chain H residue 389 THR Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 84 THR Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain I residue 215 ARG Chi-restraints excluded: chain I residue 279 GLU Chi-restraints excluded: chain I residue 290 GLU Chi-restraints excluded: chain I residue 320 LEU Chi-restraints excluded: chain I residue 361 LEU Chi-restraints excluded: chain J residue 55 GLU Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 122 MET Chi-restraints excluded: chain J residue 144 SER Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain J residue 180 ILE Chi-restraints excluded: chain J residue 227 ILE Chi-restraints excluded: chain J residue 302 VAL Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain J residue 351 LEU Chi-restraints excluded: chain J residue 360 LEU Chi-restraints excluded: chain J residue 389 THR Chi-restraints excluded: chain K residue 84 THR Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 125 CYS Chi-restraints excluded: chain K residue 146 LEU Chi-restraints excluded: chain K residue 176 SER Chi-restraints excluded: chain K residue 228 LEU Chi-restraints excluded: chain K residue 255 VAL Chi-restraints excluded: chain K residue 261 ILE Chi-restraints excluded: chain K residue 268 THR Chi-restraints excluded: chain K residue 273 VAL Chi-restraints excluded: chain K residue 302 VAL Chi-restraints excluded: chain K residue 311 TRP Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain L residue 391 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 94 optimal weight: 8.9990 chunk 41 optimal weight: 8.9990 chunk 207 optimal weight: 5.9990 chunk 396 optimal weight: 10.0000 chunk 57 optimal weight: 7.9990 chunk 83 optimal weight: 0.9990 chunk 391 optimal weight: 2.9990 chunk 211 optimal weight: 7.9990 chunk 46 optimal weight: 0.2980 chunk 11 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN A 318 GLN ** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 214 GLN F 87 ASN G 242 GLN ** I 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 318 GLN J 129 ASN J 242 GLN J 246 ASN J 352 HIS L 352 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.154839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.127475 restraints weight = 46414.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.130850 restraints weight = 26272.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.133001 restraints weight = 18371.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.134314 restraints weight = 14743.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.134990 restraints weight = 12890.736| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.6674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 33300 Z= 0.175 Angle : 0.653 9.549 44976 Z= 0.341 Chirality : 0.044 0.176 4896 Planarity : 0.005 0.069 5904 Dihedral : 6.197 112.044 4534 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.73 % Allowed : 6.54 % Favored : 92.73 % Rotamer: Outliers : 5.10 % Allowed : 18.08 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: -0.54 (0.13), residues: 4128 helix: 0.68 (0.12), residues: 1810 sheet: -0.42 (0.20), residues: 642 loop : -1.45 (0.16), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 388 TYR 0.019 0.002 TYR F 110 PHE 0.023 0.002 PHE G 186 TRP 0.024 0.002 TRP B 311 HIS 0.008 0.002 HIS H 300 Details of bonding type rmsd covalent geometry : bond 0.00404 (33300) covalent geometry : angle 0.65263 (44976) hydrogen bonds : bond 0.04940 ( 1549) hydrogen bonds : angle 5.16190 ( 4461) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 718 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 538 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ASN cc_start: 0.7238 (m-40) cc_final: 0.6864 (t0) REVERT: C 110 TYR cc_start: 0.8492 (m-80) cc_final: 0.8223 (m-80) REVERT: C 279 GLU cc_start: 0.5850 (OUTLIER) cc_final: 0.5628 (tp30) REVERT: C 368 ARG cc_start: 0.7749 (ptm160) cc_final: 0.7480 (ttp-170) REVERT: C 392 MET cc_start: 0.8691 (mmp) cc_final: 0.8307 (mmt) REVERT: D 120 MET cc_start: 0.8299 (tpp) cc_final: 0.8047 (mmm) REVERT: D 122 MET cc_start: 0.8446 (tpp) cc_final: 0.7873 (tpp) REVERT: D 212 ASP cc_start: 0.7354 (m-30) cc_final: 0.6917 (m-30) REVERT: D 213 GLN cc_start: 0.9130 (tm-30) cc_final: 0.8679 (tm-30) REVERT: D 216 ASP cc_start: 0.7150 (m-30) cc_final: 0.6481 (m-30) REVERT: D 220 ASN cc_start: 0.8300 (m-40) cc_final: 0.7811 (m-40) REVERT: D 232 GLU cc_start: 0.5633 (OUTLIER) cc_final: 0.3911 (mt-10) REVERT: D 335 GLU cc_start: 0.7412 (mt-10) cc_final: 0.7168 (mt-10) REVERT: D 392 MET cc_start: 0.7473 (tpp) cc_final: 0.7145 (mmt) REVERT: E 248 LYS cc_start: 0.6524 (OUTLIER) cc_final: 0.5571 (ttpp) REVERT: F 335 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7878 (mt-10) REVERT: F 342 LEU cc_start: 0.8662 (mm) cc_final: 0.8410 (mp) REVERT: G 72 THR cc_start: 0.9039 (m) cc_final: 0.8145 (p) REVERT: G 73 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8527 (mt) REVERT: G 76 CYS cc_start: 0.8161 (m) cc_final: 0.7561 (m) REVERT: G 153 MET cc_start: 0.7991 (tpp) cc_final: 0.7095 (tpp) REVERT: G 356 ASN cc_start: 0.8234 (p0) cc_final: 0.7847 (p0) REVERT: G 392 MET cc_start: 0.7812 (mmm) cc_final: 0.7504 (mmm) REVERT: H 153 MET cc_start: 0.7575 (tpp) cc_final: 0.7250 (tpp) REVERT: H 171 GLU cc_start: 0.5996 (mp0) cc_final: 0.5675 (pp20) REVERT: H 377 GLU cc_start: 0.5907 (mm-30) cc_final: 0.5601 (mm-30) REVERT: H 392 MET cc_start: 0.7783 (mmt) cc_final: 0.7426 (mmt) REVERT: H 393 PRO cc_start: 0.8465 (Cg_exo) cc_final: 0.8103 (Cg_endo) REVERT: I 110 TYR cc_start: 0.8059 (m-80) cc_final: 0.7815 (m-80) REVERT: I 122 MET cc_start: 0.8693 (tpp) cc_final: 0.8337 (tpp) REVERT: I 136 ARG cc_start: 0.7776 (ptp-170) cc_final: 0.6759 (mtt-85) REVERT: I 168 ARG cc_start: 0.6715 (tpt170) cc_final: 0.6289 (ttp-110) REVERT: I 215 ARG cc_start: 0.7849 (OUTLIER) cc_final: 0.7228 (ttt90) REVERT: I 245 GLU cc_start: 0.7978 (tm-30) cc_final: 0.7709 (tm-30) REVERT: J 111 MET cc_start: 0.8467 (mtt) cc_final: 0.8141 (mtt) REVERT: J 223 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8333 (mttp) REVERT: K 133 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8753 (mt) REVERT: K 304 ASP cc_start: 0.6701 (t0) cc_final: 0.6449 (t0) REVERT: K 311 TRP cc_start: 0.3784 (OUTLIER) cc_final: 0.2976 (p90) REVERT: K 318 GLN cc_start: 0.8764 (tm-30) cc_final: 0.8101 (tm-30) REVERT: K 375 MET cc_start: 0.7860 (mmt) cc_final: 0.7510 (mmt) REVERT: K 392 MET cc_start: 0.7857 (mmm) cc_final: 0.7402 (mmm) outliers start: 180 outliers final: 127 residues processed: 672 average time/residue: 0.1781 time to fit residues: 193.7959 Evaluate side-chains 623 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 488 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 311 TRP Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain B residue 111 MET Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 345 SER Chi-restraints excluded: chain D residue 346 LYS Chi-restraints excluded: chain E residue 53 ASN Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 177 GLN Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 242 GLN Chi-restraints excluded: chain E residue 248 LYS Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 279 GLU Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 313 SER Chi-restraints excluded: chain E residue 337 SER Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 203 SER Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain F residue 257 LYS Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 389 THR Chi-restraints excluded: chain F residue 390 ASP Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain G residue 112 THR Chi-restraints excluded: chain G residue 188 PHE Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 261 ILE Chi-restraints excluded: chain G residue 301 LEU Chi-restraints excluded: chain G residue 311 TRP Chi-restraints excluded: chain G residue 316 GLU Chi-restraints excluded: chain G residue 345 SER Chi-restraints excluded: chain G residue 382 THR Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 110 TYR Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 125 CYS Chi-restraints excluded: chain H residue 176 SER Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 229 SER Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 320 LEU Chi-restraints excluded: chain H residue 389 THR Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 84 THR Chi-restraints excluded: chain I residue 112 THR Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain I residue 197 ILE Chi-restraints excluded: chain I residue 215 ARG Chi-restraints excluded: chain I residue 262 LEU Chi-restraints excluded: chain I residue 279 GLU Chi-restraints excluded: chain I residue 290 GLU Chi-restraints excluded: chain I residue 367 SER Chi-restraints excluded: chain I residue 375 MET Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 122 MET Chi-restraints excluded: chain J residue 129 ASN Chi-restraints excluded: chain J residue 144 SER Chi-restraints excluded: chain J residue 180 ILE Chi-restraints excluded: chain J residue 223 LYS Chi-restraints excluded: chain J residue 227 ILE Chi-restraints excluded: chain J residue 258 ARG Chi-restraints excluded: chain J residue 302 VAL Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain J residue 351 LEU Chi-restraints excluded: chain J residue 360 LEU Chi-restraints excluded: chain J residue 389 THR Chi-restraints excluded: chain K residue 71 SER Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 84 THR Chi-restraints excluded: chain K residue 125 CYS Chi-restraints excluded: chain K residue 133 LEU Chi-restraints excluded: chain K residue 146 LEU Chi-restraints excluded: chain K residue 176 SER Chi-restraints excluded: chain K residue 255 VAL Chi-restraints excluded: chain K residue 261 ILE Chi-restraints excluded: chain K residue 268 THR Chi-restraints excluded: chain K residue 273 VAL Chi-restraints excluded: chain K residue 302 VAL Chi-restraints excluded: chain K residue 311 TRP Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 110 TYR Chi-restraints excluded: chain L residue 150 SER Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain L residue 274 THR Chi-restraints excluded: chain L residue 313 SER Chi-restraints excluded: chain L residue 389 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 80 optimal weight: 5.9990 chunk 207 optimal weight: 2.9990 chunk 117 optimal weight: 6.9990 chunk 325 optimal weight: 7.9990 chunk 13 optimal weight: 8.9990 chunk 128 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 393 optimal weight: 10.0000 chunk 329 optimal weight: 3.9990 chunk 287 optimal weight: 2.9990 chunk 274 optimal weight: 10.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 214 GLN F 87 ASN G 242 GLN ** I 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 129 ASN ** J 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 352 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.155412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.128173 restraints weight = 46107.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.131592 restraints weight = 26076.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.133763 restraints weight = 18115.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.135103 restraints weight = 14479.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.135837 restraints weight = 12620.796| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.6921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 33300 Z= 0.145 Angle : 0.625 10.521 44976 Z= 0.325 Chirality : 0.043 0.235 4896 Planarity : 0.004 0.067 5904 Dihedral : 6.018 113.504 4531 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.63 % Allowed : 6.13 % Favored : 93.24 % Rotamer: Outliers : 4.85 % Allowed : 18.82 % Favored : 76.33 % 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 aren not related in a simple way. whole: -0.35 (0.13), residues: 4128 helix: 0.87 (0.13), residues: 1768 sheet: -0.31 (0.21), residues: 572 loop : -1.31 (0.15), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 388 TYR 0.023 0.001 TYR E 105 PHE 0.021 0.002 PHE A 186 TRP 0.018 0.001 TRP B 311 HIS 0.009 0.001 HIS L 352 Details of bonding type rmsd covalent geometry : bond 0.00327 (33300) covalent geometry : angle 0.62469 (44976) hydrogen bonds : bond 0.04499 ( 1549) hydrogen bonds : angle 5.07200 ( 4461) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 706 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 535 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 ASN cc_start: 0.7267 (m-40) cc_final: 0.6892 (t0) REVERT: A 188 PHE cc_start: 0.7546 (OUTLIER) cc_final: 0.7083 (t80) REVERT: A 388 ARG cc_start: 0.8838 (mmm-85) cc_final: 0.8329 (mmm160) REVERT: C 110 TYR cc_start: 0.8462 (m-80) cc_final: 0.8248 (m-80) REVERT: C 122 MET cc_start: 0.8089 (tpt) cc_final: 0.7763 (tpt) REVERT: C 167 GLN cc_start: 0.7242 (tm-30) cc_final: 0.6817 (tm-30) REVERT: C 368 ARG cc_start: 0.7732 (ptm160) cc_final: 0.7448 (ttm170) REVERT: D 120 MET cc_start: 0.8410 (tpp) cc_final: 0.8136 (mmm) REVERT: D 122 MET cc_start: 0.8405 (tpp) cc_final: 0.7864 (ttp) REVERT: D 212 ASP cc_start: 0.7346 (m-30) cc_final: 0.6924 (m-30) REVERT: D 213 GLN cc_start: 0.9150 (tm-30) cc_final: 0.8626 (tm-30) REVERT: D 216 ASP cc_start: 0.7128 (m-30) cc_final: 0.6444 (m-30) REVERT: D 220 ASN cc_start: 0.8283 (m-40) cc_final: 0.7795 (m-40) REVERT: D 232 GLU cc_start: 0.5736 (OUTLIER) cc_final: 0.4157 (mt-10) REVERT: D 354 GLU cc_start: 0.6276 (tp30) cc_final: 0.6031 (tp30) REVERT: E 248 LYS cc_start: 0.6437 (OUTLIER) cc_final: 0.5569 (ttpp) REVERT: F 167 GLN cc_start: 0.7782 (tm-30) cc_final: 0.7553 (tt0) REVERT: F 188 PHE cc_start: 0.7601 (OUTLIER) cc_final: 0.6874 (t80) REVERT: G 72 THR cc_start: 0.9029 (m) cc_final: 0.8121 (p) REVERT: G 73 LEU cc_start: 0.8944 (mm) cc_final: 0.8535 (mt) REVERT: G 76 CYS cc_start: 0.8097 (m) cc_final: 0.7529 (m) REVERT: G 153 MET cc_start: 0.8021 (tpp) cc_final: 0.7046 (tpp) REVERT: G 356 ASN cc_start: 0.8252 (p0) cc_final: 0.7863 (p0) REVERT: G 392 MET cc_start: 0.7878 (mmm) cc_final: 0.7612 (mmm) REVERT: H 76 CYS cc_start: 0.7514 (m) cc_final: 0.7067 (m) REVERT: H 153 MET cc_start: 0.7428 (tpp) cc_final: 0.7041 (tpp) REVERT: H 393 PRO cc_start: 0.8427 (Cg_exo) cc_final: 0.8181 (Cg_endo) REVERT: I 110 TYR cc_start: 0.8104 (m-80) cc_final: 0.7718 (m-80) REVERT: I 122 MET cc_start: 0.8701 (tpp) cc_final: 0.8341 (tpp) REVERT: I 136 ARG cc_start: 0.7798 (ptp-170) cc_final: 0.6782 (mtt-85) REVERT: I 168 ARG cc_start: 0.6729 (tpt170) cc_final: 0.6295 (ttp-110) REVERT: I 215 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.7214 (ttt90) REVERT: I 389 THR cc_start: 0.8847 (m) cc_final: 0.8585 (p) REVERT: K 188 PHE cc_start: 0.8110 (OUTLIER) cc_final: 0.7629 (t80) REVERT: K 227 ILE cc_start: 0.7590 (OUTLIER) cc_final: 0.7332 (mp) REVERT: K 304 ASP cc_start: 0.6682 (t0) cc_final: 0.6403 (t0) REVERT: K 311 TRP cc_start: 0.3899 (OUTLIER) cc_final: 0.2716 (p90) REVERT: K 318 GLN cc_start: 0.8717 (tm-30) cc_final: 0.8048 (tm-30) REVERT: K 375 MET cc_start: 0.7856 (mmt) cc_final: 0.7515 (mmt) REVERT: K 392 MET cc_start: 0.7947 (mmm) cc_final: 0.7516 (mmm) REVERT: L 122 MET cc_start: 0.7877 (OUTLIER) cc_final: 0.7599 (tpp) REVERT: L 167 GLN cc_start: 0.8011 (tm-30) cc_final: 0.7533 (tm-30) outliers start: 171 outliers final: 116 residues processed: 663 average time/residue: 0.1812 time to fit residues: 195.7868 Evaluate side-chains 616 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 491 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 311 TRP Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 304 ASP Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 283 SER Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 345 SER Chi-restraints excluded: chain E residue 53 ASN Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 242 GLN Chi-restraints excluded: chain E residue 248 LYS Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 279 GLU Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 188 PHE Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 203 SER Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 389 THR Chi-restraints excluded: chain F residue 390 ASP Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain G residue 90 ARG Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 112 THR Chi-restraints excluded: chain G residue 188 PHE Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 261 ILE Chi-restraints excluded: chain G residue 301 LEU Chi-restraints excluded: chain G residue 311 TRP Chi-restraints excluded: chain G residue 316 GLU Chi-restraints excluded: chain G residue 382 THR Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 109 GLN Chi-restraints excluded: chain H residue 110 TYR Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 125 CYS Chi-restraints excluded: chain H residue 176 SER Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 229 SER Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 320 LEU Chi-restraints excluded: chain H residue 389 THR Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 112 THR Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain I residue 197 ILE Chi-restraints excluded: chain I residue 215 ARG Chi-restraints excluded: chain I residue 262 LEU Chi-restraints excluded: chain I residue 279 GLU Chi-restraints excluded: chain I residue 367 SER Chi-restraints excluded: chain I residue 375 MET Chi-restraints excluded: chain J residue 55 GLU Chi-restraints excluded: chain J residue 110 TYR Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 122 MET Chi-restraints excluded: chain J residue 144 SER Chi-restraints excluded: chain J residue 188 PHE Chi-restraints excluded: chain J residue 227 ILE Chi-restraints excluded: chain J residue 302 VAL Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain J residue 360 LEU Chi-restraints excluded: chain K residue 71 SER Chi-restraints excluded: chain K residue 84 THR Chi-restraints excluded: chain K residue 125 CYS Chi-restraints excluded: chain K residue 176 SER Chi-restraints excluded: chain K residue 188 PHE Chi-restraints excluded: chain K residue 227 ILE Chi-restraints excluded: chain K residue 255 VAL Chi-restraints excluded: chain K residue 261 ILE Chi-restraints excluded: chain K residue 268 THR Chi-restraints excluded: chain K residue 302 VAL Chi-restraints excluded: chain K residue 311 TRP Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 110 TYR Chi-restraints excluded: chain L residue 122 MET Chi-restraints excluded: chain L residue 150 SER Chi-restraints excluded: chain L residue 192 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 341 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 223 optimal weight: 20.0000 chunk 333 optimal weight: 0.9980 chunk 260 optimal weight: 5.9990 chunk 405 optimal weight: 5.9990 chunk 302 optimal weight: 6.9990 chunk 353 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 270 optimal weight: 7.9990 chunk 381 optimal weight: 5.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 HIS ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 87 ASN F 177 GLN G 182 HIS G 242 GLN ** I 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 129 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.154444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.127199 restraints weight = 46218.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.130551 restraints weight = 26004.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.132697 restraints weight = 18189.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.134008 restraints weight = 14584.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.134805 restraints weight = 12764.069| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.7233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 33300 Z= 0.156 Angle : 0.635 10.872 44976 Z= 0.330 Chirality : 0.043 0.237 4896 Planarity : 0.004 0.068 5904 Dihedral : 6.014 120.927 4531 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.63 % Allowed : 6.78 % Favored : 92.59 % Rotamer: Outliers : 4.71 % Allowed : 19.59 % Favored : 75.71 % 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 aren not related in a simple way. whole: -0.42 (0.13), residues: 4128 helix: 0.83 (0.12), residues: 1768 sheet: -0.33 (0.20), residues: 642 loop : -1.42 (0.15), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 388 TYR 0.020 0.001 TYR E 105 PHE 0.020 0.002 PHE A 186 TRP 0.018 0.001 TRP G 311 HIS 0.007 0.001 HIS H 300 Details of bonding type rmsd covalent geometry : bond 0.00358 (33300) covalent geometry : angle 0.63549 (44976) hydrogen bonds : bond 0.04618 ( 1549) hydrogen bonds : angle 5.08236 ( 4461) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 699 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 533 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ASN cc_start: 0.7334 (m-40) cc_final: 0.6968 (t0) REVERT: A 188 PHE cc_start: 0.7595 (OUTLIER) cc_final: 0.7157 (t80) REVERT: A 388 ARG cc_start: 0.8862 (mmm-85) cc_final: 0.8348 (mmm160) REVERT: C 122 MET cc_start: 0.8108 (tpt) cc_final: 0.7738 (tpt) REVERT: D 120 MET cc_start: 0.8302 (tpp) cc_final: 0.8076 (mmm) REVERT: D 122 MET cc_start: 0.8413 (OUTLIER) cc_final: 0.7796 (ttp) REVERT: D 212 ASP cc_start: 0.7373 (m-30) cc_final: 0.6936 (m-30) REVERT: D 213 GLN cc_start: 0.9121 (tm-30) cc_final: 0.8557 (tm-30) REVERT: D 216 ASP cc_start: 0.7141 (m-30) cc_final: 0.6458 (m-30) REVERT: D 220 ASN cc_start: 0.8273 (m-40) cc_final: 0.7766 (m-40) REVERT: D 232 GLU cc_start: 0.5785 (OUTLIER) cc_final: 0.4308 (mt-10) REVERT: E 160 LYS cc_start: 0.6242 (tptt) cc_final: 0.5567 (mttm) REVERT: E 188 PHE cc_start: 0.8521 (OUTLIER) cc_final: 0.8121 (t80) REVERT: E 248 LYS cc_start: 0.6119 (OUTLIER) cc_final: 0.5796 (ttpp) REVERT: F 188 PHE cc_start: 0.7642 (OUTLIER) cc_final: 0.7009 (t80) REVERT: G 72 THR cc_start: 0.9051 (m) cc_final: 0.8107 (p) REVERT: G 73 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8554 (mt) REVERT: G 76 CYS cc_start: 0.8151 (m) cc_final: 0.7514 (m) REVERT: G 356 ASN cc_start: 0.8204 (p0) cc_final: 0.7854 (p0) REVERT: H 178 LYS cc_start: 0.8500 (pttm) cc_final: 0.8266 (pttp) REVERT: H 326 THR cc_start: 0.9398 (m) cc_final: 0.9060 (p) REVERT: H 375 MET cc_start: 0.8801 (mmt) cc_final: 0.8494 (mmt) REVERT: H 393 PRO cc_start: 0.8446 (Cg_exo) cc_final: 0.8221 (Cg_endo) REVERT: I 110 TYR cc_start: 0.8089 (m-80) cc_final: 0.7789 (m-80) REVERT: I 122 MET cc_start: 0.8687 (OUTLIER) cc_final: 0.8350 (tpp) REVERT: I 136 ARG cc_start: 0.7836 (ptp-170) cc_final: 0.6851 (mtt-85) REVERT: I 168 ARG cc_start: 0.6718 (tpt170) cc_final: 0.6279 (ttp-110) REVERT: I 215 ARG cc_start: 0.7904 (OUTLIER) cc_final: 0.7232 (ttt90) REVERT: I 389 THR cc_start: 0.8801 (m) cc_final: 0.8547 (p) REVERT: K 188 PHE cc_start: 0.8125 (OUTLIER) cc_final: 0.7681 (t80) REVERT: K 227 ILE cc_start: 0.7716 (OUTLIER) cc_final: 0.7481 (mp) REVERT: K 304 ASP cc_start: 0.6629 (t0) cc_final: 0.6414 (t0) REVERT: K 311 TRP cc_start: 0.4037 (OUTLIER) cc_final: 0.2750 (p90) REVERT: K 318 GLN cc_start: 0.8722 (tm-30) cc_final: 0.8051 (tm-30) REVERT: K 375 MET cc_start: 0.7818 (mmt) cc_final: 0.7590 (mmt) REVERT: K 392 MET cc_start: 0.7945 (mmm) cc_final: 0.7590 (mmm) REVERT: L 167 GLN cc_start: 0.7879 (tm-30) cc_final: 0.7494 (tm-30) outliers start: 166 outliers final: 125 residues processed: 653 average time/residue: 0.1924 time to fit residues: 202.1532 Evaluate side-chains 626 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 489 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 311 TRP Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 122 MET Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 258 ARG Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 345 SER Chi-restraints excluded: chain D residue 367 SER Chi-restraints excluded: chain E residue 53 ASN Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 149 GLN Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 177 GLN Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 188 PHE Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 242 GLN Chi-restraints excluded: chain E residue 248 LYS Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 279 GLU Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 188 PHE Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 203 SER Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 389 THR Chi-restraints excluded: chain F residue 390 ASP Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain G residue 90 ARG Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 112 THR Chi-restraints excluded: chain G residue 188 PHE Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 261 ILE Chi-restraints excluded: chain G residue 301 LEU Chi-restraints excluded: chain G residue 311 TRP Chi-restraints excluded: chain G residue 316 GLU Chi-restraints excluded: chain G residue 382 THR Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 109 GLN Chi-restraints excluded: chain H residue 110 TYR Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 125 CYS Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 229 SER Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 320 LEU Chi-restraints excluded: chain H residue 389 THR Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 112 THR Chi-restraints excluded: chain I residue 122 MET Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain I residue 197 ILE Chi-restraints excluded: chain I residue 215 ARG Chi-restraints excluded: chain I residue 248 LYS Chi-restraints excluded: chain I residue 262 LEU Chi-restraints excluded: chain I residue 279 GLU Chi-restraints excluded: chain I residue 280 MET Chi-restraints excluded: chain I residue 367 SER Chi-restraints excluded: chain I residue 375 MET Chi-restraints excluded: chain J residue 110 TYR Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 122 MET Chi-restraints excluded: chain J residue 129 ASN Chi-restraints excluded: chain J residue 144 SER Chi-restraints excluded: chain J residue 188 PHE Chi-restraints excluded: chain J residue 227 ILE Chi-restraints excluded: chain J residue 258 ARG Chi-restraints excluded: chain J residue 302 VAL Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain J residue 360 LEU Chi-restraints excluded: chain K residue 71 SER Chi-restraints excluded: chain K residue 84 THR Chi-restraints excluded: chain K residue 125 CYS Chi-restraints excluded: chain K residue 176 SER Chi-restraints excluded: chain K residue 188 PHE Chi-restraints excluded: chain K residue 227 ILE Chi-restraints excluded: chain K residue 255 VAL Chi-restraints excluded: chain K residue 261 ILE Chi-restraints excluded: chain K residue 268 THR Chi-restraints excluded: chain K residue 302 VAL Chi-restraints excluded: chain K residue 311 TRP Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 150 SER Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain L residue 388 ARG Chi-restraints excluded: chain L residue 389 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 48 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 335 optimal weight: 7.9990 chunk 97 optimal weight: 0.0570 chunk 210 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 350 optimal weight: 9.9990 chunk 252 optimal weight: 0.9990 chunk 319 optimal weight: 3.9990 chunk 385 optimal weight: 3.9990 chunk 180 optimal weight: 5.9990 overall best weight: 1.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 HIS ** D 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 214 GLN F 87 ASN ** I 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 391 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.156872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.129646 restraints weight = 45879.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.133083 restraints weight = 25803.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.135229 restraints weight = 17915.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.136568 restraints weight = 14345.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.137232 restraints weight = 12520.017| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.7385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 33300 Z= 0.121 Angle : 0.605 9.085 44976 Z= 0.313 Chirality : 0.042 0.230 4896 Planarity : 0.004 0.062 5904 Dihedral : 5.822 123.080 4531 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.63 % Allowed : 6.03 % Favored : 93.34 % Rotamer: Outliers : 3.57 % Allowed : 20.78 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.13), residues: 4128 helix: 0.98 (0.13), residues: 1768 sheet: -0.06 (0.20), residues: 622 loop : -1.39 (0.15), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 388 TYR 0.020 0.001 TYR E 105 PHE 0.022 0.001 PHE A 186 TRP 0.016 0.001 TRP G 311 HIS 0.017 0.001 HIS L 352 Details of bonding type rmsd covalent geometry : bond 0.00267 (33300) covalent geometry : angle 0.60485 (44976) hydrogen bonds : bond 0.04043 ( 1549) hydrogen bonds : angle 4.98229 ( 4461) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 667 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 541 time to evaluate : 1.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ASN cc_start: 0.7216 (m-40) cc_final: 0.6885 (t0) REVERT: A 165 ARG cc_start: 0.7429 (ttm170) cc_final: 0.6963 (tpp80) REVERT: A 188 PHE cc_start: 0.7465 (OUTLIER) cc_final: 0.7109 (t80) REVERT: A 388 ARG cc_start: 0.8856 (mmm-85) cc_final: 0.8348 (mmm160) REVERT: B 115 GLU cc_start: 0.7931 (tp30) cc_final: 0.7608 (tp30) REVERT: B 188 PHE cc_start: 0.8108 (OUTLIER) cc_final: 0.7017 (t80) REVERT: C 122 MET cc_start: 0.8073 (tpt) cc_final: 0.7732 (tpt) REVERT: C 233 LYS cc_start: 0.4494 (ttpp) cc_final: 0.4247 (ttmt) REVERT: D 120 MET cc_start: 0.8366 (tpp) cc_final: 0.8105 (mmm) REVERT: D 122 MET cc_start: 0.8400 (OUTLIER) cc_final: 0.7814 (ttp) REVERT: D 212 ASP cc_start: 0.7275 (m-30) cc_final: 0.6851 (m-30) REVERT: D 213 GLN cc_start: 0.9081 (tm-30) cc_final: 0.8603 (tm-30) REVERT: D 216 ASP cc_start: 0.7142 (m-30) cc_final: 0.6465 (m-30) REVERT: D 220 ASN cc_start: 0.8262 (m-40) cc_final: 0.7762 (m-40) REVERT: D 232 GLU cc_start: 0.5662 (OUTLIER) cc_final: 0.4386 (mt-10) REVERT: D 277 ASP cc_start: 0.4737 (OUTLIER) cc_final: 0.3738 (t0) REVERT: D 354 GLU cc_start: 0.6359 (tp30) cc_final: 0.5939 (tp30) REVERT: D 368 ARG cc_start: 0.7954 (ttp80) cc_final: 0.7672 (ttp-170) REVERT: E 160 LYS cc_start: 0.6137 (tptt) cc_final: 0.5327 (mmtp) REVERT: E 188 PHE cc_start: 0.8491 (OUTLIER) cc_final: 0.8198 (t80) REVERT: E 248 LYS cc_start: 0.6258 (OUTLIER) cc_final: 0.5938 (ttpp) REVERT: F 167 GLN cc_start: 0.7997 (tm-30) cc_final: 0.7755 (tt0) REVERT: F 188 PHE cc_start: 0.7409 (OUTLIER) cc_final: 0.6996 (t80) REVERT: G 72 THR cc_start: 0.9005 (m) cc_final: 0.8077 (p) REVERT: G 73 LEU cc_start: 0.8905 (mm) cc_final: 0.8526 (mt) REVERT: G 76 CYS cc_start: 0.8102 (m) cc_final: 0.7478 (m) REVERT: G 356 ASN cc_start: 0.8163 (p0) cc_final: 0.7811 (p0) REVERT: H 325 TYR cc_start: 0.9185 (m-80) cc_final: 0.8773 (m-80) REVERT: H 326 THR cc_start: 0.9388 (m) cc_final: 0.9017 (p) REVERT: H 375 MET cc_start: 0.8808 (mmt) cc_final: 0.8530 (mmt) REVERT: H 393 PRO cc_start: 0.8474 (Cg_exo) cc_final: 0.8265 (Cg_endo) REVERT: I 122 MET cc_start: 0.8661 (OUTLIER) cc_final: 0.8391 (tpp) REVERT: I 168 ARG cc_start: 0.6686 (tpt170) cc_final: 0.6469 (ttp-110) REVERT: I 290 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7586 (tp30) REVERT: I 389 THR cc_start: 0.8809 (m) cc_final: 0.8575 (p) REVERT: K 188 PHE cc_start: 0.8002 (OUTLIER) cc_final: 0.7654 (t80) REVERT: K 227 ILE cc_start: 0.7509 (OUTLIER) cc_final: 0.7223 (mp) REVERT: K 311 TRP cc_start: 0.3917 (OUTLIER) cc_final: 0.2655 (p90) REVERT: K 318 GLN cc_start: 0.8670 (tm-30) cc_final: 0.8044 (tm-30) REVERT: K 375 MET cc_start: 0.7759 (mmt) cc_final: 0.7545 (mmt) REVERT: K 392 MET cc_start: 0.7942 (mmm) cc_final: 0.7480 (mmt) REVERT: L 111 MET cc_start: 0.7974 (mtm) cc_final: 0.7637 (mtm) REVERT: L 122 MET cc_start: 0.7993 (tpp) cc_final: 0.7586 (tpp) REVERT: L 167 GLN cc_start: 0.7832 (tm-30) cc_final: 0.7466 (tm-30) REVERT: L 188 PHE cc_start: 0.8333 (OUTLIER) cc_final: 0.7646 (t80) outliers start: 126 outliers final: 98 residues processed: 633 average time/residue: 0.1770 time to fit residues: 181.5043 Evaluate side-chains 631 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 519 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 311 TRP Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 188 PHE Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 122 MET Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 258 ARG Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 345 SER Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 177 GLN Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 188 PHE Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 203 SER Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 242 GLN Chi-restraints excluded: chain E residue 248 LYS Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 279 GLU Chi-restraints excluded: chain E residue 313 SER Chi-restraints excluded: chain E residue 377 GLU Chi-restraints excluded: chain F residue 87 ASN Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 188 PHE Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 203 SER Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 389 THR Chi-restraints excluded: chain G residue 90 ARG Chi-restraints excluded: chain G residue 188 PHE Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 261 ILE Chi-restraints excluded: chain G residue 311 TRP Chi-restraints excluded: chain G residue 316 GLU Chi-restraints excluded: chain G residue 382 THR Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 109 GLN Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 229 SER Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 263 GLU Chi-restraints excluded: chain H residue 320 LEU Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 112 THR Chi-restraints excluded: chain I residue 122 MET Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain I residue 197 ILE Chi-restraints excluded: chain I residue 248 LYS Chi-restraints excluded: chain I residue 262 LEU Chi-restraints excluded: chain I residue 279 GLU Chi-restraints excluded: chain I residue 290 GLU Chi-restraints excluded: chain I residue 375 MET Chi-restraints excluded: chain J residue 110 TYR Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 122 MET Chi-restraints excluded: chain J residue 144 SER Chi-restraints excluded: chain J residue 188 PHE Chi-restraints excluded: chain J residue 258 ARG Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain J residue 360 LEU Chi-restraints excluded: chain K residue 111 MET Chi-restraints excluded: chain K residue 125 CYS Chi-restraints excluded: chain K residue 176 SER Chi-restraints excluded: chain K residue 188 PHE Chi-restraints excluded: chain K residue 227 ILE Chi-restraints excluded: chain K residue 255 VAL Chi-restraints excluded: chain K residue 261 ILE Chi-restraints excluded: chain K residue 268 THR Chi-restraints excluded: chain K residue 302 VAL Chi-restraints excluded: chain K residue 311 TRP Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 110 TYR Chi-restraints excluded: chain L residue 150 SER Chi-restraints excluded: chain L residue 188 PHE Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain L residue 281 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 147 optimal weight: 20.0000 chunk 2 optimal weight: 0.9990 chunk 352 optimal weight: 6.9990 chunk 240 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 chunk 185 optimal weight: 10.0000 chunk 137 optimal weight: 5.9990 chunk 231 optimal weight: 1.9990 chunk 375 optimal weight: 4.9990 chunk 260 optimal weight: 0.5980 chunk 17 optimal weight: 10.0000 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 214 GLN F 87 ASN H 177 GLN H 391 ASN ** I 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 391 ASN ** J 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 246 ASN J 391 ASN K 384 ASN L 318 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.155546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.128332 restraints weight = 45762.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.131697 restraints weight = 25633.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.133852 restraints weight = 17852.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.135184 restraints weight = 14284.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.135848 restraints weight = 12454.853| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.7502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 33300 Z= 0.138 Angle : 0.620 8.338 44976 Z= 0.321 Chirality : 0.042 0.231 4896 Planarity : 0.004 0.064 5904 Dihedral : 5.810 123.405 4530 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.63 % Allowed : 6.49 % Favored : 92.88 % Rotamer: Outliers : 3.80 % Allowed : 21.06 % Favored : 75.14 % 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 aren not related in a simple way. whole: -0.23 (0.13), residues: 4128 helix: 0.99 (0.13), residues: 1764 sheet: -0.05 (0.20), residues: 624 loop : -1.39 (0.15), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 388 TYR 0.021 0.001 TYR E 105 PHE 0.020 0.002 PHE G 188 TRP 0.017 0.001 TRP G 311 HIS 0.019 0.001 HIS L 352 Details of bonding type rmsd covalent geometry : bond 0.00313 (33300) covalent geometry : angle 0.62000 (44976) hydrogen bonds : bond 0.04239 ( 1549) hydrogen bonds : angle 4.98007 ( 4461) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 518 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ASN cc_start: 0.7257 (m-40) cc_final: 0.6895 (t0) REVERT: A 188 PHE cc_start: 0.7582 (OUTLIER) cc_final: 0.7150 (t80) REVERT: A 388 ARG cc_start: 0.8901 (mmm-85) cc_final: 0.8460 (mmm160) REVERT: B 172 TYR cc_start: 0.7224 (m-80) cc_final: 0.6997 (m-80) REVERT: B 188 PHE cc_start: 0.8120 (OUTLIER) cc_final: 0.7039 (t80) REVERT: C 122 MET cc_start: 0.8128 (tpt) cc_final: 0.7769 (tpt) REVERT: D 120 MET cc_start: 0.8363 (tpp) cc_final: 0.8118 (mmm) REVERT: D 122 MET cc_start: 0.8409 (OUTLIER) cc_final: 0.7794 (ttp) REVERT: D 212 ASP cc_start: 0.7291 (m-30) cc_final: 0.6875 (m-30) REVERT: D 213 GLN cc_start: 0.9127 (tm-30) cc_final: 0.8888 (tm-30) REVERT: D 216 ASP cc_start: 0.7159 (m-30) cc_final: 0.6360 (m-30) REVERT: D 220 ASN cc_start: 0.8291 (m-40) cc_final: 0.7813 (m-40) REVERT: D 232 GLU cc_start: 0.5695 (OUTLIER) cc_final: 0.4405 (mt-10) REVERT: D 368 ARG cc_start: 0.7965 (ttp80) cc_final: 0.7759 (ttp-170) REVERT: E 188 PHE cc_start: 0.8493 (OUTLIER) cc_final: 0.8264 (t80) REVERT: E 248 LYS cc_start: 0.6235 (OUTLIER) cc_final: 0.5993 (ttpp) REVERT: F 111 MET cc_start: 0.8583 (ptp) cc_final: 0.8088 (ptp) REVERT: F 167 GLN cc_start: 0.8082 (tm-30) cc_final: 0.7875 (tt0) REVERT: F 188 PHE cc_start: 0.7511 (OUTLIER) cc_final: 0.7062 (t80) REVERT: G 72 THR cc_start: 0.9044 (m) cc_final: 0.8103 (p) REVERT: G 73 LEU cc_start: 0.8900 (mm) cc_final: 0.8557 (mt) REVERT: G 76 CYS cc_start: 0.8112 (m) cc_final: 0.7508 (m) REVERT: G 356 ASN cc_start: 0.8186 (p0) cc_final: 0.7821 (p0) REVERT: H 165 ARG cc_start: 0.7579 (tpt-90) cc_final: 0.7300 (tpp80) REVERT: H 326 THR cc_start: 0.9418 (m) cc_final: 0.9079 (p) REVERT: H 375 MET cc_start: 0.8853 (mmt) cc_final: 0.8625 (mmt) REVERT: I 122 MET cc_start: 0.8637 (OUTLIER) cc_final: 0.8375 (tpp) REVERT: I 290 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7598 (tp30) REVERT: I 389 THR cc_start: 0.8827 (m) cc_final: 0.8615 (p) REVERT: J 111 MET cc_start: 0.8321 (mtt) cc_final: 0.8102 (mtt) REVERT: K 122 MET cc_start: 0.8393 (tpp) cc_final: 0.8179 (tpp) REVERT: K 188 PHE cc_start: 0.8028 (OUTLIER) cc_final: 0.7667 (t80) REVERT: K 227 ILE cc_start: 0.7460 (OUTLIER) cc_final: 0.7163 (mp) REVERT: K 311 TRP cc_start: 0.4139 (OUTLIER) cc_final: 0.2894 (p90) REVERT: K 318 GLN cc_start: 0.8681 (tm-30) cc_final: 0.8036 (tm-30) REVERT: K 375 MET cc_start: 0.7829 (mmt) cc_final: 0.7623 (mmt) REVERT: K 392 MET cc_start: 0.7903 (mmm) cc_final: 0.7476 (mmt) REVERT: L 111 MET cc_start: 0.7997 (mtm) cc_final: 0.7615 (mtm) REVERT: L 167 GLN cc_start: 0.7887 (tm-30) cc_final: 0.7467 (tm-30) REVERT: L 188 PHE cc_start: 0.8474 (OUTLIER) cc_final: 0.7698 (t80) outliers start: 134 outliers final: 105 residues processed: 615 average time/residue: 0.2100 time to fit residues: 208.7844 Evaluate side-chains 613 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 495 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 311 TRP Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 188 PHE Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 122 MET Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 258 ARG Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 345 SER Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 177 GLN Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 188 PHE Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 203 SER Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 242 GLN Chi-restraints excluded: chain E residue 248 LYS Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 279 GLU Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 313 SER Chi-restraints excluded: chain E residue 377 GLU Chi-restraints excluded: chain F residue 87 ASN Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 188 PHE Chi-restraints excluded: chain F residue 203 SER Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 389 THR Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain G residue 90 ARG Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 188 PHE Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 261 ILE Chi-restraints excluded: chain G residue 311 TRP Chi-restraints excluded: chain G residue 316 GLU Chi-restraints excluded: chain G residue 382 THR Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 109 GLN Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 229 SER Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain H residue 320 LEU Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 112 THR Chi-restraints excluded: chain I residue 122 MET Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain I residue 197 ILE Chi-restraints excluded: chain I residue 248 LYS Chi-restraints excluded: chain I residue 262 LEU Chi-restraints excluded: chain I residue 279 GLU Chi-restraints excluded: chain I residue 290 GLU Chi-restraints excluded: chain I residue 375 MET Chi-restraints excluded: chain J residue 110 TYR Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 122 MET Chi-restraints excluded: chain J residue 144 SER Chi-restraints excluded: chain J residue 188 PHE Chi-restraints excluded: chain J residue 258 ARG Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain J residue 360 LEU Chi-restraints excluded: chain J residue 389 THR Chi-restraints excluded: chain K residue 71 SER Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 111 MET Chi-restraints excluded: chain K residue 125 CYS Chi-restraints excluded: chain K residue 176 SER Chi-restraints excluded: chain K residue 188 PHE Chi-restraints excluded: chain K residue 227 ILE Chi-restraints excluded: chain K residue 255 VAL Chi-restraints excluded: chain K residue 261 ILE Chi-restraints excluded: chain K residue 268 THR Chi-restraints excluded: chain K residue 302 VAL Chi-restraints excluded: chain K residue 311 TRP Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 150 SER Chi-restraints excluded: chain L residue 188 PHE Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain L residue 281 MET Chi-restraints excluded: chain L residue 318 GLN Chi-restraints excluded: chain L residue 388 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 190 optimal weight: 4.9990 chunk 376 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 chunk 331 optimal weight: 6.9990 chunk 302 optimal weight: 5.9990 chunk 216 optimal weight: 9.9990 chunk 227 optimal weight: 1.9990 chunk 41 optimal weight: 7.9990 chunk 323 optimal weight: 9.9990 chunk 56 optimal weight: 0.7980 chunk 248 optimal weight: 6.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 GLN ** D 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 391 ASN E 214 GLN F 87 ASN ** I 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 226 GLN J 246 ASN J 391 ASN L 318 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.151299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.124252 restraints weight = 46406.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.127596 restraints weight = 26125.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.129732 restraints weight = 18195.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.131025 restraints weight = 14554.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.131772 restraints weight = 12708.887| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.7652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 33300 Z= 0.205 Angle : 0.692 9.134 44976 Z= 0.358 Chirality : 0.045 0.245 4896 Planarity : 0.005 0.071 5904 Dihedral : 6.098 131.435 4530 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.65 % Allowed : 7.00 % Favored : 92.34 % Rotamer: Outliers : 3.74 % Allowed : 20.92 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.53 (0.13), residues: 4128 helix: 0.73 (0.12), residues: 1806 sheet: -0.45 (0.20), residues: 660 loop : -1.49 (0.16), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 388 TYR 0.022 0.002 TYR E 105 PHE 0.025 0.002 PHE L 186 TRP 0.022 0.002 TRP G 311 HIS 0.016 0.002 HIS L 352 Details of bonding type rmsd covalent geometry : bond 0.00480 (33300) covalent geometry : angle 0.69151 (44976) hydrogen bonds : bond 0.05139 ( 1549) hydrogen bonds : angle 5.16756 ( 4461) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 491 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ASN cc_start: 0.7305 (m-40) cc_final: 0.6952 (t0) REVERT: A 165 ARG cc_start: 0.7550 (ttm110) cc_final: 0.6977 (ttm-80) REVERT: A 178 LYS cc_start: 0.7901 (tptt) cc_final: 0.7561 (tptm) REVERT: A 188 PHE cc_start: 0.7656 (OUTLIER) cc_final: 0.7166 (t80) REVERT: A 388 ARG cc_start: 0.8878 (mmm-85) cc_final: 0.8319 (mmm160) REVERT: B 188 PHE cc_start: 0.8284 (OUTLIER) cc_final: 0.7121 (t80) REVERT: C 188 PHE cc_start: 0.8700 (OUTLIER) cc_final: 0.8247 (t80) REVERT: C 233 LYS cc_start: 0.4766 (ttpp) cc_final: 0.4431 (ttmt) REVERT: D 120 MET cc_start: 0.8311 (tpp) cc_final: 0.8073 (mmm) REVERT: D 122 MET cc_start: 0.8490 (OUTLIER) cc_final: 0.7845 (ttp) REVERT: D 212 ASP cc_start: 0.7319 (m-30) cc_final: 0.6891 (m-30) REVERT: D 213 GLN cc_start: 0.9143 (tm-30) cc_final: 0.8564 (tm-30) REVERT: D 216 ASP cc_start: 0.7179 (m-30) cc_final: 0.6594 (m-30) REVERT: D 220 ASN cc_start: 0.8391 (m-40) cc_final: 0.7928 (m-40) REVERT: D 232 GLU cc_start: 0.5684 (OUTLIER) cc_final: 0.4262 (mt-10) REVERT: D 368 ARG cc_start: 0.8058 (ttp80) cc_final: 0.7787 (ttp-170) REVERT: E 188 PHE cc_start: 0.8558 (OUTLIER) cc_final: 0.8234 (t80) REVERT: F 111 MET cc_start: 0.8769 (ptp) cc_final: 0.8352 (ptp) REVERT: F 188 PHE cc_start: 0.7690 (OUTLIER) cc_final: 0.7203 (t80) REVERT: F 277 ASP cc_start: 0.5410 (OUTLIER) cc_final: 0.4634 (t0) REVERT: G 72 THR cc_start: 0.9081 (m) cc_final: 0.8113 (p) REVERT: G 73 LEU cc_start: 0.8947 (mm) cc_final: 0.8567 (mt) REVERT: G 76 CYS cc_start: 0.8124 (m) cc_final: 0.7510 (m) REVERT: G 120 MET cc_start: 0.8723 (mmm) cc_final: 0.8382 (tpt) REVERT: G 356 ASN cc_start: 0.8239 (p0) cc_final: 0.7875 (p0) REVERT: H 326 THR cc_start: 0.9383 (m) cc_final: 0.9063 (p) REVERT: I 122 MET cc_start: 0.8672 (OUTLIER) cc_final: 0.8396 (tpp) REVERT: I 389 THR cc_start: 0.8922 (m) cc_final: 0.8688 (p) REVERT: K 188 PHE cc_start: 0.8179 (OUTLIER) cc_final: 0.7736 (t80) REVERT: K 311 TRP cc_start: 0.4214 (OUTLIER) cc_final: 0.3056 (p-90) REVERT: K 318 GLN cc_start: 0.8750 (tm-30) cc_final: 0.8040 (tm-30) REVERT: K 392 MET cc_start: 0.7945 (mmm) cc_final: 0.7487 (mmt) REVERT: L 111 MET cc_start: 0.8143 (mtm) cc_final: 0.7808 (mtm) REVERT: L 167 GLN cc_start: 0.7942 (tm-30) cc_final: 0.7540 (tm-30) outliers start: 132 outliers final: 105 residues processed: 590 average time/residue: 0.1880 time to fit residues: 178.2242 Evaluate side-chains 579 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 463 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 311 TRP Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 188 PHE Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 122 MET Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 258 ARG Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 345 SER Chi-restraints excluded: chain D residue 367 SER Chi-restraints excluded: chain E residue 53 ASN Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 177 GLN Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 188 PHE Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 203 SER Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 242 GLN Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 279 GLU Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 313 SER Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 87 ASN Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 188 PHE Chi-restraints excluded: chain F residue 203 SER Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 277 ASP Chi-restraints excluded: chain F residue 389 THR Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain G residue 90 ARG Chi-restraints excluded: chain G residue 112 THR Chi-restraints excluded: chain G residue 188 PHE Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 261 ILE Chi-restraints excluded: chain G residue 311 TRP Chi-restraints excluded: chain G residue 316 GLU Chi-restraints excluded: chain G residue 382 THR Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 229 SER Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain H residue 320 LEU Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 112 THR Chi-restraints excluded: chain I residue 122 MET Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain I residue 197 ILE Chi-restraints excluded: chain I residue 248 LYS Chi-restraints excluded: chain I residue 262 LEU Chi-restraints excluded: chain I residue 279 GLU Chi-restraints excluded: chain I residue 375 MET Chi-restraints excluded: chain J residue 110 TYR Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 122 MET Chi-restraints excluded: chain J residue 144 SER Chi-restraints excluded: chain J residue 183 LEU Chi-restraints excluded: chain J residue 188 PHE Chi-restraints excluded: chain J residue 302 VAL Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain J residue 360 LEU Chi-restraints excluded: chain K residue 71 SER Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 111 MET Chi-restraints excluded: chain K residue 176 SER Chi-restraints excluded: chain K residue 188 PHE Chi-restraints excluded: chain K residue 255 VAL Chi-restraints excluded: chain K residue 261 ILE Chi-restraints excluded: chain K residue 268 THR Chi-restraints excluded: chain K residue 302 VAL Chi-restraints excluded: chain K residue 311 TRP Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 150 SER Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain L residue 281 MET Chi-restraints excluded: chain L residue 318 GLN Chi-restraints excluded: chain L residue 388 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 268 optimal weight: 9.9990 chunk 196 optimal weight: 1.9990 chunk 373 optimal weight: 6.9990 chunk 287 optimal weight: 0.9990 chunk 290 optimal weight: 6.9990 chunk 145 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 282 optimal weight: 10.0000 chunk 149 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 115 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 GLN ** D 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 214 GLN E 384 ASN F 87 ASN ** I 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 129 ASN J 391 ASN L 318 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.151872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.124868 restraints weight = 46380.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.128226 restraints weight = 25909.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.130367 restraints weight = 17972.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.131686 restraints weight = 14342.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.132344 restraints weight = 12482.665| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.7750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 33300 Z= 0.177 Angle : 0.667 8.545 44976 Z= 0.346 Chirality : 0.044 0.246 4896 Planarity : 0.005 0.072 5904 Dihedral : 5.997 135.448 4526 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.65 % Allowed : 6.86 % Favored : 92.49 % Rotamer: Outliers : 3.68 % Allowed : 21.03 % Favored : 75.28 % 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 aren not related in a simple way. whole: -0.50 (0.13), residues: 4128 helix: 0.78 (0.13), residues: 1770 sheet: -0.49 (0.20), residues: 660 loop : -1.44 (0.15), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 388 TYR 0.021 0.002 TYR E 105 PHE 0.021 0.002 PHE L 186 TRP 0.021 0.001 TRP G 311 HIS 0.012 0.001 HIS L 352 Details of bonding type rmsd covalent geometry : bond 0.00414 (33300) covalent geometry : angle 0.66683 (44976) hydrogen bonds : bond 0.04818 ( 1549) hydrogen bonds : angle 5.14278 ( 4461) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5491.63 seconds wall clock time: 95 minutes 33.99 seconds (5733.99 seconds total)