Starting phenix.real_space_refine on Thu May 29 12:28:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fql_29392/05_2025/8fql_29392.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fql_29392/05_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_29392/05_2025/8fql_29392.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fql_29392/05_2025/8fql_29392.map" model { file = "/net/cci-nas-00/data/ceres_data/8fql_29392/05_2025/8fql_29392.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fql_29392/05_2025/8fql_29392.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 20.15, per 1000 atoms: 0.62 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: 7.85 Conformation dependent library (CDL) restraints added in 4.1 seconds 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: 3.65 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: 12.91 Time building geometry restraints manager: 9.11 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: 0.03 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: 4.450 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: 0.030 Extract box with map and model: 1.240 Check model and map are aligned: 0.230 Set scattering table: 0.340 Process input model: 72.890 Find NCS groups from input model: 1.340 Set up NCS constraints: 0.290 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: 0.020 Load rotamer database and sin/cos tables:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.940 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (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 TRP 0.118 0.021 TRP F 260 HIS 0.013 0.004 HIS J 300 PHE 0.069 0.017 PHE K 218 TYR 0.179 0.022 TYR I 172 ARG 0.011 0.001 ARG B 258 Details of bonding type rmsd hydrogen bonds : bond 0.16397 ( 1549) hydrogen bonds : angle 8.19612 ( 4461) covalent geometry : bond 0.01186 (33300) covalent geometry : angle 1.78272 (44976) *********************** 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 : 3.766 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: 0.4846 time to fit residues: 882.8300 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 : 3.456 ------------------------------------------------------------------------------- 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 344 optimal weight: 6.9990 chunk 309 optimal weight: 6.9990 chunk 171 optimal weight: 2.9990 chunk 105 optimal weight: 7.9990 chunk 208 optimal weight: 0.9980 chunk 165 optimal weight: 1.9990 chunk 319 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 194 optimal weight: 5.9990 chunk 238 optimal weight: 3.9990 chunk 370 optimal weight: 9.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 ASN B 86 GLN B 318 GLN C 86 GLN C 182 HIS C 226 GLN C 246 ASN D 86 GLN D 318 GLN D 352 HIS E 59 GLN E 86 GLN E 89 ASN E 324 GLN F 86 GLN F 87 ASN F 318 GLN G 86 GLN G 214 GLN G 242 GLN H 86 GLN H 149 GLN I 86 GLN ** I 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 167 GLN 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.168293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.140163 restraints weight = 46365.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.143574 restraints weight = 27246.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.145757 restraints weight = 19529.997| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 33300 Z= 0.187 Angle : 0.783 9.589 44976 Z= 0.416 Chirality : 0.045 0.157 4896 Planarity : 0.005 0.042 5904 Dihedral : 7.481 108.551 4565 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.85 % Allowed : 5.79 % Favored : 93.36 % Rotamer: Outliers : 3.74 % Allowed : 14.06 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.13), residues: 4128 helix: 0.45 (0.12), residues: 1756 sheet: -0.88 (0.19), residues: 688 loop : -1.57 (0.15), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP H 311 HIS 0.006 0.001 HIS C 352 PHE 0.032 0.003 PHE H 186 TYR 0.020 0.002 TYR H 105 ARG 0.008 0.001 ARG J 362 Details of bonding type rmsd hydrogen bonds : bond 0.05301 ( 1549) hydrogen bonds : angle 5.62696 ( 4461) covalent geometry : bond 0.00418 (33300) covalent geometry : angle 0.78325 (44976) *********************** 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 833 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 701 time to evaluate : 3.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ASN cc_start: 0.7963 (m-40) cc_final: 0.7658 (m-40) REVERT: A 242 GLN cc_start: 0.8170 (mm110) cc_final: 0.7631 (pp30) REVERT: C 85 ASP cc_start: 0.6968 (OUTLIER) cc_final: 0.6579 (p0) REVERT: C 112 THR cc_start: 0.8740 (OUTLIER) cc_final: 0.8466 (p) REVERT: C 168 ARG cc_start: 0.7449 (ttp-170) cc_final: 0.6798 (ptt-90) REVERT: C 215 ARG cc_start: 0.8109 (ttt-90) cc_final: 0.7801 (ttp80) REVERT: C 347 ASP cc_start: 0.6060 (m-30) cc_final: 0.5711 (m-30) REVERT: D 88 ASP cc_start: 0.8142 (t0) cc_final: 0.7926 (t0) REVERT: D 212 ASP cc_start: 0.7229 (m-30) cc_final: 0.6995 (m-30) REVERT: D 215 ARG cc_start: 0.7822 (tmm-80) cc_final: 0.7576 (tmm-80) REVERT: D 216 ASP cc_start: 0.7458 (m-30) cc_final: 0.6621 (m-30) REVERT: D 220 ASN cc_start: 0.7802 (m-40) cc_final: 0.7526 (m-40) REVERT: D 346 LYS cc_start: 0.6650 (OUTLIER) cc_final: 0.6017 (ptmt) REVERT: D 347 ASP cc_start: 0.7332 (m-30) cc_final: 0.7113 (m-30) REVERT: E 58 LEU cc_start: 0.8969 (tp) cc_final: 0.8736 (tt) REVERT: E 166 TYR cc_start: 0.7790 (t80) cc_final: 0.7431 (t80) REVERT: E 248 LYS cc_start: 0.7201 (OUTLIER) cc_final: 0.5635 (ttpp) REVERT: E 279 GLU cc_start: 0.5659 (OUTLIER) cc_final: 0.4370 (tm-30) REVERT: E 280 MET cc_start: 0.7384 (tpp) cc_final: 0.7085 (tpp) REVERT: F 111 MET cc_start: 0.6904 (mtt) cc_final: 0.6691 (mtt) REVERT: F 316 GLU cc_start: 0.8031 (tt0) cc_final: 0.7776 (tt0) REVERT: G 72 THR cc_start: 0.8554 (m) cc_final: 0.8053 (p) REVERT: G 76 CYS cc_start: 0.8303 (m) cc_final: 0.7701 (m) REVERT: G 214 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.8090 (tm130) REVERT: G 392 MET cc_start: 0.6711 (mmm) cc_final: 0.6278 (mmm) REVERT: H 392 MET cc_start: 0.7466 (mmt) cc_final: 0.7085 (mmt) REVERT: I 143 ILE cc_start: 0.7609 (pt) cc_final: 0.7356 (tp) REVERT: I 168 ARG cc_start: 0.6787 (tpt170) cc_final: 0.6475 (tmt170) REVERT: I 215 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.7342 (ttt90) REVERT: I 245 GLU cc_start: 0.7861 (tm-30) cc_final: 0.7583 (tm-30) REVERT: I 261 ILE cc_start: 0.5891 (OUTLIER) cc_final: 0.5451 (pt) REVERT: I 318 GLN cc_start: 0.7251 (OUTLIER) cc_final: 0.6726 (mt0) REVERT: J 350 ARG cc_start: 0.6703 (mtm110) cc_final: 0.6156 (ttp80) REVERT: K 184 LYS cc_start: 0.7111 (OUTLIER) cc_final: 0.6558 (ttpt) REVERT: K 311 TRP cc_start: 0.3505 (OUTLIER) cc_final: 0.3037 (p90) REVERT: K 318 GLN cc_start: 0.8492 (tm-30) cc_final: 0.7858 (tm-30) REVERT: L 318 GLN cc_start: 0.7362 (mm-40) cc_final: 0.7150 (mm-40) outliers start: 132 outliers final: 67 residues processed: 799 average time/residue: 0.4393 time to fit residues: 555.0067 Evaluate side-chains 629 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 551 time to evaluate : 3.569 ------------------------------------------------------------------------------- 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 228 LEU Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain B residue 155 VAL 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 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 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 346 LYS 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 248 LYS Chi-restraints excluded: chain E residue 279 GLU 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 129 ASN 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 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 134 VAL Chi-restraints excluded: chain G residue 214 GLN Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 311 TRP 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 227 ILE 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 134 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 318 GLN 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 192 VAL Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 227 ILE Chi-restraints excluded: chain J residue 389 THR 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 313 SER 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 80 optimal weight: 8.9990 chunk 107 optimal weight: 4.9990 chunk 188 optimal weight: 1.9990 chunk 195 optimal weight: 9.9990 chunk 242 optimal weight: 2.9990 chunk 373 optimal weight: 2.9990 chunk 248 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 318 optimal weight: 4.9990 chunk 40 optimal weight: 9.9990 chunk 9 optimal weight: 8.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 89 ASN C 276 GLN D 239 GLN D 276 GLN E 182 HIS F 87 ASN F 214 GLN ** F 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 220 ASN G 242 GLN H 182 HIS H 226 GLN H 242 GLN H 339 GLN I 129 ASN I 182 HIS I 214 GLN I 319 ASN ** J 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 287 GLN J 324 GLN K 89 ASN L 89 ASN L 182 HIS L 276 GLN L 287 GLN L 352 HIS ** L 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.159942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.131578 restraints weight = 46942.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.134998 restraints weight = 27127.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.137171 restraints weight = 19303.282| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.5529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 33300 Z= 0.182 Angle : 0.705 10.223 44976 Z= 0.374 Chirality : 0.045 0.162 4896 Planarity : 0.005 0.046 5904 Dihedral : 6.364 105.130 4537 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.75 % Allowed : 6.30 % Favored : 92.95 % Rotamer: Outliers : 4.68 % Allowed : 15.65 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.13), residues: 4128 helix: 0.71 (0.12), residues: 1744 sheet: -0.50 (0.21), residues: 588 loop : -1.43 (0.15), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP E 260 HIS 0.007 0.002 HIS I 355 PHE 0.026 0.002 PHE F 186 TYR 0.019 0.002 TYR A 131 ARG 0.010 0.001 ARG H 90 Details of bonding type rmsd hydrogen bonds : bond 0.05198 ( 1549) hydrogen bonds : angle 5.26963 ( 4461) covalent geometry : bond 0.00412 (33300) covalent geometry : angle 0.70491 (44976) *********************** 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 787 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 622 time to evaluate : 3.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 GLN cc_start: 0.8066 (mm110) cc_final: 0.7820 (pp30) REVERT: B 356 ASN cc_start: 0.7932 (OUTLIER) cc_final: 0.7602 (t0) REVERT: C 110 TYR cc_start: 0.8361 (m-80) cc_final: 0.8119 (m-80) REVERT: C 168 ARG cc_start: 0.7418 (ttp-170) cc_final: 0.7102 (ptt-90) REVERT: C 368 ARG cc_start: 0.7605 (ptm160) cc_final: 0.7202 (ttp-170) REVERT: C 375 MET cc_start: 0.8203 (mmp) cc_final: 0.7967 (mmt) REVERT: C 392 MET cc_start: 0.8170 (mmp) cc_final: 0.7587 (mmt) REVERT: D 88 ASP cc_start: 0.8154 (t0) cc_final: 0.7896 (t0) REVERT: D 120 MET cc_start: 0.8389 (tpp) cc_final: 0.8060 (mmm) REVERT: D 212 ASP cc_start: 0.7320 (m-30) cc_final: 0.6970 (m-30) REVERT: D 215 ARG cc_start: 0.7919 (tmm-80) cc_final: 0.7714 (tmm-80) REVERT: D 216 ASP cc_start: 0.7225 (m-30) cc_final: 0.6433 (m-30) REVERT: D 220 ASN cc_start: 0.8260 (m-40) cc_final: 0.7824 (m110) REVERT: E 153 MET cc_start: 0.7675 (tpp) cc_final: 0.7309 (ttp) REVERT: E 248 LYS cc_start: 0.7004 (OUTLIER) cc_final: 0.5764 (ttpp) REVERT: E 301 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.9135 (mt) REVERT: F 111 MET cc_start: 0.7853 (mtt) cc_final: 0.7634 (mtt) REVERT: F 197 ILE cc_start: 0.8721 (OUTLIER) cc_final: 0.8478 (tp) REVERT: F 343 ILE cc_start: 0.8359 (mt) cc_final: 0.8149 (mt) REVERT: G 72 THR cc_start: 0.8990 (m) cc_final: 0.8266 (p) REVERT: G 73 LEU cc_start: 0.8788 (mm) cc_final: 0.8518 (mt) REVERT: G 76 CYS cc_start: 0.8417 (m) cc_final: 0.7910 (m) REVERT: G 178 LYS cc_start: 0.8143 (tptt) cc_final: 0.7907 (tppt) REVERT: G 356 ASN cc_start: 0.8305 (p0) cc_final: 0.7913 (p0) REVERT: G 392 MET cc_start: 0.7779 (mmm) cc_final: 0.7450 (mmm) REVERT: H 72 THR cc_start: 0.8803 (m) cc_final: 0.8373 (p) REVERT: H 76 CYS cc_start: 0.7885 (m) cc_final: 0.7265 (m) REVERT: H 122 MET cc_start: 0.8235 (tpp) cc_final: 0.7946 (ttp) REVERT: H 392 MET cc_start: 0.7559 (mmt) cc_final: 0.6894 (mmt) REVERT: H 393 PRO cc_start: 0.8073 (Cg_exo) cc_final: 0.7271 (Cg_endo) REVERT: I 82 PHE cc_start: 0.8066 (m-80) cc_final: 0.7767 (m-10) REVERT: I 136 ARG cc_start: 0.7539 (ptp-170) cc_final: 0.7149 (ptp-110) REVERT: I 168 ARG cc_start: 0.6676 (tpt170) cc_final: 0.6180 (ttp-110) REVERT: I 215 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.7273 (ttt90) REVERT: I 245 GLU cc_start: 0.8006 (tm-30) cc_final: 0.7724 (tm-30) REVERT: I 279 GLU cc_start: 0.6785 (OUTLIER) cc_final: 0.5615 (tm-30) REVERT: J 76 CYS cc_start: 0.7654 (m) cc_final: 0.6894 (p) REVERT: J 77 LEU cc_start: 0.8799 (mt) cc_final: 0.8572 (mt) REVERT: J 111 MET cc_start: 0.8414 (mtt) cc_final: 0.8103 (mtt) REVERT: K 91 LYS cc_start: 0.7869 (tppt) cc_final: 0.7637 (tptm) REVERT: K 311 TRP cc_start: 0.3758 (OUTLIER) cc_final: 0.3256 (p-90) REVERT: K 318 GLN cc_start: 0.8468 (tm-30) cc_final: 0.7873 (tm-30) REVERT: K 375 MET cc_start: 0.7900 (mmt) cc_final: 0.7665 (mmt) REVERT: L 352 HIS cc_start: 0.6392 (t70) cc_final: 0.5110 (t-170) outliers start: 165 outliers final: 93 residues processed: 751 average time/residue: 0.4518 time to fit residues: 543.2106 Evaluate side-chains 608 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 508 time to evaluate : 3.642 ------------------------------------------------------------------------------- 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 189 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 273 VAL 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 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 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 93 VAL Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 125 CYS 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 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 180 ILE Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 197 ILE 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 301 LEU 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 192 VAL Chi-restraints excluded: chain F residue 197 ILE 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 255 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 G residue 112 THR Chi-restraints excluded: chain G residue 122 MET 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 155 VAL 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 351 LEU 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 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 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 360 LEU 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 135 ASP 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 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 155 VAL Chi-restraints excluded: chain L residue 192 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 163 optimal weight: 0.8980 chunk 306 optimal weight: 10.0000 chunk 170 optimal weight: 10.0000 chunk 227 optimal weight: 2.9990 chunk 184 optimal weight: 5.9990 chunk 14 optimal weight: 8.9990 chunk 124 optimal weight: 7.9990 chunk 382 optimal weight: 4.9990 chunk 288 optimal weight: 9.9990 chunk 180 optimal weight: 8.9990 chunk 187 optimal weight: 20.0000 overall best weight: 4.5788 ------------------------------------------------------------------------------- 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 318 GLN D 239 GLN E 214 GLN E 220 ASN F 87 ASN F 182 HIS G 177 GLN G 182 HIS G 214 GLN G 242 GLN G 352 HIS ** H 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 391 ASN I 220 ASN I 318 GLN ** J 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 213 GLN ** J 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 391 ASN ** L 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.151720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.123909 restraints weight = 47050.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.127153 restraints weight = 27373.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.129217 restraints weight = 19543.759| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.6436 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= 0.229 Angle : 0.721 9.149 44976 Z= 0.378 Chirality : 0.046 0.186 4896 Planarity : 0.005 0.068 5904 Dihedral : 6.364 116.080 4531 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.68 % Allowed : 6.30 % Favored : 93.02 % Rotamer: Outliers : 5.16 % Allowed : 17.09 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.13), residues: 4128 helix: 0.58 (0.12), residues: 1748 sheet: -0.76 (0.20), residues: 656 loop : -1.38 (0.15), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP J 311 HIS 0.007 0.002 HIS H 300 PHE 0.025 0.002 PHE E 186 TYR 0.019 0.002 TYR I 127 ARG 0.006 0.001 ARG F 284 Details of bonding type rmsd hydrogen bonds : bond 0.05538 ( 1549) hydrogen bonds : angle 5.36285 ( 4461) covalent geometry : bond 0.00540 (33300) covalent geometry : angle 0.72128 (44976) *********************** 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 732 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 550 time to evaluate : 3.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.7444 (OUTLIER) cc_final: 0.7018 (ttp) REVERT: A 167 GLN cc_start: 0.8301 (tm-30) cc_final: 0.7962 (tm-30) REVERT: A 242 GLN cc_start: 0.8029 (mm110) cc_final: 0.7813 (pp30) REVERT: C 250 ILE cc_start: 0.0941 (OUTLIER) cc_final: 0.0621 (mp) REVERT: C 279 GLU cc_start: 0.5921 (OUTLIER) cc_final: 0.5561 (tp30) REVERT: C 368 ARG cc_start: 0.7750 (ptm160) cc_final: 0.7432 (ttp-170) REVERT: C 392 MET cc_start: 0.8646 (mmp) cc_final: 0.8137 (mmt) REVERT: D 120 MET cc_start: 0.8247 (tpp) cc_final: 0.8008 (mmm) REVERT: D 122 MET cc_start: 0.8447 (tpp) cc_final: 0.7967 (tpp) REVERT: D 212 ASP cc_start: 0.7420 (m-30) cc_final: 0.7049 (m-30) REVERT: D 213 GLN cc_start: 0.9126 (tm-30) cc_final: 0.8604 (tm-30) REVERT: D 216 ASP cc_start: 0.7303 (m-30) cc_final: 0.6697 (m-30) REVERT: D 220 ASN cc_start: 0.8313 (m-40) cc_final: 0.8089 (m-40) REVERT: D 277 ASP cc_start: 0.5769 (OUTLIER) cc_final: 0.5055 (t0) REVERT: E 58 LEU cc_start: 0.9335 (tp) cc_final: 0.8856 (tt) REVERT: E 157 LEU cc_start: 0.5055 (pt) cc_final: 0.4768 (mp) REVERT: E 248 LYS cc_start: 0.6629 (OUTLIER) cc_final: 0.5617 (ttpp) REVERT: E 281 MET cc_start: 0.7906 (mmp) cc_final: 0.7619 (mmp) REVERT: G 72 THR cc_start: 0.9035 (m) cc_final: 0.8175 (p) REVERT: G 73 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8510 (mt) REVERT: G 76 CYS cc_start: 0.8229 (m) cc_final: 0.7624 (m) REVERT: G 80 ASP cc_start: 0.7483 (m-30) cc_final: 0.7158 (t0) REVERT: G 153 MET cc_start: 0.8039 (tpp) cc_final: 0.7216 (tpp) REVERT: G 316 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7726 (mp0) REVERT: G 356 ASN cc_start: 0.8374 (p0) cc_final: 0.7965 (p0) REVERT: G 392 MET cc_start: 0.7889 (mmm) cc_final: 0.7570 (mmm) REVERT: H 72 THR cc_start: 0.8793 (m) cc_final: 0.8527 (p) REVERT: H 120 MET cc_start: 0.7144 (tpp) cc_final: 0.6934 (mmp) REVERT: H 136 ARG cc_start: 0.4965 (ptp-110) cc_final: 0.4457 (ptm160) REVERT: H 171 GLU cc_start: 0.6199 (mp0) cc_final: 0.5815 (pp20) REVERT: H 377 GLU cc_start: 0.6019 (mm-30) cc_final: 0.5715 (mm-30) REVERT: H 392 MET cc_start: 0.7849 (mmt) cc_final: 0.7440 (mmt) REVERT: H 393 PRO cc_start: 0.8381 (Cg_exo) cc_final: 0.7991 (Cg_endo) REVERT: I 110 TYR cc_start: 0.8078 (m-80) cc_final: 0.7363 (m-80) REVERT: I 136 ARG cc_start: 0.7783 (ptp-170) cc_final: 0.7355 (mtm110) REVERT: I 168 ARG cc_start: 0.6720 (tpt170) cc_final: 0.6263 (ttp-110) REVERT: I 215 ARG cc_start: 0.7914 (OUTLIER) cc_final: 0.7329 (ttt90) REVERT: I 245 GLU cc_start: 0.8014 (tm-30) cc_final: 0.7788 (tm-30) REVERT: I 279 GLU cc_start: 0.6580 (OUTLIER) cc_final: 0.5539 (tm-30) REVERT: I 362 ARG cc_start: 0.8973 (ptm160) cc_final: 0.8635 (ptm160) REVERT: J 76 CYS cc_start: 0.7873 (m) cc_final: 0.7173 (p) REVERT: J 168 ARG cc_start: 0.7034 (ptp-110) cc_final: 0.6697 (ttp-170) REVERT: J 242 GLN cc_start: 0.6064 (OUTLIER) cc_final: 0.5710 (pp30) REVERT: K 311 TRP cc_start: 0.4078 (OUTLIER) cc_final: 0.3451 (p-90) REVERT: K 318 GLN cc_start: 0.8617 (tm-30) cc_final: 0.8012 (tm-30) REVERT: K 392 MET cc_start: 0.7724 (mmm) cc_final: 0.7361 (mmm) outliers start: 182 outliers final: 123 residues processed: 689 average time/residue: 0.4221 time to fit residues: 466.8233 Evaluate side-chains 631 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 497 time to evaluate : 3.464 ------------------------------------------------------------------------------- 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 122 MET 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 273 VAL 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 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 150 SER Chi-restraints excluded: chain C residue 250 ILE 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 180 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 277 ASP 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 146 LEU 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 302 VAL Chi-restraints excluded: chain E residue 337 SER 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 155 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 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 57 ILE Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 112 THR Chi-restraints excluded: chain G residue 141 ASP 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 311 TRP Chi-restraints excluded: chain G residue 316 GLU Chi-restraints excluded: chain G residue 345 SER 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 192 VAL 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 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 197 ILE 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 290 GLU Chi-restraints excluded: chain I residue 318 GLN Chi-restraints excluded: chain I residue 320 LEU Chi-restraints excluded: chain I residue 375 MET Chi-restraints excluded: chain J residue 88 ASP 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 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 242 GLN 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 81 VAL Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 122 MET Chi-restraints excluded: chain K residue 146 LEU Chi-restraints excluded: chain K residue 163 VAL 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 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 274 THR Chi-restraints excluded: chain L residue 313 SER Chi-restraints excluded: chain L residue 327 LEU Chi-restraints excluded: chain L residue 367 SER Chi-restraints excluded: chain L residue 389 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 396 optimal weight: 5.9990 chunk 74 optimal weight: 9.9990 chunk 183 optimal weight: 0.8980 chunk 38 optimal weight: 10.0000 chunk 75 optimal weight: 4.9990 chunk 129 optimal weight: 0.9980 chunk 331 optimal weight: 7.9990 chunk 347 optimal weight: 0.9990 chunk 76 optimal weight: 9.9990 chunk 137 optimal weight: 0.9980 chunk 308 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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** D 239 GLN ** D 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 214 GLN E 324 GLN F 87 ASN G 220 ASN G 242 GLN H 152 ASN I 177 GLN ** I 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 226 GLN I 318 GLN I 319 ASN J 129 ASN J 246 ASN J 324 GLN J 352 HIS J 391 ASN K 89 ASN K 287 GLN ** L 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 391 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.157890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.130138 restraints weight = 46166.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.133588 restraints weight = 26180.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.135792 restraints weight = 18304.082| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.6668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 33300 Z= 0.118 Angle : 0.599 7.669 44976 Z= 0.314 Chirality : 0.042 0.253 4896 Planarity : 0.004 0.065 5904 Dihedral : 5.913 119.897 4531 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.65 % Allowed : 6.01 % Favored : 93.34 % Rotamer: Outliers : 3.97 % Allowed : 18.71 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.13), residues: 4128 helix: 0.88 (0.12), residues: 1761 sheet: -0.40 (0.20), residues: 661 loop : -1.29 (0.16), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP J 311 HIS 0.007 0.001 HIS H 300 PHE 0.023 0.001 PHE A 186 TYR 0.017 0.001 TYR F 110 ARG 0.004 0.000 ARG D 388 Details of bonding type rmsd hydrogen bonds : bond 0.04157 ( 1549) hydrogen bonds : angle 5.04986 ( 4461) covalent geometry : bond 0.00248 (33300) covalent geometry : angle 0.59944 (44976) *********************** 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 715 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 575 time to evaluate : 3.729 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 ASN cc_start: 0.7487 (m-40) cc_final: 0.6931 (t0) REVERT: A 242 GLN cc_start: 0.8033 (mm110) cc_final: 0.7826 (pp30) REVERT: A 336 ASN cc_start: 0.8788 (m-40) cc_final: 0.8568 (m-40) REVERT: A 375 MET cc_start: 0.8124 (mmt) cc_final: 0.7836 (mmt) REVERT: B 214 GLN cc_start: 0.8444 (tt0) cc_final: 0.8135 (tt0) REVERT: C 110 TYR cc_start: 0.8424 (m-80) cc_final: 0.8166 (m-80) REVERT: C 168 ARG cc_start: 0.6388 (ptt-90) cc_final: 0.6095 (ptt-90) REVERT: C 368 ARG cc_start: 0.7670 (ptm160) cc_final: 0.7448 (ttp-170) REVERT: C 392 MET cc_start: 0.8668 (mmp) cc_final: 0.8273 (mmt) REVERT: D 90 ARG cc_start: 0.7488 (mtt180) cc_final: 0.6912 (mtt180) REVERT: D 120 MET cc_start: 0.8390 (tpp) cc_final: 0.8068 (mmm) REVERT: D 122 MET cc_start: 0.8339 (tpp) cc_final: 0.7821 (tpp) REVERT: D 212 ASP cc_start: 0.7360 (m-30) cc_final: 0.6953 (m-30) REVERT: D 213 GLN cc_start: 0.9084 (tm-30) cc_final: 0.8554 (tm-30) REVERT: D 216 ASP cc_start: 0.7141 (m-30) cc_final: 0.6549 (m-30) REVERT: D 220 ASN cc_start: 0.8263 (m-40) cc_final: 0.7970 (m-40) REVERT: D 232 GLU cc_start: 0.5670 (OUTLIER) cc_final: 0.4045 (mt-10) REVERT: D 239 GLN cc_start: 0.5806 (tp-100) cc_final: 0.4280 (pt0) REVERT: E 58 LEU cc_start: 0.9276 (tp) cc_final: 0.8820 (tt) REVERT: E 248 LYS cc_start: 0.6416 (OUTLIER) cc_final: 0.5526 (ttpp) REVERT: E 279 GLU cc_start: 0.5650 (OUTLIER) cc_final: 0.4691 (tm-30) REVERT: F 188 PHE cc_start: 0.7156 (OUTLIER) cc_final: 0.6509 (t80) REVERT: F 210 MET cc_start: 0.8763 (mtm) cc_final: 0.8525 (mtt) REVERT: F 279 GLU cc_start: 0.5549 (mm-30) cc_final: 0.5140 (mm-30) REVERT: G 72 THR cc_start: 0.9029 (m) cc_final: 0.8128 (p) REVERT: G 73 LEU cc_start: 0.8908 (mm) cc_final: 0.8529 (mt) REVERT: G 76 CYS cc_start: 0.8129 (m) cc_final: 0.7494 (m) REVERT: G 153 MET cc_start: 0.8029 (tpp) cc_final: 0.7208 (tpp) REVERT: G 316 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7862 (mp0) REVERT: G 356 ASN cc_start: 0.8228 (p0) cc_final: 0.7808 (p0) REVERT: G 392 MET cc_start: 0.7886 (mmm) cc_final: 0.7602 (mmm) REVERT: H 72 THR cc_start: 0.8863 (m) cc_final: 0.8571 (p) REVERT: H 393 PRO cc_start: 0.8349 (Cg_exo) cc_final: 0.8024 (Cg_endo) REVERT: I 110 TYR cc_start: 0.8139 (m-80) cc_final: 0.7717 (m-80) REVERT: I 122 MET cc_start: 0.8826 (tpt) cc_final: 0.8375 (tpt) REVERT: I 136 ARG cc_start: 0.7740 (ptp-170) cc_final: 0.7319 (mtm110) REVERT: I 168 ARG cc_start: 0.6665 (tpt170) cc_final: 0.6261 (ttp-110) REVERT: I 215 ARG cc_start: 0.7943 (OUTLIER) cc_final: 0.7242 (ttt90) REVERT: I 279 GLU cc_start: 0.6390 (OUTLIER) cc_final: 0.5350 (tm-30) REVERT: I 362 ARG cc_start: 0.8921 (ptm160) cc_final: 0.8623 (ptm160) REVERT: J 76 CYS cc_start: 0.7444 (m) cc_final: 0.6760 (p) REVERT: J 168 ARG cc_start: 0.6983 (ptp-110) cc_final: 0.6685 (ttp-170) REVERT: K 304 ASP cc_start: 0.6823 (t0) cc_final: 0.6489 (t0) REVERT: K 311 TRP cc_start: 0.3874 (OUTLIER) cc_final: 0.2835 (p90) REVERT: K 318 GLN cc_start: 0.8578 (tm-30) cc_final: 0.7984 (tm-30) REVERT: K 392 MET cc_start: 0.7803 (mmm) cc_final: 0.7393 (mmm) outliers start: 140 outliers final: 86 residues processed: 672 average time/residue: 0.4425 time to fit residues: 475.9226 Evaluate side-chains 607 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 513 time to evaluate : 3.571 ------------------------------------------------------------------------------- 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 189 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 273 VAL 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 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 C residue 72 THR Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 102 LEU 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 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 345 SER Chi-restraints excluded: chain E residue 53 ASN Chi-restraints excluded: chain E residue 177 GLN Chi-restraints excluded: chain E residue 180 ILE 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 261 ILE Chi-restraints excluded: chain E residue 279 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 137 ASN Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 188 PHE Chi-restraints excluded: chain F residue 197 ILE 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 G residue 112 THR Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain G residue 149 GLN 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 311 TRP Chi-restraints excluded: chain G residue 316 GLU Chi-restraints excluded: chain H residue 110 TYR Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 189 THR 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 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 215 ARG Chi-restraints excluded: chain I residue 279 GLU Chi-restraints excluded: chain J residue 88 ASP 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 227 ILE Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain J residue 360 LEU Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 122 MET 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 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 192 VAL Chi-restraints excluded: chain L residue 327 LEU Chi-restraints excluded: chain L residue 391 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 131 optimal weight: 10.0000 chunk 181 optimal weight: 0.7980 chunk 137 optimal weight: 1.9990 chunk 143 optimal weight: 4.9990 chunk 150 optimal weight: 9.9990 chunk 375 optimal weight: 4.9990 chunk 197 optimal weight: 7.9990 chunk 389 optimal weight: 5.9990 chunk 302 optimal weight: 7.9990 chunk 73 optimal weight: 8.9990 chunk 169 optimal weight: 7.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 182 HIS C 149 GLN C 167 GLN D 318 GLN ** D 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 214 GLN E 324 GLN F 87 ASN G 242 GLN ** H 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 214 GLN I 319 ASN J 129 ASN ** J 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 324 GLN L 318 GLN L 352 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.152963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.125671 restraints weight = 46308.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.128997 restraints weight = 26028.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.131106 restraints weight = 18193.553| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.7036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 33300 Z= 0.191 Angle : 0.665 10.204 44976 Z= 0.347 Chirality : 0.044 0.246 4896 Planarity : 0.005 0.070 5904 Dihedral : 6.006 118.268 4529 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.65 % Allowed : 6.42 % Favored : 92.93 % Rotamer: Outliers : 4.56 % Allowed : 19.08 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.13), residues: 4128 helix: 0.63 (0.12), residues: 1810 sheet: -0.19 (0.22), residues: 522 loop : -1.45 (0.15), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP J 311 HIS 0.011 0.002 HIS L 352 PHE 0.021 0.002 PHE B 186 TYR 0.018 0.002 TYR F 110 ARG 0.005 0.001 ARG D 168 Details of bonding type rmsd hydrogen bonds : bond 0.05093 ( 1549) hydrogen bonds : angle 5.13245 ( 4461) covalent geometry : bond 0.00449 (33300) covalent geometry : angle 0.66522 (44976) *********************** 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 700 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 539 time to evaluate : 3.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ASN cc_start: 0.7416 (m-40) cc_final: 0.7009 (t0) REVERT: A 388 ARG cc_start: 0.8859 (mmm-85) cc_final: 0.8305 (mmm160) REVERT: C 168 ARG cc_start: 0.6401 (ptt-90) cc_final: 0.6041 (ptt-90) REVERT: C 368 ARG cc_start: 0.7836 (ptm160) cc_final: 0.7390 (ttp-170) REVERT: C 392 MET cc_start: 0.8712 (mmp) cc_final: 0.8386 (mmt) REVERT: D 120 MET cc_start: 0.8303 (tpp) cc_final: 0.8047 (mmm) REVERT: D 122 MET cc_start: 0.8451 (OUTLIER) cc_final: 0.7633 (ttt) REVERT: D 135 ASP cc_start: 0.7615 (t0) cc_final: 0.7352 (t0) REVERT: D 212 ASP cc_start: 0.7411 (m-30) cc_final: 0.6947 (m-30) REVERT: D 216 ASP cc_start: 0.7175 (m-30) cc_final: 0.6583 (m-30) REVERT: D 220 ASN cc_start: 0.8346 (m-40) cc_final: 0.8029 (m-40) REVERT: D 232 GLU cc_start: 0.5663 (OUTLIER) cc_final: 0.4001 (mt-10) REVERT: D 354 GLU cc_start: 0.6105 (mt-10) cc_final: 0.5804 (mt-10) REVERT: E 188 PHE cc_start: 0.8630 (OUTLIER) cc_final: 0.8291 (t80) REVERT: E 248 LYS cc_start: 0.6318 (OUTLIER) cc_final: 0.5644 (ttpp) REVERT: E 256 LYS cc_start: 0.7011 (mmtt) cc_final: 0.6576 (mtmm) REVERT: F 188 PHE cc_start: 0.7511 (OUTLIER) cc_final: 0.6921 (t80) REVERT: G 72 THR cc_start: 0.9055 (m) cc_final: 0.8134 (p) REVERT: G 73 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8526 (mt) REVERT: G 76 CYS cc_start: 0.8092 (m) cc_final: 0.7510 (m) REVERT: G 356 ASN cc_start: 0.8293 (p0) cc_final: 0.7867 (p0) REVERT: G 392 MET cc_start: 0.7955 (mmm) cc_final: 0.7612 (mmm) REVERT: H 72 THR cc_start: 0.8853 (m) cc_final: 0.8539 (p) REVERT: H 153 MET cc_start: 0.7620 (tpp) cc_final: 0.7256 (tpp) REVERT: H 281 MET cc_start: 0.7963 (mmm) cc_final: 0.7759 (mmm) REVERT: H 393 PRO cc_start: 0.8364 (Cg_exo) cc_final: 0.8102 (Cg_endo) REVERT: I 110 TYR cc_start: 0.8135 (m-80) cc_final: 0.7698 (m-80) REVERT: I 136 ARG cc_start: 0.7880 (ptp-170) cc_final: 0.6803 (mtt-85) REVERT: I 168 ARG cc_start: 0.6701 (tpt170) cc_final: 0.6330 (ttp-110) REVERT: I 215 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.7286 (ttt90) REVERT: I 279 GLU cc_start: 0.6460 (OUTLIER) cc_final: 0.5499 (tm-30) REVERT: J 168 ARG cc_start: 0.7090 (ptp-110) cc_final: 0.6818 (ttp-170) REVERT: K 91 LYS cc_start: 0.8033 (tptt) cc_final: 0.7710 (tptm) REVERT: K 188 PHE cc_start: 0.8221 (OUTLIER) cc_final: 0.7662 (t80) REVERT: K 304 ASP cc_start: 0.6774 (t0) cc_final: 0.6497 (t0) REVERT: K 311 TRP cc_start: 0.3931 (OUTLIER) cc_final: 0.3132 (p90) REVERT: K 318 GLN cc_start: 0.8646 (tm-30) cc_final: 0.7978 (tm-30) REVERT: K 392 MET cc_start: 0.7819 (mmm) cc_final: 0.7366 (mmm) outliers start: 161 outliers final: 119 residues processed: 652 average time/residue: 0.4312 time to fit residues: 448.6917 Evaluate side-chains 634 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 505 time to evaluate : 3.913 ------------------------------------------------------------------------------- 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 189 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 273 VAL 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 304 ASP 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 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 358 ASP 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 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 126 PHE 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 228 LEU 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 268 THR 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 389 THR 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 250 ILE Chi-restraints excluded: chain F residue 257 LYS Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 351 LEU Chi-restraints excluded: chain F residue 389 THR 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 112 THR Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain G residue 149 GLN 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 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 186 PHE Chi-restraints excluded: chain H residue 189 THR 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 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 84 THR Chi-restraints excluded: chain I residue 112 THR Chi-restraints excluded: chain I residue 163 VAL 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 375 MET Chi-restraints excluded: chain I residue 389 THR Chi-restraints excluded: chain J residue 95 LEU 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 180 ILE Chi-restraints excluded: chain J residue 188 PHE Chi-restraints excluded: chain J residue 227 ILE Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain J residue 360 LEU Chi-restraints excluded: chain K residue 122 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 288 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 313 SER Chi-restraints excluded: chain L residue 388 ARG Chi-restraints excluded: chain L residue 389 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 83 optimal weight: 2.9990 chunk 402 optimal weight: 7.9990 chunk 302 optimal weight: 5.9990 chunk 387 optimal weight: 6.9990 chunk 306 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 chunk 99 optimal weight: 4.9990 chunk 160 optimal weight: 10.0000 chunk 349 optimal weight: 5.9990 chunk 310 optimal weight: 5.9990 chunk 378 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 GLN ** D 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 214 GLN E 324 GLN F 87 ASN G 242 GLN ** I 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 318 GLN ** J 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 226 GLN ** J 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 246 ASN J 391 ASN L 318 GLN ** L 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.149146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.122127 restraints weight = 46741.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.125423 restraints weight = 26228.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.127490 restraints weight = 18296.300| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.7455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 33300 Z= 0.242 Angle : 0.719 10.286 44976 Z= 0.375 Chirality : 0.046 0.264 4896 Planarity : 0.005 0.076 5904 Dihedral : 6.256 127.194 4528 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.70 % Allowed : 7.24 % Favored : 92.05 % Rotamer: Outliers : 5.13 % Allowed : 19.02 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.13), residues: 4128 helix: 0.47 (0.12), residues: 1800 sheet: -0.44 (0.21), residues: 588 loop : -1.55 (0.15), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP G 311 HIS 0.013 0.002 HIS L 352 PHE 0.023 0.002 PHE B 186 TYR 0.027 0.002 TYR E 105 ARG 0.008 0.001 ARG D 368 Details of bonding type rmsd hydrogen bonds : bond 0.05566 ( 1549) hydrogen bonds : angle 5.34629 ( 4461) covalent geometry : bond 0.00572 (33300) covalent geometry : angle 0.71924 (44976) *********************** 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 705 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 524 time to evaluate : 3.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ASN cc_start: 0.7514 (m-40) cc_final: 0.7134 (t0) REVERT: A 122 MET cc_start: 0.7527 (OUTLIER) cc_final: 0.7057 (ttp) REVERT: A 281 MET cc_start: 0.8171 (mmt) cc_final: 0.7948 (mmt) REVERT: A 388 ARG cc_start: 0.8825 (mmm-85) cc_final: 0.8255 (mmm160) REVERT: B 83 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8272 (tt0) REVERT: B 210 MET cc_start: 0.8852 (OUTLIER) cc_final: 0.8435 (mtp) REVERT: B 283 SER cc_start: 0.8482 (p) cc_final: 0.8247 (t) REVERT: C 171 GLU cc_start: 0.7780 (mp0) cc_final: 0.7101 (pp20) REVERT: C 233 LYS cc_start: 0.4610 (ttpp) cc_final: 0.4339 (ttmt) REVERT: C 368 ARG cc_start: 0.7925 (ptm160) cc_final: 0.7616 (ttp-170) REVERT: C 392 MET cc_start: 0.8920 (mmp) cc_final: 0.8650 (mmt) REVERT: D 122 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.7653 (ttt) REVERT: D 188 PHE cc_start: 0.8027 (OUTLIER) cc_final: 0.7661 (t80) REVERT: D 212 ASP cc_start: 0.7440 (m-30) cc_final: 0.7056 (m-30) REVERT: D 213 GLN cc_start: 0.9110 (tm-30) cc_final: 0.8656 (tm-30) REVERT: D 216 ASP cc_start: 0.7163 (m-30) cc_final: 0.6631 (m-30) REVERT: D 220 ASN cc_start: 0.8364 (m-40) cc_final: 0.7882 (m-40) REVERT: D 232 GLU cc_start: 0.5502 (OUTLIER) cc_final: 0.3986 (mt-10) REVERT: D 368 ARG cc_start: 0.8019 (ttp80) cc_final: 0.7794 (ttp-170) REVERT: E 160 LYS cc_start: 0.6280 (tptt) cc_final: 0.5602 (mttm) REVERT: E 188 PHE cc_start: 0.8666 (OUTLIER) cc_final: 0.8339 (t80) REVERT: E 248 LYS cc_start: 0.6139 (OUTLIER) cc_final: 0.5898 (ttpp) REVERT: F 167 GLN cc_start: 0.7986 (tm-30) cc_final: 0.7761 (tm-30) REVERT: F 188 PHE cc_start: 0.7734 (OUTLIER) cc_final: 0.7091 (t80) REVERT: F 277 ASP cc_start: 0.5334 (OUTLIER) cc_final: 0.4463 (t0) REVERT: G 72 THR cc_start: 0.9061 (m) cc_final: 0.8111 (p) REVERT: G 73 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8548 (mt) REVERT: G 76 CYS cc_start: 0.8041 (m) cc_final: 0.7478 (m) REVERT: G 83 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7653 (mt-10) REVERT: G 356 ASN cc_start: 0.8420 (p0) cc_final: 0.8060 (p0) REVERT: H 72 THR cc_start: 0.8966 (m) cc_final: 0.8709 (p) REVERT: H 165 ARG cc_start: 0.7639 (tpt-90) cc_final: 0.7393 (tpp80) REVERT: H 178 LYS cc_start: 0.8704 (pttm) cc_final: 0.8481 (pttp) REVERT: H 375 MET cc_start: 0.8983 (mmt) cc_final: 0.8772 (mmt) REVERT: I 168 ARG cc_start: 0.6715 (tpt170) cc_final: 0.6306 (ttp-110) REVERT: I 215 ARG cc_start: 0.7935 (OUTLIER) cc_final: 0.7347 (ttt90) REVERT: I 279 GLU cc_start: 0.6581 (OUTLIER) cc_final: 0.5368 (tm-30) REVERT: I 290 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7656 (tp30) REVERT: I 386 MET cc_start: 0.8419 (mtm) cc_final: 0.8122 (mtp) REVERT: K 91 LYS cc_start: 0.8138 (tptt) cc_final: 0.7686 (tptm) REVERT: K 188 PHE cc_start: 0.8353 (OUTLIER) cc_final: 0.7785 (t80) REVERT: K 304 ASP cc_start: 0.6719 (t0) cc_final: 0.6431 (t0) REVERT: K 311 TRP cc_start: 0.4119 (OUTLIER) cc_final: 0.3473 (p-90) REVERT: K 318 GLN cc_start: 0.8682 (tm-30) cc_final: 0.8015 (tm-30) REVERT: K 392 MET cc_start: 0.7858 (mmm) cc_final: 0.7415 (mmt) outliers start: 181 outliers final: 128 residues processed: 658 average time/residue: 0.4447 time to fit residues: 464.4561 Evaluate side-chains 643 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 499 time to evaluate : 4.132 ------------------------------------------------------------------------------- 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 122 MET Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 273 VAL 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 68 SER Chi-restraints excluded: chain B residue 83 GLU 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 210 MET 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 82 PHE 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 186 PHE Chi-restraints excluded: chain C residue 255 VAL 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 99 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 188 PHE 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 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 126 PHE 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 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 268 THR 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 389 THR Chi-restraints excluded: chain F residue 76 CYS 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 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 257 LYS Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 277 ASP Chi-restraints excluded: chain F residue 313 SER Chi-restraints excluded: chain F residue 351 LEU Chi-restraints excluded: chain F residue 389 THR 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 112 THR Chi-restraints excluded: chain G residue 141 ASP 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 327 LEU 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 186 PHE Chi-restraints excluded: chain H residue 189 THR 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 263 GLU 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 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 248 LYS 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 95 LEU 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 162 VAL Chi-restraints excluded: chain J residue 180 ILE 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 122 MET Chi-restraints excluded: chain K residue 146 LEU 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 288 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 150 SER Chi-restraints excluded: chain L residue 188 PHE Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain L residue 313 SER 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 232 optimal weight: 0.9980 chunk 259 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 37 optimal weight: 8.9990 chunk 281 optimal weight: 0.9990 chunk 396 optimal weight: 8.9990 chunk 190 optimal weight: 5.9990 chunk 227 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 GLN ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 214 GLN E 324 GLN F 87 ASN G 242 GLN ** I 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 129 ASN J 391 ASN L 318 GLN ** L 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.153739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.126874 restraints weight = 46238.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.130235 restraints weight = 25628.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.132359 restraints weight = 17784.292| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.7558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 33300 Z= 0.133 Angle : 0.625 8.801 44976 Z= 0.325 Chirality : 0.043 0.233 4896 Planarity : 0.004 0.072 5904 Dihedral : 5.870 123.689 4528 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.63 % Allowed : 6.64 % Favored : 92.73 % Rotamer: Outliers : 3.94 % Allowed : 20.07 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.13), residues: 4128 helix: 0.73 (0.12), residues: 1768 sheet: -0.26 (0.21), residues: 592 loop : -1.43 (0.15), residues: 1768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 311 HIS 0.016 0.001 HIS L 352 PHE 0.031 0.001 PHE G 188 TYR 0.023 0.001 TYR E 105 ARG 0.012 0.000 ARG A 240 Details of bonding type rmsd hydrogen bonds : bond 0.04379 ( 1549) hydrogen bonds : angle 5.11723 ( 4461) covalent geometry : bond 0.00295 (33300) covalent geometry : angle 0.62458 (44976) *********************** 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 679 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 540 time to evaluate : 3.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 PHE cc_start: 0.8512 (m-80) cc_final: 0.8280 (m-10) REVERT: A 89 ASN cc_start: 0.7499 (m-40) cc_final: 0.7113 (t0) REVERT: A 122 MET cc_start: 0.7246 (OUTLIER) cc_final: 0.6769 (ttp) REVERT: A 259 LEU cc_start: 0.5587 (OUTLIER) cc_final: 0.5160 (mm) REVERT: A 388 ARG cc_start: 0.8832 (mmm-85) cc_final: 0.8280 (mmm160) REVERT: B 115 GLU cc_start: 0.7931 (tp30) cc_final: 0.7565 (tp30) REVERT: C 171 GLU cc_start: 0.7733 (mp0) cc_final: 0.7093 (pp20) REVERT: C 233 LYS cc_start: 0.4628 (ttpp) cc_final: 0.4369 (ttmt) REVERT: C 368 ARG cc_start: 0.7772 (ptm160) cc_final: 0.7472 (ttp-170) REVERT: C 392 MET cc_start: 0.8895 (mmp) cc_final: 0.8421 (mmt) REVERT: D 122 MET cc_start: 0.8375 (OUTLIER) cc_final: 0.7556 (ttt) REVERT: D 212 ASP cc_start: 0.7365 (m-30) cc_final: 0.6900 (m-30) REVERT: D 213 GLN cc_start: 0.9071 (tm-30) cc_final: 0.8515 (tm-30) REVERT: D 216 ASP cc_start: 0.7101 (m-30) cc_final: 0.6517 (m-30) REVERT: D 220 ASN cc_start: 0.8288 (m-40) cc_final: 0.7774 (m-40) REVERT: D 232 GLU cc_start: 0.5678 (OUTLIER) cc_final: 0.4249 (mt-10) REVERT: E 58 LEU cc_start: 0.9324 (tp) cc_final: 0.8878 (tt) REVERT: E 160 LYS cc_start: 0.6215 (tptt) cc_final: 0.5419 (mmtp) REVERT: E 171 GLU cc_start: 0.6380 (mp0) cc_final: 0.6178 (mp0) REVERT: E 248 LYS cc_start: 0.6135 (OUTLIER) cc_final: 0.5879 (ttpp) REVERT: F 105 TYR cc_start: 0.8634 (t80) cc_final: 0.8367 (t80) REVERT: F 188 PHE cc_start: 0.7435 (OUTLIER) cc_final: 0.6886 (t80) REVERT: G 72 THR cc_start: 0.9042 (m) cc_final: 0.8067 (p) REVERT: G 73 LEU cc_start: 0.8916 (mm) cc_final: 0.8501 (mt) REVERT: G 76 CYS cc_start: 0.7985 (m) cc_final: 0.7379 (m) REVERT: G 356 ASN cc_start: 0.8364 (p0) cc_final: 0.7948 (p0) REVERT: H 165 ARG cc_start: 0.7513 (tpt-90) cc_final: 0.7173 (tpp80) REVERT: H 167 GLN cc_start: 0.7900 (tm-30) cc_final: 0.7539 (mt0) REVERT: H 178 LYS cc_start: 0.8608 (pttm) cc_final: 0.8401 (pttp) REVERT: H 326 THR cc_start: 0.9450 (m) cc_final: 0.9136 (p) REVERT: H 375 MET cc_start: 0.8863 (mmt) cc_final: 0.8626 (mmt) REVERT: H 393 PRO cc_start: 0.8663 (Cg_exo) cc_final: 0.8454 (Cg_endo) REVERT: I 122 MET cc_start: 0.8846 (tpt) cc_final: 0.8390 (tpt) REVERT: I 168 ARG cc_start: 0.6721 (tpt170) cc_final: 0.6505 (ttp-110) REVERT: I 188 PHE cc_start: 0.8158 (OUTLIER) cc_final: 0.7796 (t80) REVERT: I 215 ARG cc_start: 0.7840 (OUTLIER) cc_final: 0.7256 (ttt90) REVERT: I 279 GLU cc_start: 0.6259 (OUTLIER) cc_final: 0.5078 (tm-30) REVERT: I 290 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7560 (tp30) REVERT: J 157 LEU cc_start: 0.6778 (pt) cc_final: 0.6510 (tt) REVERT: K 91 LYS cc_start: 0.8071 (tptt) cc_final: 0.7615 (tptm) REVERT: K 188 PHE cc_start: 0.8122 (OUTLIER) cc_final: 0.7710 (t80) REVERT: K 304 ASP cc_start: 0.6572 (t0) cc_final: 0.6328 (t0) REVERT: K 311 TRP cc_start: 0.4170 (OUTLIER) cc_final: 0.2879 (p90) REVERT: K 318 GLN cc_start: 0.8602 (tm-30) cc_final: 0.7956 (tm-30) REVERT: K 392 MET cc_start: 0.7828 (mmm) cc_final: 0.7398 (mmt) REVERT: L 167 GLN cc_start: 0.8001 (tm-30) cc_final: 0.7595 (tm-30) outliers start: 139 outliers final: 118 residues processed: 642 average time/residue: 0.4657 time to fit residues: 479.1687 Evaluate side-chains 633 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 503 time to evaluate : 5.470 ------------------------------------------------------------------------------- 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 122 MET Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 273 VAL 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 68 SER 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 210 MET Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 77 LEU 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 358 ASP 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 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 126 PHE Chi-restraints excluded: chain E residue 146 LEU 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 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 268 THR 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 76 CYS 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 197 ILE 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 351 LEU 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 141 ASP Chi-restraints excluded: chain G residue 149 GLN Chi-restraints excluded: chain G residue 188 PHE Chi-restraints excluded: chain G residue 227 ILE Chi-restraints excluded: chain G residue 301 LEU Chi-restraints excluded: chain G residue 311 TRP 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 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 263 GLU 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 163 VAL Chi-restraints excluded: chain I residue 188 PHE 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 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 180 ILE Chi-restraints excluded: chain J residue 188 PHE Chi-restraints excluded: chain J residue 227 ILE Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain J residue 343 ILE Chi-restraints excluded: chain J residue 360 LEU Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 111 MET Chi-restraints excluded: chain K residue 122 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 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 229 optimal weight: 4.9990 chunk 349 optimal weight: 9.9990 chunk 366 optimal weight: 10.0000 chunk 344 optimal weight: 10.0000 chunk 185 optimal weight: 9.9990 chunk 152 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 289 optimal weight: 1.9990 chunk 384 optimal weight: 0.0000 chunk 110 optimal weight: 8.9990 chunk 165 optimal weight: 9.9990 overall best weight: 4.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 214 GLN E 324 GLN F 87 ASN F 167 GLN G 242 GLN ** I 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3682 r_free = 0.3682 target = 0.150013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.123133 restraints weight = 46471.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.126385 restraints weight = 25995.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.128469 restraints weight = 18137.153| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.7702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 33300 Z= 0.207 Angle : 0.688 9.448 44976 Z= 0.358 Chirality : 0.045 0.237 4896 Planarity : 0.005 0.078 5904 Dihedral : 6.026 128.091 4528 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.70 % Allowed : 7.24 % Favored : 92.05 % Rotamer: Outliers : 4.51 % Allowed : 20.21 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.13), residues: 4128 helix: 0.55 (0.12), residues: 1806 sheet: -0.37 (0.21), residues: 588 loop : -1.59 (0.15), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP G 311 HIS 0.016 0.002 HIS L 352 PHE 0.031 0.002 PHE G 188 TYR 0.021 0.002 TYR E 105 ARG 0.016 0.001 ARG C 168 Details of bonding type rmsd hydrogen bonds : bond 0.05227 ( 1549) hydrogen bonds : angle 5.23277 ( 4461) covalent geometry : bond 0.00488 (33300) covalent geometry : angle 0.68844 (44976) *********************** 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: 159 poor density : 493 time to evaluate : 3.540 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: 0.7466 (m-40) cc_final: 0.7155 (t0) REVERT: A 122 MET cc_start: 0.7498 (OUTLIER) cc_final: 0.7028 (ttp) REVERT: A 259 LEU cc_start: 0.5315 (OUTLIER) cc_final: 0.4875 (mm) REVERT: A 388 ARG cc_start: 0.8850 (mmm-85) cc_final: 0.8272 (mmm160) REVERT: B 172 TYR cc_start: 0.7463 (m-80) cc_final: 0.7262 (m-80) REVERT: B 283 SER cc_start: 0.8421 (p) cc_final: 0.8167 (t) REVERT: C 122 MET cc_start: 0.8209 (tpt) cc_final: 0.7838 (tpt) REVERT: C 171 GLU cc_start: 0.7722 (mp0) cc_final: 0.7191 (pp20) REVERT: C 240 ARG cc_start: 0.7577 (tpp80) cc_final: 0.7008 (ptp-170) REVERT: C 368 ARG cc_start: 0.7861 (ptm160) cc_final: 0.7586 (ttp-170) REVERT: C 392 MET cc_start: 0.8919 (mmp) cc_final: 0.8501 (mmt) REVERT: D 122 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.7692 (ttt) REVERT: D 212 ASP cc_start: 0.7406 (m-30) cc_final: 0.7005 (m-30) REVERT: D 213 GLN cc_start: 0.9117 (tm-30) cc_final: 0.8511 (tm-30) REVERT: D 216 ASP cc_start: 0.7191 (m-30) cc_final: 0.6638 (m-30) REVERT: D 220 ASN cc_start: 0.8347 (m-40) cc_final: 0.7839 (m-40) REVERT: D 232 GLU cc_start: 0.5736 (OUTLIER) cc_final: 0.4294 (mt-10) REVERT: D 277 ASP cc_start: 0.5234 (OUTLIER) cc_final: 0.4501 (t70) REVERT: E 160 LYS cc_start: 0.6244 (tptt) cc_final: 0.5452 (mmtp) REVERT: E 171 GLU cc_start: 0.6467 (mp0) cc_final: 0.6262 (mp0) REVERT: F 105 TYR cc_start: 0.8688 (t80) cc_final: 0.8435 (t80) REVERT: F 188 PHE cc_start: 0.7653 (OUTLIER) cc_final: 0.7147 (t80) REVERT: G 72 THR cc_start: 0.9064 (m) cc_final: 0.8102 (p) REVERT: G 73 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8508 (mt) REVERT: G 76 CYS cc_start: 0.8034 (m) cc_final: 0.7469 (m) REVERT: G 356 ASN cc_start: 0.8399 (p0) cc_final: 0.8010 (p0) REVERT: H 165 ARG cc_start: 0.7562 (tpt-90) cc_final: 0.7270 (tpp80) REVERT: H 167 GLN cc_start: 0.7885 (tm-30) cc_final: 0.7638 (mt0) REVERT: H 326 THR cc_start: 0.9398 (m) cc_final: 0.9113 (p) REVERT: I 122 MET cc_start: 0.8846 (tpt) cc_final: 0.8422 (tpt) REVERT: I 131 TYR cc_start: 0.8769 (m-80) cc_final: 0.8513 (m-80) REVERT: I 168 ARG cc_start: 0.6745 (tpt170) cc_final: 0.6522 (ttp-110) REVERT: I 188 PHE cc_start: 0.8123 (OUTLIER) cc_final: 0.7703 (t80) REVERT: I 215 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.7317 (ttt90) REVERT: I 279 GLU cc_start: 0.6441 (OUTLIER) cc_final: 0.5270 (tm-30) REVERT: I 290 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7599 (tp30) REVERT: J 157 LEU cc_start: 0.6787 (pt) cc_final: 0.6568 (tt) REVERT: K 91 LYS cc_start: 0.8141 (tptt) cc_final: 0.7671 (tptm) REVERT: K 188 PHE cc_start: 0.8241 (OUTLIER) cc_final: 0.7781 (t80) REVERT: K 304 ASP cc_start: 0.6648 (t0) cc_final: 0.6390 (t0) REVERT: K 311 TRP cc_start: 0.4421 (OUTLIER) cc_final: 0.3577 (p-90) REVERT: K 318 GLN cc_start: 0.8648 (tm-30) cc_final: 0.7986 (tm-30) REVERT: K 392 MET cc_start: 0.7859 (mmm) cc_final: 0.7443 (mmt) REVERT: L 167 GLN cc_start: 0.8001 (tm-30) cc_final: 0.7609 (tm-30) outliers start: 159 outliers final: 129 residues processed: 610 average time/residue: 0.4304 time to fit residues: 419.8846 Evaluate side-chains 625 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 483 time to evaluate : 3.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 273 VAL 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 68 SER Chi-restraints excluded: chain B residue 84 THR 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 210 MET Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 150 SER 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 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 188 PHE 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 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 126 PHE Chi-restraints excluded: chain E residue 146 LEU 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 197 ILE 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 268 THR 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 389 THR Chi-restraints excluded: chain F residue 76 CYS Chi-restraints excluded: chain F residue 87 ASN 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 257 LYS Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 313 SER Chi-restraints excluded: chain F residue 351 LEU 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 112 THR Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain G residue 188 PHE Chi-restraints excluded: chain G residue 227 ILE 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 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 186 PHE 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 263 GLU 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 163 VAL Chi-restraints excluded: chain I residue 188 PHE 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 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 180 ILE Chi-restraints excluded: chain J residue 183 LEU Chi-restraints excluded: chain J residue 188 PHE Chi-restraints excluded: chain J residue 227 ILE Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain J residue 360 LEU Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 111 MET Chi-restraints excluded: chain K residue 122 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 188 PHE Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain L residue 281 MET 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 64 optimal weight: 8.9990 chunk 306 optimal weight: 8.9990 chunk 90 optimal weight: 0.3980 chunk 169 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 320 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 93 optimal weight: 10.0000 chunk 343 optimal weight: 8.9990 chunk 116 optimal weight: 1.9990 chunk 275 optimal weight: 6.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 318 GLN C 149 GLN ** D 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 214 GLN E 324 GLN F 87 ASN F 167 GLN ** I 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 220 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.157760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.131471 restraints weight = 46500.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.135103 restraints weight = 24842.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.137368 restraints weight = 16791.417| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.7851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 33300 Z= 0.179 Angle : 0.666 9.817 44976 Z= 0.346 Chirality : 0.044 0.236 4896 Planarity : 0.005 0.077 5904 Dihedral : 5.900 128.805 4524 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.68 % Allowed : 6.59 % Favored : 92.73 % Rotamer: Outliers : 4.11 % Allowed : 20.58 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.13), residues: 4128 helix: 0.67 (0.12), residues: 1764 sheet: -0.31 (0.22), residues: 588 loop : -1.55 (0.15), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP G 311 HIS 0.016 0.001 HIS L 352 PHE 0.028 0.002 PHE G 188 TYR 0.014 0.002 TYR E 330 ARG 0.009 0.000 ARG C 168 Details of bonding type rmsd hydrogen bonds : bond 0.04849 ( 1549) hydrogen bonds : angle 5.20315 ( 4461) covalent geometry : bond 0.00417 (33300) covalent geometry : angle 0.66571 (44976) ********************** 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 636 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 491 time to evaluate : 3.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ASN cc_start: 0.7539 (m-40) cc_final: 0.7201 (t0) REVERT: A 122 MET cc_start: 0.7589 (OUTLIER) cc_final: 0.7077 (ttp) REVERT: A 165 ARG cc_start: 0.7423 (tpp80) cc_final: 0.7062 (mmt90) REVERT: A 259 LEU cc_start: 0.5303 (OUTLIER) cc_final: 0.4881 (mm) REVERT: A 388 ARG cc_start: 0.8901 (mmm-85) cc_final: 0.8268 (mmm160) REVERT: B 283 SER cc_start: 0.8544 (p) cc_final: 0.8206 (t) REVERT: C 122 MET cc_start: 0.8260 (tpt) cc_final: 0.7798 (tpt) REVERT: C 171 GLU cc_start: 0.7710 (mp0) cc_final: 0.7117 (pp20) REVERT: C 188 PHE cc_start: 0.8714 (OUTLIER) cc_final: 0.8212 (t80) REVERT: C 368 ARG cc_start: 0.7912 (ptm160) cc_final: 0.7527 (ttp-170) REVERT: C 392 MET cc_start: 0.9024 (mmp) cc_final: 0.8643 (mmt) REVERT: D 122 MET cc_start: 0.8413 (OUTLIER) cc_final: 0.7708 (ttt) REVERT: D 212 ASP cc_start: 0.7514 (m-30) cc_final: 0.7090 (m-30) REVERT: D 213 GLN cc_start: 0.9099 (tm-30) cc_final: 0.8456 (tm-30) REVERT: D 216 ASP cc_start: 0.7217 (m-30) cc_final: 0.6630 (m-30) REVERT: D 220 ASN cc_start: 0.8344 (m-40) cc_final: 0.7876 (m-40) REVERT: D 232 GLU cc_start: 0.5604 (OUTLIER) cc_final: 0.4374 (mt-10) REVERT: E 160 LYS cc_start: 0.6160 (tptt) cc_final: 0.5380 (mmtp) REVERT: E 171 GLU cc_start: 0.6387 (mp0) cc_final: 0.6175 (mp0) REVERT: F 105 TYR cc_start: 0.8675 (t80) cc_final: 0.8436 (t80) REVERT: F 111 MET cc_start: 0.8824 (ptp) cc_final: 0.8247 (ptp) REVERT: F 188 PHE cc_start: 0.7505 (OUTLIER) cc_final: 0.7075 (t80) REVERT: G 72 THR cc_start: 0.9035 (m) cc_final: 0.8055 (p) REVERT: G 73 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8445 (mt) REVERT: G 76 CYS cc_start: 0.8000 (m) cc_final: 0.7462 (m) REVERT: G 356 ASN cc_start: 0.8405 (p0) cc_final: 0.8058 (p0) REVERT: G 375 MET cc_start: 0.9067 (mmt) cc_final: 0.8723 (mmt) REVERT: H 167 GLN cc_start: 0.7923 (tm-30) cc_final: 0.7600 (mt0) REVERT: H 281 MET cc_start: 0.8017 (OUTLIER) cc_final: 0.7441 (mmp) REVERT: H 326 THR cc_start: 0.9425 (m) cc_final: 0.9095 (p) REVERT: H 393 PRO cc_start: 0.8719 (Cg_exo) cc_final: 0.8517 (Cg_endo) REVERT: I 122 MET cc_start: 0.8928 (tpt) cc_final: 0.8479 (tpt) REVERT: I 168 ARG cc_start: 0.6690 (tpt170) cc_final: 0.6430 (ttp-110) REVERT: I 188 PHE cc_start: 0.8161 (OUTLIER) cc_final: 0.7827 (t80) REVERT: I 215 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.7341 (ttt90) REVERT: I 279 GLU cc_start: 0.6441 (OUTLIER) cc_final: 0.5379 (tm-30) REVERT: I 290 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7627 (tp30) REVERT: J 157 LEU cc_start: 0.6932 (pt) cc_final: 0.6637 (tt) REVERT: K 91 LYS cc_start: 0.8191 (tptt) cc_final: 0.7692 (tptm) REVERT: K 188 PHE cc_start: 0.8160 (OUTLIER) cc_final: 0.7703 (t80) REVERT: K 311 TRP cc_start: 0.4273 (OUTLIER) cc_final: 0.3256 (p-90) REVERT: K 318 GLN cc_start: 0.8638 (tm-30) cc_final: 0.7955 (tm-30) REVERT: K 392 MET cc_start: 0.7962 (mmm) cc_final: 0.7628 (mmt) REVERT: L 167 GLN cc_start: 0.8027 (tm-30) cc_final: 0.7604 (tm-30) outliers start: 145 outliers final: 120 residues processed: 596 average time/residue: 0.4215 time to fit residues: 404.6404 Evaluate side-chains 608 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 474 time to evaluate : 3.539 ------------------------------------------------------------------------------- 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 122 MET Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 273 VAL 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 68 SER 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 320 LEU Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 255 VAL 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 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 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 126 PHE Chi-restraints excluded: chain E residue 146 LEU 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 197 ILE 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 268 THR 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 112 THR 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 257 LYS Chi-restraints excluded: chain F residue 313 SER Chi-restraints excluded: chain F residue 351 LEU 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 112 THR Chi-restraints excluded: chain G residue 135 ASP Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain G residue 188 PHE Chi-restraints excluded: chain G residue 227 ILE 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 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 186 PHE 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 263 GLU Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain H residue 281 MET Chi-restraints excluded: chain H residue 320 LEU Chi-restraints excluded: chain H residue 386 MET 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 188 PHE 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 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 122 MET Chi-restraints excluded: chain J residue 144 SER Chi-restraints excluded: chain J residue 162 VAL Chi-restraints excluded: chain J residue 180 ILE 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 67 VAL Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 111 MET Chi-restraints excluded: chain K residue 122 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 188 PHE Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain L residue 281 MET 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 398 optimal weight: 0.9990 chunk 263 optimal weight: 8.9990 chunk 59 optimal weight: 8.9990 chunk 376 optimal weight: 4.9990 chunk 365 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 343 optimal weight: 10.0000 chunk 303 optimal weight: 4.9990 chunk 333 optimal weight: 0.9990 chunk 255 optimal weight: 7.9990 chunk 115 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 391 ASN B 167 GLN B 318 GLN ** D 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 214 GLN E 324 GLN F 87 ASN F 167 GLN H 339 GLN ** I 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.157745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.131555 restraints weight = 46282.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.135140 restraints weight = 24682.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.137405 restraints weight = 16712.541| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.7947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 33300 Z= 0.171 Angle : 0.658 9.587 44976 Z= 0.342 Chirality : 0.044 0.244 4896 Planarity : 0.005 0.076 5904 Dihedral : 5.821 129.854 4522 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.19 % Favored : 92.13 % Rotamer: Outliers : 4.25 % Allowed : 20.58 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.13), residues: 4128 helix: 0.69 (0.12), residues: 1764 sheet: -0.29 (0.22), residues: 588 loop : -1.57 (0.15), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP K 311 HIS 0.014 0.001 HIS L 352 PHE 0.029 0.002 PHE A 186 TYR 0.022 0.002 TYR E 105 ARG 0.009 0.000 ARG C 168 Details of bonding type rmsd hydrogen bonds : bond 0.04780 ( 1549) hydrogen bonds : angle 5.16819 ( 4461) covalent geometry : bond 0.00398 (33300) covalent geometry : angle 0.65831 (44976) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11472.03 seconds wall clock time: 201 minutes 13.67 seconds (12073.67 seconds total)