Starting phenix.real_space_refine on Wed Mar 4 19:57:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6v0f_20996/03_2026/6v0f_20996.cif Found real_map, /net/cci-nas-00/data/ceres_data/6v0f_20996/03_2026/6v0f_20996.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6v0f_20996/03_2026/6v0f_20996.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6v0f_20996/03_2026/6v0f_20996.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6v0f_20996/03_2026/6v0f_20996.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6v0f_20996/03_2026/6v0f_20996.map" } resolution = 2.96 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 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 24 5.16 5 C 10128 2.51 5 N 2688 2.21 5 O 3102 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15942 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2657 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 19, 'TRANS': 331} Restraints were copied for chains: B, C, D, E, F Time building chain proxies: 2.21, per 1000 atoms: 0.14 Number of scatterers: 15942 At special positions: 0 Unit cell: (113.97, 103.49, 119.21, 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 24 16.00 O 3102 8.00 N 2688 7.00 C 10128 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.19 Conformation dependent library (CDL) restraints added in 716.6 milliseconds 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3804 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 30 sheets defined 17.1% alpha, 33.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 209 through 214 removed outlier: 3.701A pdb=" N THR A 212 " --> pdb=" O ARG A 209 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ASP A 213 " --> pdb=" O ARG A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 249 removed outlier: 4.085A pdb=" N VAL A 247 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASN A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 278 removed outlier: 3.736A pdb=" N GLN A 278 " --> pdb=" O ALA A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 334 removed outlier: 3.730A pdb=" N THR A 333 " --> pdb=" O SER A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 361 Processing helix chain 'A' and resid 381 through 386 removed outlier: 4.332A pdb=" N LEU A 386 " --> pdb=" O GLY A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 445 Processing helix chain 'A' and resid 472 through 479 Processing helix chain 'A' and resid 500 through 506 Processing helix chain 'B' and resid 209 through 214 removed outlier: 3.702A pdb=" N THR B 212 " --> pdb=" O ARG B 209 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ASP B 213 " --> pdb=" O ARG B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 249 removed outlier: 4.085A pdb=" N VAL B 247 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASN B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 278 removed outlier: 3.736A pdb=" N GLN B 278 " --> pdb=" O ALA B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 334 removed outlier: 3.731A pdb=" N THR B 333 " --> pdb=" O SER B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 361 Processing helix chain 'B' and resid 381 through 386 removed outlier: 4.333A pdb=" N LEU B 386 " --> pdb=" O GLY B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 445 Processing helix chain 'B' and resid 472 through 479 Processing helix chain 'B' and resid 500 through 506 Processing helix chain 'C' and resid 209 through 214 removed outlier: 3.702A pdb=" N THR C 212 " --> pdb=" O ARG C 209 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ASP C 213 " --> pdb=" O ARG C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 249 removed outlier: 4.085A pdb=" N VAL C 247 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASN C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 278 removed outlier: 3.737A pdb=" N GLN C 278 " --> pdb=" O ALA C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 334 removed outlier: 3.730A pdb=" N THR C 333 " --> pdb=" O SER C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 361 Processing helix chain 'C' and resid 381 through 386 removed outlier: 4.333A pdb=" N LEU C 386 " --> pdb=" O GLY C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 445 Processing helix chain 'C' and resid 472 through 479 Processing helix chain 'C' and resid 500 through 506 Processing helix chain 'D' and resid 209 through 214 removed outlier: 3.702A pdb=" N THR D 212 " --> pdb=" O ARG D 209 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ASP D 213 " --> pdb=" O ARG D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 249 removed outlier: 4.085A pdb=" N VAL D 247 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASN D 248 " --> pdb=" O ALA D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 278 removed outlier: 3.736A pdb=" N GLN D 278 " --> pdb=" O ALA D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 334 removed outlier: 3.730A pdb=" N THR D 333 " --> pdb=" O SER D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 361 Processing helix chain 'D' and resid 381 through 386 removed outlier: 4.333A pdb=" N LEU D 386 " --> pdb=" O GLY D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 445 Processing helix chain 'D' and resid 472 through 479 Processing helix chain 'D' and resid 500 through 506 Processing helix chain 'E' and resid 209 through 214 removed outlier: 3.701A pdb=" N THR E 212 " --> pdb=" O ARG E 209 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ASP E 213 " --> pdb=" O ARG E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 249 removed outlier: 4.085A pdb=" N VAL E 247 " --> pdb=" O LEU E 243 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASN E 248 " --> pdb=" O ALA E 244 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 278 removed outlier: 3.736A pdb=" N GLN E 278 " --> pdb=" O ALA E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 334 removed outlier: 3.731A pdb=" N THR E 333 " --> pdb=" O SER E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 361 Processing helix chain 'E' and resid 381 through 386 removed outlier: 4.333A pdb=" N LEU E 386 " --> pdb=" O GLY E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 445 Processing helix chain 'E' and resid 472 through 479 Processing helix chain 'E' and resid 500 through 506 Processing helix chain 'F' and resid 209 through 214 removed outlier: 3.701A pdb=" N THR F 212 " --> pdb=" O ARG F 209 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ASP F 213 " --> pdb=" O ARG F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 249 removed outlier: 4.085A pdb=" N VAL F 247 " --> pdb=" O LEU F 243 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASN F 248 " --> pdb=" O ALA F 244 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 278 removed outlier: 3.736A pdb=" N GLN F 278 " --> pdb=" O ALA F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 334 removed outlier: 3.731A pdb=" N THR F 333 " --> pdb=" O SER F 330 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 361 Processing helix chain 'F' and resid 381 through 386 removed outlier: 4.333A pdb=" N LEU F 386 " --> pdb=" O GLY F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 438 through 445 Processing helix chain 'F' and resid 472 through 479 Processing helix chain 'F' and resid 500 through 506 Processing sheet with id=AA1, first strand: chain 'A' and resid 161 through 167 removed outlier: 7.018A pdb=" N VAL A 202 " --> pdb=" O TYR A 192 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N TYR A 192 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ASP A 204 " --> pdb=" O TYR A 190 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL A 179 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N PHE A 221 " --> pdb=" O TYR A 271 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 227 through 230 removed outlier: 3.850A pdb=" N VAL A 227 " --> pdb=" O LEU B 240 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 237 through 240 removed outlier: 3.842A pdb=" N VAL F 227 " --> pdb=" O LEU A 240 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 340 through 344 removed outlier: 6.115A pdb=" N LEU A 300 " --> pdb=" O VAL A 307 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N LEU A 310 " --> pdb=" O THR A 326 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N THR A 326 " --> pdb=" O LEU A 310 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N PHE A 377 " --> pdb=" O ILE A 282 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LYS A 284 " --> pdb=" O PHE A 377 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 449 through 453 removed outlier: 3.592A pdb=" N ILE A 481 " --> pdb=" O PRO A 410 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N LEU A 411 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N VAL A 421 " --> pdb=" O ALA A 436 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ALA A 436 " --> pdb=" O VAL A 421 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR A 495 " --> pdb=" O THR A 396 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 459 through 460 removed outlier: 3.895A pdb=" N GLU A 467 " --> pdb=" O LYS A 460 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 161 through 167 removed outlier: 7.018A pdb=" N VAL B 202 " --> pdb=" O TYR B 192 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N TYR B 192 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ASP B 204 " --> pdb=" O TYR B 190 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL B 179 " --> pdb=" O VAL B 186 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N PHE B 221 " --> pdb=" O TYR B 271 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 227 through 230 removed outlier: 3.831A pdb=" N VAL B 227 " --> pdb=" O LEU C 240 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 340 through 344 removed outlier: 6.114A pdb=" N LEU B 300 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N LEU B 310 " --> pdb=" O THR B 326 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N THR B 326 " --> pdb=" O LEU B 310 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N PHE B 377 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LYS B 284 " --> pdb=" O PHE B 377 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 449 through 453 removed outlier: 3.592A pdb=" N ILE B 481 " --> pdb=" O PRO B 410 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LEU B 411 " --> pdb=" O VAL B 418 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N VAL B 421 " --> pdb=" O ALA B 436 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ALA B 436 " --> pdb=" O VAL B 421 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR B 495 " --> pdb=" O THR B 396 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 459 through 460 removed outlier: 3.894A pdb=" N GLU B 467 " --> pdb=" O LYS B 460 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 161 through 167 removed outlier: 7.018A pdb=" N VAL C 202 " --> pdb=" O TYR C 192 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N TYR C 192 " --> pdb=" O VAL C 202 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ASP C 204 " --> pdb=" O TYR C 190 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL C 179 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N PHE C 221 " --> pdb=" O TYR C 271 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 227 through 230 removed outlier: 3.861A pdb=" N VAL C 227 " --> pdb=" O LEU D 240 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 340 through 344 removed outlier: 6.115A pdb=" N LEU C 300 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N LEU C 310 " --> pdb=" O THR C 326 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N THR C 326 " --> pdb=" O LEU C 310 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N PHE C 377 " --> pdb=" O ILE C 282 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LYS C 284 " --> pdb=" O PHE C 377 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 449 through 453 removed outlier: 3.592A pdb=" N ILE C 481 " --> pdb=" O PRO C 410 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N LEU C 411 " --> pdb=" O VAL C 418 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N VAL C 421 " --> pdb=" O ALA C 436 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ALA C 436 " --> pdb=" O VAL C 421 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR C 495 " --> pdb=" O THR C 396 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 459 through 460 removed outlier: 3.894A pdb=" N GLU C 467 " --> pdb=" O LYS C 460 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 161 through 167 removed outlier: 7.018A pdb=" N VAL D 202 " --> pdb=" O TYR D 192 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N TYR D 192 " --> pdb=" O VAL D 202 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ASP D 204 " --> pdb=" O TYR D 190 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL D 179 " --> pdb=" O VAL D 186 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N PHE D 221 " --> pdb=" O TYR D 271 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 227 through 230 removed outlier: 3.848A pdb=" N VAL D 227 " --> pdb=" O LEU E 240 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 340 through 344 removed outlier: 6.115A pdb=" N LEU D 300 " --> pdb=" O VAL D 307 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N LEU D 310 " --> pdb=" O THR D 326 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N THR D 326 " --> pdb=" O LEU D 310 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N PHE D 377 " --> pdb=" O ILE D 282 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LYS D 284 " --> pdb=" O PHE D 377 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 449 through 453 removed outlier: 3.592A pdb=" N ILE D 481 " --> pdb=" O PRO D 410 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LEU D 411 " --> pdb=" O VAL D 418 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N VAL D 421 " --> pdb=" O ALA D 436 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ALA D 436 " --> pdb=" O VAL D 421 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR D 495 " --> pdb=" O THR D 396 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 459 through 460 removed outlier: 3.895A pdb=" N GLU D 467 " --> pdb=" O LYS D 460 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 161 through 167 removed outlier: 7.018A pdb=" N VAL E 202 " --> pdb=" O TYR E 192 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N TYR E 192 " --> pdb=" O VAL E 202 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ASP E 204 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL E 179 " --> pdb=" O VAL E 186 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N PHE E 221 " --> pdb=" O TYR E 271 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 227 through 230 removed outlier: 3.835A pdb=" N VAL E 227 " --> pdb=" O LEU F 240 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 340 through 344 removed outlier: 6.115A pdb=" N LEU E 300 " --> pdb=" O VAL E 307 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N LEU E 310 " --> pdb=" O THR E 326 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N THR E 326 " --> pdb=" O LEU E 310 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N PHE E 377 " --> pdb=" O ILE E 282 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LYS E 284 " --> pdb=" O PHE E 377 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 449 through 453 removed outlier: 3.592A pdb=" N ILE E 481 " --> pdb=" O PRO E 410 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LEU E 411 " --> pdb=" O VAL E 418 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N VAL E 421 " --> pdb=" O ALA E 436 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ALA E 436 " --> pdb=" O VAL E 421 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR E 495 " --> pdb=" O THR E 396 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 459 through 460 removed outlier: 3.894A pdb=" N GLU E 467 " --> pdb=" O LYS E 460 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 161 through 167 removed outlier: 7.018A pdb=" N VAL F 202 " --> pdb=" O TYR F 192 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N TYR F 192 " --> pdb=" O VAL F 202 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ASP F 204 " --> pdb=" O TYR F 190 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL F 179 " --> pdb=" O VAL F 186 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N PHE F 221 " --> pdb=" O TYR F 271 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 340 through 344 removed outlier: 6.116A pdb=" N LEU F 300 " --> pdb=" O VAL F 307 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N LEU F 310 " --> pdb=" O THR F 326 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N THR F 326 " --> pdb=" O LEU F 310 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N PHE F 377 " --> pdb=" O ILE F 282 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LYS F 284 " --> pdb=" O PHE F 377 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 449 through 453 removed outlier: 3.592A pdb=" N ILE F 481 " --> pdb=" O PRO F 410 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N LEU F 411 " --> pdb=" O VAL F 418 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N VAL F 421 " --> pdb=" O ALA F 436 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ALA F 436 " --> pdb=" O VAL F 421 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR F 495 " --> pdb=" O THR F 396 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 459 through 460 removed outlier: 3.895A pdb=" N GLU F 467 " --> pdb=" O LYS F 460 " (cutoff:3.500A) 552 hydrogen bonds defined for protein. 1404 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.49 Time building geometry restraints manager: 1.64 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: 4263 1.33 - 1.44: 2353 1.44 - 1.56: 9542 1.56 - 1.68: 6 1.68 - 1.79: 48 Bond restraints: 16212 Sorted by residual: bond pdb=" CB VAL B 307 " pdb=" CG1 VAL B 307 " ideal model delta sigma weight residual 1.521 1.423 0.098 3.30e-02 9.18e+02 8.75e+00 bond pdb=" CB VAL C 307 " pdb=" CG1 VAL C 307 " ideal model delta sigma weight residual 1.521 1.424 0.097 3.30e-02 9.18e+02 8.70e+00 bond pdb=" CB VAL D 307 " pdb=" CG1 VAL D 307 " ideal model delta sigma weight residual 1.521 1.424 0.097 3.30e-02 9.18e+02 8.68e+00 bond pdb=" CB VAL A 307 " pdb=" CG1 VAL A 307 " ideal model delta sigma weight residual 1.521 1.424 0.097 3.30e-02 9.18e+02 8.68e+00 bond pdb=" CB VAL F 307 " pdb=" CG1 VAL F 307 " ideal model delta sigma weight residual 1.521 1.424 0.097 3.30e-02 9.18e+02 8.64e+00 ... (remaining 16207 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.98: 21525 3.98 - 7.96: 411 7.96 - 11.95: 48 11.95 - 15.93: 6 15.93 - 19.91: 6 Bond angle restraints: 21996 Sorted by residual: angle pdb=" N LEU C 444 " pdb=" CA LEU C 444 " pdb=" C LEU C 444 " ideal model delta sigma weight residual 111.33 119.87 -8.54 1.21e+00 6.83e-01 4.98e+01 angle pdb=" N LEU E 444 " pdb=" CA LEU E 444 " pdb=" C LEU E 444 " ideal model delta sigma weight residual 111.33 119.86 -8.53 1.21e+00 6.83e-01 4.98e+01 angle pdb=" N LEU A 444 " pdb=" CA LEU A 444 " pdb=" C LEU A 444 " ideal model delta sigma weight residual 111.33 119.84 -8.51 1.21e+00 6.83e-01 4.94e+01 angle pdb=" N LEU F 444 " pdb=" CA LEU F 444 " pdb=" C LEU F 444 " ideal model delta sigma weight residual 111.33 119.84 -8.51 1.21e+00 6.83e-01 4.94e+01 angle pdb=" N LEU D 444 " pdb=" CA LEU D 444 " pdb=" C LEU D 444 " ideal model delta sigma weight residual 111.33 119.82 -8.49 1.21e+00 6.83e-01 4.92e+01 ... (remaining 21991 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.79: 9339 15.79 - 31.58: 401 31.58 - 47.37: 82 47.37 - 63.16: 6 63.16 - 78.95: 24 Dihedral angle restraints: 9852 sinusoidal: 3900 harmonic: 5952 Sorted by residual: dihedral pdb=" CA LEU F 411 " pdb=" C LEU F 411 " pdb=" N ILE F 412 " pdb=" CA ILE F 412 " ideal model delta harmonic sigma weight residual -180.00 -153.33 -26.67 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" CA LEU E 411 " pdb=" C LEU E 411 " pdb=" N ILE E 412 " pdb=" CA ILE E 412 " ideal model delta harmonic sigma weight residual 180.00 -153.34 -26.66 0 5.00e+00 4.00e-02 2.84e+01 dihedral pdb=" CA LEU A 411 " pdb=" C LEU A 411 " pdb=" N ILE A 412 " pdb=" CA ILE A 412 " ideal model delta harmonic sigma weight residual -180.00 -153.36 -26.64 0 5.00e+00 4.00e-02 2.84e+01 ... (remaining 9849 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1594 0.059 - 0.118: 723 0.118 - 0.177: 195 0.177 - 0.236: 40 0.236 - 0.294: 34 Chirality restraints: 2586 Sorted by residual: chirality pdb=" CA ASN A 338 " pdb=" N ASN A 338 " pdb=" C ASN A 338 " pdb=" CB ASN A 338 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" CA ASN B 338 " pdb=" N ASN B 338 " pdb=" C ASN B 338 " pdb=" CB ASN B 338 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" CA ASN C 338 " pdb=" N ASN C 338 " pdb=" C ASN C 338 " pdb=" CB ASN C 338 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.15e+00 ... (remaining 2583 not shown) Planarity restraints: 2856 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET C 491 " 0.018 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C MET C 491 " -0.064 2.00e-02 2.50e+03 pdb=" O MET C 491 " 0.025 2.00e-02 2.50e+03 pdb=" N LYS C 492 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET F 491 " -0.018 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C MET F 491 " 0.064 2.00e-02 2.50e+03 pdb=" O MET F 491 " -0.025 2.00e-02 2.50e+03 pdb=" N LYS F 492 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET E 491 " 0.018 2.00e-02 2.50e+03 3.69e-02 1.36e+01 pdb=" C MET E 491 " -0.064 2.00e-02 2.50e+03 pdb=" O MET E 491 " 0.025 2.00e-02 2.50e+03 pdb=" N LYS E 492 " 0.021 2.00e-02 2.50e+03 ... (remaining 2853 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.93: 6270 2.93 - 3.42: 14154 3.42 - 3.91: 25028 3.91 - 4.41: 27013 4.41 - 4.90: 47875 Nonbonded interactions: 120340 Sorted by model distance: nonbonded pdb=" NH1 ARG D 220 " pdb=" OH TYR D 271 " model vdw 2.433 3.120 nonbonded pdb=" NH1 ARG C 220 " pdb=" OH TYR C 271 " model vdw 2.433 3.120 nonbonded pdb=" NH1 ARG E 220 " pdb=" OH TYR E 271 " model vdw 2.433 3.120 nonbonded pdb=" NH1 ARG F 220 " pdb=" OH TYR F 271 " model vdw 2.433 3.120 nonbonded pdb=" NH1 ARG A 220 " pdb=" OH TYR A 271 " model vdw 2.433 3.120 ... (remaining 120335 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.140 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: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.380 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 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 : 0.010 0.098 16212 Z= 0.407 Angle : 1.332 19.912 21996 Z= 0.712 Chirality : 0.074 0.294 2586 Planarity : 0.009 0.061 2856 Dihedral : 10.493 78.952 6048 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 0.34 % Allowed : 3.70 % Favored : 95.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.57 (0.15), residues: 2094 helix: -2.11 (0.28), residues: 234 sheet: -1.13 (0.19), residues: 666 loop : -1.99 (0.14), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 374 TYR 0.011 0.002 TYR F 403 PHE 0.036 0.004 PHE C 221 TRP 0.023 0.003 TRP A 222 HIS 0.020 0.006 HIS C 441 Details of bonding type rmsd covalent geometry : bond 0.00973 (16212) covalent geometry : angle 1.33196 (21996) hydrogen bonds : bond 0.19041 ( 552) hydrogen bonds : angle 10.36466 ( 1404) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 455 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 ARG cc_start: 0.8671 (mtt-85) cc_final: 0.8318 (mtp180) REVERT: A 248 ASN cc_start: 0.6725 (t0) cc_final: 0.6513 (p0) REVERT: A 278 GLN cc_start: 0.8294 (mm-40) cc_final: 0.8063 (mp10) REVERT: A 456 ARG cc_start: 0.7594 (mtm110) cc_final: 0.6706 (mmm160) REVERT: B 278 GLN cc_start: 0.8332 (mm-40) cc_final: 0.8080 (mp10) REVERT: B 312 LYS cc_start: 0.8195 (tttt) cc_final: 0.7986 (tttp) REVERT: B 314 ASP cc_start: 0.7171 (m-30) cc_final: 0.6929 (m-30) REVERT: B 425 LYS cc_start: 0.8026 (tttm) cc_final: 0.7809 (mttm) REVERT: C 220 ARG cc_start: 0.8764 (mtt-85) cc_final: 0.8545 (mtp180) REVERT: C 273 ASP cc_start: 0.7799 (t0) cc_final: 0.7554 (t0) REVERT: C 297 SER cc_start: 0.8480 (m) cc_final: 0.8219 (t) REVERT: C 312 LYS cc_start: 0.8293 (tttt) cc_final: 0.8088 (tttm) REVERT: C 425 LYS cc_start: 0.8011 (tttm) cc_final: 0.7745 (mttm) REVERT: D 246 LEU cc_start: 0.8359 (mp) cc_final: 0.8039 (tm) REVERT: D 278 GLN cc_start: 0.8276 (mm-40) cc_final: 0.8065 (mp10) REVERT: D 456 ARG cc_start: 0.7558 (mtm110) cc_final: 0.6650 (mmm160) REVERT: E 314 ASP cc_start: 0.7194 (m-30) cc_final: 0.6945 (m-30) REVERT: F 297 SER cc_start: 0.8458 (m) cc_final: 0.8213 (t) outliers start: 6 outliers final: 6 residues processed: 461 average time/residue: 0.6456 time to fit residues: 323.4461 Evaluate side-chains 244 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 238 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain D residue 248 ASN Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 354 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.3980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 HIS A 316 ASN A 345 ASN ** A 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 440 GLN ** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 HIS B 174 ASN B 345 ASN B 417 GLN B 440 GLN ** B 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 HIS ** C 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 440 GLN ** C 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 HIS D 345 ASN D 417 GLN D 440 GLN ** D 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 HIS E 174 ASN E 345 ASN ** E 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 417 GLN E 440 GLN ** E 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 HIS ** F 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 440 GLN ** F 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.145859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.115673 restraints weight = 20489.207| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 3.17 r_work: 0.3323 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16212 Z= 0.173 Angle : 0.738 11.213 21996 Z= 0.369 Chirality : 0.050 0.159 2586 Planarity : 0.005 0.049 2856 Dihedral : 5.673 32.894 2238 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 3.92 % Allowed : 17.18 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.16), residues: 2094 helix: -2.55 (0.21), residues: 258 sheet: -0.35 (0.19), residues: 684 loop : -1.66 (0.15), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 442 TYR 0.012 0.001 TYR C 192 PHE 0.014 0.002 PHE D 364 TRP 0.013 0.002 TRP D 222 HIS 0.004 0.001 HIS D 441 Details of bonding type rmsd covalent geometry : bond 0.00408 (16212) covalent geometry : angle 0.73841 (21996) hydrogen bonds : bond 0.04898 ( 552) hydrogen bonds : angle 7.55974 ( 1404) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 259 time to evaluate : 0.494 Fit side-chains revert: symmetry clash REVERT: A 248 ASN cc_start: 0.6741 (t0) cc_final: 0.6215 (p0) REVERT: A 278 GLN cc_start: 0.8435 (mm-40) cc_final: 0.8144 (mp10) REVERT: A 302 TYR cc_start: 0.9048 (t80) cc_final: 0.8844 (t80) REVERT: A 409 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.8329 (mt0) REVERT: A 456 ARG cc_start: 0.7505 (mtm110) cc_final: 0.6340 (mmm160) REVERT: A 482 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.7573 (ttt90) REVERT: A 502 GLU cc_start: 0.8450 (pp20) cc_final: 0.8225 (pp20) REVERT: A 505 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8755 (mm) REVERT: B 169 ASP cc_start: 0.8713 (p0) cc_final: 0.8507 (p0) REVERT: B 174 ASN cc_start: 0.8263 (m-40) cc_final: 0.7621 (p0) REVERT: B 278 GLN cc_start: 0.8605 (mm-40) cc_final: 0.8230 (mp10) REVERT: B 312 LYS cc_start: 0.8153 (tttt) cc_final: 0.7886 (tttm) REVERT: B 372 GLU cc_start: 0.7620 (mm-30) cc_final: 0.7302 (pt0) REVERT: B 376 GLU cc_start: 0.7754 (pt0) cc_final: 0.7487 (tt0) REVERT: B 425 LYS cc_start: 0.8110 (tttm) cc_final: 0.7497 (mttm) REVERT: B 491 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.8421 (mmm) REVERT: C 273 ASP cc_start: 0.8303 (t0) cc_final: 0.7946 (t0) REVERT: C 278 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.7929 (mp10) REVERT: C 297 SER cc_start: 0.8739 (m) cc_final: 0.8328 (t) REVERT: C 312 LYS cc_start: 0.8230 (tttt) cc_final: 0.7496 (ttpt) REVERT: C 347 LYS cc_start: 0.7285 (pttt) cc_final: 0.7012 (tptm) REVERT: C 416 VAL cc_start: 0.8044 (OUTLIER) cc_final: 0.7801 (m) REVERT: C 425 LYS cc_start: 0.8087 (tttm) cc_final: 0.7516 (mttm) REVERT: D 169 ASP cc_start: 0.8777 (p0) cc_final: 0.8573 (p0) REVERT: D 174 ASN cc_start: 0.8185 (m-40) cc_final: 0.7848 (p0) REVERT: D 246 LEU cc_start: 0.7807 (mp) cc_final: 0.7606 (tp) REVERT: D 278 GLN cc_start: 0.8356 (mm-40) cc_final: 0.8087 (mp10) REVERT: D 302 TYR cc_start: 0.9027 (t80) cc_final: 0.8805 (t80) REVERT: D 312 LYS cc_start: 0.8082 (OUTLIER) cc_final: 0.7327 (ttpt) REVERT: D 409 GLN cc_start: 0.8939 (mm-40) cc_final: 0.8642 (mt0) REVERT: D 417 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.8193 (tt0) REVERT: D 456 ARG cc_start: 0.7492 (mtm110) cc_final: 0.6307 (mmm160) REVERT: E 169 ASP cc_start: 0.8748 (p0) cc_final: 0.8546 (p0) REVERT: E 174 ASN cc_start: 0.8184 (m-40) cc_final: 0.7661 (p0) REVERT: E 402 SER cc_start: 0.8972 (OUTLIER) cc_final: 0.8756 (p) REVERT: E 409 GLN cc_start: 0.8920 (mm-40) cc_final: 0.8433 (mt0) REVERT: E 456 ARG cc_start: 0.7217 (mtt180) cc_final: 0.6911 (mtt180) REVERT: E 482 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7881 (ttt90) REVERT: E 491 MET cc_start: 0.8544 (OUTLIER) cc_final: 0.8311 (mmm) REVERT: F 169 ASP cc_start: 0.8263 (p0) cc_final: 0.8021 (p0) REVERT: F 174 ASN cc_start: 0.8208 (m-40) cc_final: 0.7710 (p0) REVERT: F 278 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.7833 (mp10) REVERT: F 297 SER cc_start: 0.8558 (m) cc_final: 0.8128 (t) REVERT: F 347 LYS cc_start: 0.7257 (pttt) cc_final: 0.6956 (tptm) outliers start: 69 outliers final: 16 residues processed: 302 average time/residue: 0.6000 time to fit residues: 198.4520 Evaluate side-chains 256 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 228 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 482 ARG Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 491 MET Chi-restraints excluded: chain C residue 278 GLN Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 395 LEU Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 312 LYS Chi-restraints excluded: chain D residue 417 GLN Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 297 SER Chi-restraints excluded: chain E residue 402 SER Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 482 ARG Chi-restraints excluded: chain E residue 491 MET Chi-restraints excluded: chain F residue 278 GLN Chi-restraints excluded: chain F residue 354 ASN Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain F residue 416 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 131 optimal weight: 1.9990 chunk 187 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 116 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 190 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 GLN ** B 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 316 ASN C 354 ASN C 420 GLN ** D 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 316 ASN E 417 GLN ** E 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 354 ASN F 420 GLN ** F 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.143799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.113225 restraints weight = 20741.854| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 3.19 r_work: 0.3284 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16212 Z= 0.175 Angle : 0.675 9.417 21996 Z= 0.342 Chirality : 0.049 0.153 2586 Planarity : 0.005 0.046 2856 Dihedral : 5.318 31.667 2230 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 4.89 % Allowed : 18.09 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.17), residues: 2094 helix: -2.77 (0.22), residues: 216 sheet: -0.04 (0.20), residues: 684 loop : -1.27 (0.16), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG F 456 TYR 0.007 0.001 TYR D 302 PHE 0.014 0.002 PHE C 364 TRP 0.013 0.002 TRP D 222 HIS 0.003 0.001 HIS D 441 Details of bonding type rmsd covalent geometry : bond 0.00414 (16212) covalent geometry : angle 0.67512 (21996) hydrogen bonds : bond 0.04252 ( 552) hydrogen bonds : angle 7.17567 ( 1404) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 246 time to evaluate : 0.579 Fit side-chains REVERT: A 263 GLU cc_start: 0.8626 (pm20) cc_final: 0.8095 (pm20) REVERT: A 409 GLN cc_start: 0.8877 (OUTLIER) cc_final: 0.8318 (mt0) REVERT: A 456 ARG cc_start: 0.7480 (mtm110) cc_final: 0.6388 (mmm160) REVERT: A 482 ARG cc_start: 0.7986 (OUTLIER) cc_final: 0.7432 (ttt90) REVERT: A 501 LEU cc_start: 0.8824 (tp) cc_final: 0.8539 (tm) REVERT: A 502 GLU cc_start: 0.8363 (pp20) cc_final: 0.8107 (pp20) REVERT: B 174 ASN cc_start: 0.8347 (m-40) cc_final: 0.7734 (p0) REVERT: B 278 GLN cc_start: 0.8619 (mm-40) cc_final: 0.8184 (mp10) REVERT: B 294 THR cc_start: 0.8482 (m) cc_final: 0.8113 (t) REVERT: B 312 LYS cc_start: 0.8234 (tttt) cc_final: 0.7699 (ttpt) REVERT: B 372 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7307 (pt0) REVERT: B 376 GLU cc_start: 0.7938 (pt0) cc_final: 0.7627 (tt0) REVERT: B 395 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7508 (mt) REVERT: B 425 LYS cc_start: 0.8141 (tttm) cc_final: 0.7447 (mttm) REVERT: B 456 ARG cc_start: 0.7420 (mtt180) cc_final: 0.7179 (mtt180) REVERT: C 206 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8578 (tp) REVERT: C 209 ARG cc_start: 0.6175 (OUTLIER) cc_final: 0.4554 (ttt90) REVERT: C 273 ASP cc_start: 0.8201 (t0) cc_final: 0.7949 (t0) REVERT: C 278 GLN cc_start: 0.8610 (OUTLIER) cc_final: 0.8036 (mp10) REVERT: C 294 THR cc_start: 0.8519 (m) cc_final: 0.8297 (t) REVERT: C 297 SER cc_start: 0.8769 (m) cc_final: 0.8294 (t) REVERT: C 347 LYS cc_start: 0.7521 (pttt) cc_final: 0.7072 (tptm) REVERT: C 386 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8195 (tp) REVERT: C 416 VAL cc_start: 0.8045 (OUTLIER) cc_final: 0.7793 (m) REVERT: C 425 LYS cc_start: 0.8134 (tttm) cc_final: 0.7496 (mttm) REVERT: D 169 ASP cc_start: 0.8711 (p0) cc_final: 0.8497 (p0) REVERT: D 174 ASN cc_start: 0.8404 (m-40) cc_final: 0.7975 (p0) REVERT: D 246 LEU cc_start: 0.7797 (mp) cc_final: 0.7585 (tm) REVERT: D 278 GLN cc_start: 0.8417 (mm-40) cc_final: 0.8138 (mp10) REVERT: D 312 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7564 (ttpt) REVERT: D 409 GLN cc_start: 0.8956 (mt0) cc_final: 0.8696 (mt0) REVERT: D 417 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.8514 (tt0) REVERT: D 456 ARG cc_start: 0.7446 (mtm110) cc_final: 0.6379 (mmm160) REVERT: E 174 ASN cc_start: 0.8356 (m-40) cc_final: 0.7778 (p0) REVERT: E 278 GLN cc_start: 0.7897 (OUTLIER) cc_final: 0.6795 (mp10) REVERT: E 294 THR cc_start: 0.8494 (OUTLIER) cc_final: 0.8081 (t) REVERT: E 402 SER cc_start: 0.9027 (OUTLIER) cc_final: 0.8794 (p) REVERT: F 271 TYR cc_start: 0.8538 (m-80) cc_final: 0.8253 (m-10) REVERT: F 273 ASP cc_start: 0.8286 (t0) cc_final: 0.8048 (t0) REVERT: F 278 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.7668 (mp10) REVERT: F 297 SER cc_start: 0.8720 (m) cc_final: 0.8392 (t) REVERT: F 347 LYS cc_start: 0.7480 (pttt) cc_final: 0.7016 (tptm) REVERT: F 386 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8173 (tp) outliers start: 86 outliers final: 30 residues processed: 303 average time/residue: 0.5606 time to fit residues: 186.8687 Evaluate side-chains 261 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 216 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 443 GLU Chi-restraints excluded: chain A residue 482 ARG Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 209 ARG Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 278 GLN Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 395 LEU Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 443 GLU Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 312 LYS Chi-restraints excluded: chain D residue 354 ASN Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 417 GLN Chi-restraints excluded: chain D residue 443 GLU Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 278 GLN Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 297 SER Chi-restraints excluded: chain E residue 402 SER Chi-restraints excluded: chain E residue 412 ILE Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain F residue 278 GLN Chi-restraints excluded: chain F residue 354 ASN Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain F residue 416 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 110 optimal weight: 0.7980 chunk 78 optimal weight: 4.9990 chunk 172 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 188 optimal weight: 0.9990 chunk 86 optimal weight: 0.5980 chunk 58 optimal weight: 0.8980 chunk 46 optimal weight: 0.2980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 GLN C 354 ASN C 420 GLN D 316 ASN ** D 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 417 GLN ** E 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 417 GLN F 354 ASN F 420 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.143866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.113414 restraints weight = 20590.783| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 3.17 r_work: 0.3290 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16212 Z= 0.146 Angle : 0.636 9.077 21996 Z= 0.323 Chirality : 0.048 0.148 2586 Planarity : 0.004 0.044 2856 Dihedral : 5.080 30.415 2230 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 5.23 % Allowed : 17.92 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.17), residues: 2094 helix: -2.91 (0.23), residues: 252 sheet: 0.09 (0.20), residues: 684 loop : -1.28 (0.17), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 442 TYR 0.006 0.001 TYR D 302 PHE 0.011 0.001 PHE E 451 TRP 0.011 0.002 TRP C 222 HIS 0.004 0.001 HIS A 441 Details of bonding type rmsd covalent geometry : bond 0.00342 (16212) covalent geometry : angle 0.63574 (21996) hydrogen bonds : bond 0.03822 ( 552) hydrogen bonds : angle 6.97241 ( 1404) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 226 time to evaluate : 0.485 Fit side-chains REVERT: A 208 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7465 (mm-30) REVERT: A 209 ARG cc_start: 0.5919 (OUTLIER) cc_final: 0.4696 (ttt90) REVERT: A 278 GLN cc_start: 0.8190 (OUTLIER) cc_final: 0.7089 (mp10) REVERT: A 302 TYR cc_start: 0.9030 (t80) cc_final: 0.8704 (t80) REVERT: A 376 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7530 (tm-30) REVERT: A 409 GLN cc_start: 0.8919 (OUTLIER) cc_final: 0.8351 (mt0) REVERT: A 456 ARG cc_start: 0.7560 (mtm110) cc_final: 0.6543 (mmm160) REVERT: A 482 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.7526 (ttt90) REVERT: A 501 LEU cc_start: 0.8962 (tp) cc_final: 0.8664 (tm) REVERT: B 174 ASN cc_start: 0.8253 (m-40) cc_final: 0.7631 (p0) REVERT: B 278 GLN cc_start: 0.8610 (mm-40) cc_final: 0.8206 (mp10) REVERT: B 294 THR cc_start: 0.8209 (m) cc_final: 0.7791 (t) REVERT: B 312 LYS cc_start: 0.8290 (tttt) cc_final: 0.7817 (ttpt) REVERT: B 372 GLU cc_start: 0.7627 (mm-30) cc_final: 0.7359 (pt0) REVERT: B 376 GLU cc_start: 0.7731 (pt0) cc_final: 0.7457 (tt0) REVERT: B 425 LYS cc_start: 0.8147 (tttm) cc_final: 0.7460 (mttm) REVERT: B 456 ARG cc_start: 0.7389 (mtt180) cc_final: 0.7082 (mtt180) REVERT: C 209 ARG cc_start: 0.6074 (OUTLIER) cc_final: 0.4348 (ttt90) REVERT: C 273 ASP cc_start: 0.8159 (t0) cc_final: 0.7947 (t0) REVERT: C 278 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.7835 (mp10) REVERT: C 297 SER cc_start: 0.8757 (m) cc_final: 0.8439 (t) REVERT: C 347 LYS cc_start: 0.7617 (pttt) cc_final: 0.7113 (tptm) REVERT: C 425 LYS cc_start: 0.8074 (tttm) cc_final: 0.7468 (mttm) REVERT: C 502 GLU cc_start: 0.8067 (pp20) cc_final: 0.7829 (pp20) REVERT: D 169 ASP cc_start: 0.8688 (p0) cc_final: 0.8442 (p0) REVERT: D 174 ASN cc_start: 0.8383 (m-40) cc_final: 0.7985 (p0) REVERT: D 246 LEU cc_start: 0.7818 (mp) cc_final: 0.7588 (tm) REVERT: D 302 TYR cc_start: 0.9013 (t80) cc_final: 0.8728 (t80) REVERT: D 312 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.7646 (ttpt) REVERT: D 409 GLN cc_start: 0.8921 (mt0) cc_final: 0.8581 (mt0) REVERT: D 456 ARG cc_start: 0.7546 (mtm110) cc_final: 0.6504 (mmm160) REVERT: D 501 LEU cc_start: 0.8883 (tp) cc_final: 0.8410 (tm) REVERT: E 174 ASN cc_start: 0.8201 (m-40) cc_final: 0.7611 (p0) REVERT: E 278 GLN cc_start: 0.8062 (OUTLIER) cc_final: 0.7030 (mp10) REVERT: E 286 GLU cc_start: 0.8005 (tt0) cc_final: 0.7681 (tt0) REVERT: E 402 SER cc_start: 0.9104 (OUTLIER) cc_final: 0.8823 (p) REVERT: E 456 ARG cc_start: 0.7279 (mtt180) cc_final: 0.6211 (mmt180) REVERT: F 271 TYR cc_start: 0.8480 (m-80) cc_final: 0.8226 (m-10) REVERT: F 278 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.7763 (mp10) REVERT: F 294 THR cc_start: 0.8538 (m) cc_final: 0.8209 (t) REVERT: F 297 SER cc_start: 0.8691 (m) cc_final: 0.8238 (t) REVERT: F 347 LYS cc_start: 0.7626 (pttt) cc_final: 0.7070 (tptm) REVERT: F 395 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7726 (mp) outliers start: 92 outliers final: 30 residues processed: 288 average time/residue: 0.5632 time to fit residues: 178.4271 Evaluate side-chains 246 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 203 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 209 ARG Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 376 GLU Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 443 GLU Chi-restraints excluded: chain A residue 482 ARG Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 209 ARG Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 278 GLN Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 395 LEU Chi-restraints excluded: chain C residue 443 GLU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 312 LYS Chi-restraints excluded: chain D residue 354 ASN Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 443 GLU Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 278 GLN Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 402 SER Chi-restraints excluded: chain E residue 412 ILE Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain F residue 278 GLN Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain F residue 416 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 160 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 174 optimal weight: 0.9980 chunk 195 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 180 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 GLN ** C 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 420 GLN ** D 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 417 GLN ** F 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 420 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.140178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.110486 restraints weight = 20969.900| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 3.14 r_work: 0.3245 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16212 Z= 0.183 Angle : 0.661 9.324 21996 Z= 0.334 Chirality : 0.049 0.150 2586 Planarity : 0.005 0.045 2856 Dihedral : 5.067 21.998 2226 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 6.09 % Allowed : 17.97 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.17), residues: 2094 helix: -2.84 (0.24), residues: 252 sheet: 0.33 (0.20), residues: 672 loop : -1.22 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 456 TYR 0.006 0.001 TYR D 302 PHE 0.012 0.002 PHE C 364 TRP 0.014 0.002 TRP D 222 HIS 0.004 0.001 HIS D 441 Details of bonding type rmsd covalent geometry : bond 0.00438 (16212) covalent geometry : angle 0.66139 (21996) hydrogen bonds : bond 0.03915 ( 552) hydrogen bonds : angle 6.97365 ( 1404) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 219 time to evaluate : 0.523 Fit side-chains REVERT: A 206 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8514 (mp) REVERT: A 208 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7549 (mm-30) REVERT: A 209 ARG cc_start: 0.5875 (OUTLIER) cc_final: 0.4489 (ttt90) REVERT: A 271 TYR cc_start: 0.8458 (m-80) cc_final: 0.8185 (m-10) REVERT: A 278 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.7118 (mp10) REVERT: A 302 TYR cc_start: 0.9027 (t80) cc_final: 0.8760 (t80) REVERT: A 376 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7445 (tm-30) REVERT: A 456 ARG cc_start: 0.7570 (mtm110) cc_final: 0.6531 (mmm160) REVERT: A 482 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7623 (ttt90) REVERT: A 491 MET cc_start: 0.8558 (mmm) cc_final: 0.8326 (tpt) REVERT: A 501 LEU cc_start: 0.8961 (tp) cc_final: 0.8728 (tp) REVERT: A 505 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8640 (mm) REVERT: B 174 ASN cc_start: 0.8243 (m-40) cc_final: 0.7637 (p0) REVERT: B 278 GLN cc_start: 0.8681 (mm-40) cc_final: 0.8303 (mp10) REVERT: B 312 LYS cc_start: 0.8262 (tttt) cc_final: 0.7784 (ttpt) REVERT: B 372 GLU cc_start: 0.7609 (mm-30) cc_final: 0.7338 (pt0) REVERT: B 376 GLU cc_start: 0.7780 (pt0) cc_final: 0.7404 (tt0) REVERT: B 425 LYS cc_start: 0.8108 (tttm) cc_final: 0.7454 (mttm) REVERT: B 456 ARG cc_start: 0.7349 (mtt180) cc_final: 0.7045 (mtt180) REVERT: C 206 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8438 (mp) REVERT: C 209 ARG cc_start: 0.6402 (OUTLIER) cc_final: 0.4535 (ttt90) REVERT: C 271 TYR cc_start: 0.8499 (m-80) cc_final: 0.8243 (m-10) REVERT: C 278 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.7885 (mp10) REVERT: C 297 SER cc_start: 0.8745 (m) cc_final: 0.8439 (t) REVERT: C 347 LYS cc_start: 0.7641 (pttt) cc_final: 0.7049 (tptp) REVERT: C 425 LYS cc_start: 0.8107 (tttm) cc_final: 0.7511 (mttm) REVERT: D 169 ASP cc_start: 0.8704 (p0) cc_final: 0.8389 (p0) REVERT: D 174 ASN cc_start: 0.8199 (m-40) cc_final: 0.7769 (p0) REVERT: D 206 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8491 (mp) REVERT: D 209 ARG cc_start: 0.6139 (OUTLIER) cc_final: 0.4670 (ttt90) REVERT: D 246 LEU cc_start: 0.7795 (mp) cc_final: 0.7586 (tm) REVERT: D 278 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.7055 (mp10) REVERT: D 312 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7635 (ttpt) REVERT: D 409 GLN cc_start: 0.9123 (mt0) cc_final: 0.8755 (mt0) REVERT: D 456 ARG cc_start: 0.7556 (mtm110) cc_final: 0.6479 (mmm160) REVERT: D 501 LEU cc_start: 0.8950 (tp) cc_final: 0.8542 (tm) REVERT: E 174 ASN cc_start: 0.8180 (m-40) cc_final: 0.7585 (p0) REVERT: E 278 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.7043 (mp10) REVERT: E 286 GLU cc_start: 0.8071 (tt0) cc_final: 0.7691 (tt0) REVERT: E 456 ARG cc_start: 0.7213 (mtt180) cc_final: 0.6910 (mtt180) REVERT: F 206 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8682 (tp) REVERT: F 271 TYR cc_start: 0.8492 (m-80) cc_final: 0.8244 (m-10) REVERT: F 273 ASP cc_start: 0.8334 (t0) cc_final: 0.8106 (t0) REVERT: F 278 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.7688 (mp10) REVERT: F 294 THR cc_start: 0.8524 (m) cc_final: 0.8190 (t) REVERT: F 297 SER cc_start: 0.8583 (m) cc_final: 0.8149 (t) REVERT: F 347 LYS cc_start: 0.7605 (pttt) cc_final: 0.7001 (tptp) REVERT: F 502 GLU cc_start: 0.8128 (pp20) cc_final: 0.7900 (pp20) outliers start: 107 outliers final: 40 residues processed: 292 average time/residue: 0.5409 time to fit residues: 174.6452 Evaluate side-chains 264 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 207 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 209 ARG Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 376 GLU Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 443 GLU Chi-restraints excluded: chain A residue 482 ARG Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 443 GLU Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 209 ARG Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 278 GLN Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain D residue 278 GLN Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 312 LYS Chi-restraints excluded: chain D residue 354 ASN Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 443 GLU Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 278 GLN Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 412 ILE Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain F residue 162 MET Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 206 LEU Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain F residue 278 GLN Chi-restraints excluded: chain F residue 286 GLU Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 354 ASN Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 452 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 200 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 168 optimal weight: 0.7980 chunk 153 optimal weight: 3.9990 chunk 190 optimal weight: 0.6980 chunk 140 optimal weight: 2.9990 chunk 154 optimal weight: 0.9990 chunk 48 optimal weight: 0.0370 chunk 137 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 overall best weight: 0.6260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 GLN ** C 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 417 GLN ** F 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.142020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.111850 restraints weight = 20654.982| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 3.16 r_work: 0.3267 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.3897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16212 Z= 0.141 Angle : 0.644 8.475 21996 Z= 0.319 Chirality : 0.047 0.146 2586 Planarity : 0.004 0.046 2856 Dihedral : 4.846 21.281 2226 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 5.01 % Allowed : 19.80 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.17), residues: 2094 helix: -2.73 (0.25), residues: 252 sheet: 0.40 (0.20), residues: 672 loop : -1.18 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 442 TYR 0.007 0.001 TYR C 302 PHE 0.009 0.001 PHE C 253 TRP 0.012 0.002 TRP F 222 HIS 0.003 0.001 HIS D 441 Details of bonding type rmsd covalent geometry : bond 0.00335 (16212) covalent geometry : angle 0.64448 (21996) hydrogen bonds : bond 0.03606 ( 552) hydrogen bonds : angle 6.75031 ( 1404) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 224 time to evaluate : 0.597 Fit side-chains REVERT: A 208 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7593 (mm-30) REVERT: A 209 ARG cc_start: 0.5802 (OUTLIER) cc_final: 0.4457 (ttt90) REVERT: A 278 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7058 (mp10) REVERT: A 294 THR cc_start: 0.8572 (m) cc_final: 0.8223 (t) REVERT: A 376 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7433 (tm-30) REVERT: A 456 ARG cc_start: 0.7523 (mtm110) cc_final: 0.6536 (mmm160) REVERT: A 482 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7600 (ttt90) REVERT: A 501 LEU cc_start: 0.8958 (tp) cc_final: 0.8744 (tp) REVERT: A 505 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8607 (mm) REVERT: B 174 ASN cc_start: 0.8234 (m-40) cc_final: 0.7649 (p0) REVERT: B 278 GLN cc_start: 0.8675 (mm-40) cc_final: 0.8260 (mp10) REVERT: B 312 LYS cc_start: 0.8225 (tttt) cc_final: 0.7731 (ttpt) REVERT: B 372 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7322 (pt0) REVERT: B 409 GLN cc_start: 0.8990 (mm-40) cc_final: 0.8358 (mt0) REVERT: B 425 LYS cc_start: 0.8108 (tttm) cc_final: 0.7456 (mttm) REVERT: B 456 ARG cc_start: 0.7319 (mtt180) cc_final: 0.7007 (mtt180) REVERT: C 209 ARG cc_start: 0.6359 (OUTLIER) cc_final: 0.4556 (ttt90) REVERT: C 278 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.7825 (mp10) REVERT: C 297 SER cc_start: 0.8726 (m) cc_final: 0.8424 (t) REVERT: C 347 LYS cc_start: 0.7500 (pttt) cc_final: 0.6934 (tptp) REVERT: C 425 LYS cc_start: 0.8153 (tttm) cc_final: 0.7533 (mttm) REVERT: D 169 ASP cc_start: 0.8656 (p0) cc_final: 0.8336 (p0) REVERT: D 174 ASN cc_start: 0.8139 (m-40) cc_final: 0.7741 (p0) REVERT: D 294 THR cc_start: 0.8544 (m) cc_final: 0.8160 (t) REVERT: D 312 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7635 (ttpt) REVERT: D 409 GLN cc_start: 0.9078 (mt0) cc_final: 0.8783 (mt0) REVERT: D 456 ARG cc_start: 0.7505 (mtm110) cc_final: 0.6481 (mmm160) REVERT: D 501 LEU cc_start: 0.8969 (tp) cc_final: 0.8564 (tm) REVERT: E 174 ASN cc_start: 0.8159 (m-40) cc_final: 0.7606 (p0) REVERT: E 278 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.7018 (mp10) REVERT: E 286 GLU cc_start: 0.8016 (tt0) cc_final: 0.7711 (tt0) REVERT: E 312 LYS cc_start: 0.8293 (tttp) cc_final: 0.7789 (ttpt) REVERT: E 402 SER cc_start: 0.9134 (OUTLIER) cc_final: 0.8863 (p) REVERT: E 409 GLN cc_start: 0.8987 (mm-40) cc_final: 0.8348 (mt0) REVERT: E 456 ARG cc_start: 0.7171 (mtt180) cc_final: 0.6007 (mmp-170) REVERT: F 271 TYR cc_start: 0.8505 (m-80) cc_final: 0.8254 (m-10) REVERT: F 294 THR cc_start: 0.8363 (m) cc_final: 0.7993 (t) REVERT: F 297 SER cc_start: 0.8641 (m) cc_final: 0.8205 (t) REVERT: F 347 LYS cc_start: 0.7524 (pttt) cc_final: 0.6894 (tptp) outliers start: 88 outliers final: 40 residues processed: 278 average time/residue: 0.5637 time to fit residues: 173.6208 Evaluate side-chains 264 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 213 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 209 ARG Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 376 GLU Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 443 GLU Chi-restraints excluded: chain A residue 482 ARG Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain C residue 162 MET Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 209 ARG Chi-restraints excluded: chain C residue 278 GLN Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain D residue 162 MET Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 312 LYS Chi-restraints excluded: chain D residue 354 ASN Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 443 GLU Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 278 GLN Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 402 SER Chi-restraints excluded: chain E residue 412 ILE Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain F residue 162 MET Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 354 ASN Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 452 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 65 optimal weight: 5.9990 chunk 100 optimal weight: 8.9990 chunk 132 optimal weight: 0.5980 chunk 206 optimal weight: 6.9990 chunk 134 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 200 optimal weight: 0.4980 chunk 15 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 440 GLN ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 420 GLN ** D 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 417 GLN ** F 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.141069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.110845 restraints weight = 20778.909| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 3.22 r_work: 0.3250 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.4038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16212 Z= 0.155 Angle : 0.660 9.152 21996 Z= 0.327 Chirality : 0.048 0.147 2586 Planarity : 0.004 0.044 2856 Dihedral : 4.852 21.950 2226 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 5.29 % Allowed : 20.31 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.17), residues: 2094 helix: -2.76 (0.24), residues: 258 sheet: 0.45 (0.20), residues: 672 loop : -1.14 (0.17), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 442 TYR 0.007 0.001 TYR D 302 PHE 0.011 0.001 PHE E 451 TRP 0.011 0.002 TRP C 222 HIS 0.004 0.001 HIS D 441 Details of bonding type rmsd covalent geometry : bond 0.00371 (16212) covalent geometry : angle 0.66037 (21996) hydrogen bonds : bond 0.03629 ( 552) hydrogen bonds : angle 6.74169 ( 1404) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 221 time to evaluate : 0.591 Fit side-chains REVERT: A 208 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7488 (mm-30) REVERT: A 209 ARG cc_start: 0.5814 (OUTLIER) cc_final: 0.4463 (ttt90) REVERT: A 271 TYR cc_start: 0.8396 (m-80) cc_final: 0.8135 (m-10) REVERT: A 278 GLN cc_start: 0.8110 (OUTLIER) cc_final: 0.7019 (mp10) REVERT: A 294 THR cc_start: 0.8501 (m) cc_final: 0.8130 (t) REVERT: A 302 TYR cc_start: 0.8953 (t80) cc_final: 0.8622 (t80) REVERT: A 376 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7371 (tm-30) REVERT: A 417 GLN cc_start: 0.8685 (tt0) cc_final: 0.8417 (tt0) REVERT: A 456 ARG cc_start: 0.7483 (mtm110) cc_final: 0.6462 (mmm160) REVERT: A 482 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.7561 (ttt90) REVERT: A 491 MET cc_start: 0.8534 (mmm) cc_final: 0.8268 (mmm) REVERT: A 501 LEU cc_start: 0.8942 (tp) cc_final: 0.8735 (tp) REVERT: A 505 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8575 (mm) REVERT: B 174 ASN cc_start: 0.8291 (m-40) cc_final: 0.7689 (p0) REVERT: B 278 GLN cc_start: 0.8657 (mm-40) cc_final: 0.8222 (mp10) REVERT: B 312 LYS cc_start: 0.8125 (tttt) cc_final: 0.7582 (ttpt) REVERT: B 376 GLU cc_start: 0.7663 (pt0) cc_final: 0.7293 (tt0) REVERT: B 409 GLN cc_start: 0.8965 (mm-40) cc_final: 0.8406 (mt0) REVERT: B 411 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7667 (tt) REVERT: B 425 LYS cc_start: 0.8088 (tttm) cc_final: 0.7381 (mttm) REVERT: B 456 ARG cc_start: 0.7231 (mtt180) cc_final: 0.6925 (mtt180) REVERT: C 209 ARG cc_start: 0.6390 (OUTLIER) cc_final: 0.4568 (ttt90) REVERT: C 233 ILE cc_start: 0.5150 (OUTLIER) cc_final: 0.4748 (mp) REVERT: C 278 GLN cc_start: 0.8307 (OUTLIER) cc_final: 0.7800 (mp10) REVERT: C 284 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8061 (mtmm) REVERT: C 297 SER cc_start: 0.8675 (m) cc_final: 0.8373 (t) REVERT: C 347 LYS cc_start: 0.7547 (pttt) cc_final: 0.6881 (tptp) REVERT: C 425 LYS cc_start: 0.8100 (tttm) cc_final: 0.7428 (mttm) REVERT: D 169 ASP cc_start: 0.8661 (p0) cc_final: 0.8320 (p0) REVERT: D 174 ASN cc_start: 0.8198 (m-40) cc_final: 0.7810 (p0) REVERT: D 209 ARG cc_start: 0.6376 (OUTLIER) cc_final: 0.4840 (ttt90) REVERT: D 271 TYR cc_start: 0.8407 (m-80) cc_final: 0.8128 (m-10) REVERT: D 278 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7068 (mp10) REVERT: D 294 THR cc_start: 0.8474 (m) cc_final: 0.8067 (t) REVERT: D 312 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7562 (ttpt) REVERT: D 409 GLN cc_start: 0.9083 (mt0) cc_final: 0.8783 (mt0) REVERT: D 456 ARG cc_start: 0.7478 (mtm110) cc_final: 0.6412 (mmm160) REVERT: D 501 LEU cc_start: 0.8908 (tp) cc_final: 0.8508 (tm) REVERT: E 174 ASN cc_start: 0.8224 (m-40) cc_final: 0.7617 (p0) REVERT: E 209 ARG cc_start: 0.6780 (OUTLIER) cc_final: 0.4972 (ttt180) REVERT: E 278 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.7032 (mp10) REVERT: E 286 GLU cc_start: 0.8018 (tt0) cc_final: 0.7693 (tt0) REVERT: E 312 LYS cc_start: 0.8171 (tttp) cc_final: 0.7675 (ttpt) REVERT: E 402 SER cc_start: 0.9091 (OUTLIER) cc_final: 0.8820 (p) REVERT: E 409 GLN cc_start: 0.8946 (mm-40) cc_final: 0.8317 (mt0) REVERT: E 411 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7574 (tt) REVERT: F 271 TYR cc_start: 0.8442 (m-80) cc_final: 0.8179 (m-10) REVERT: F 278 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.7673 (mp10) REVERT: F 294 THR cc_start: 0.8403 (m) cc_final: 0.8036 (t) REVERT: F 297 SER cc_start: 0.8488 (m) cc_final: 0.8060 (t) REVERT: F 347 LYS cc_start: 0.7508 (pttt) cc_final: 0.6830 (tptp) outliers start: 93 outliers final: 44 residues processed: 282 average time/residue: 0.5607 time to fit residues: 174.3021 Evaluate side-chains 272 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 209 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 209 ARG Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 376 GLU Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 443 GLU Chi-restraints excluded: chain A residue 482 ARG Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 209 ARG Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 278 GLN Chi-restraints excluded: chain C residue 284 LYS Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain D residue 278 GLN Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 312 LYS Chi-restraints excluded: chain D residue 354 ASN Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 443 GLU Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 209 ARG Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 278 GLN Chi-restraints excluded: chain E residue 297 SER Chi-restraints excluded: chain E residue 359 LEU Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 402 SER Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 412 ILE Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 443 GLU Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain F residue 278 GLN Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 354 ASN Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 452 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 117 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 162 optimal weight: 2.9990 chunk 116 optimal weight: 0.5980 chunk 209 optimal weight: 0.5980 chunk 159 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 144 optimal weight: 0.9980 chunk 182 optimal weight: 2.9990 chunk 147 optimal weight: 7.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 420 GLN ** D 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 417 GLN ** F 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.140537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.110674 restraints weight = 20904.820| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 3.16 r_work: 0.3246 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16212 Z= 0.159 Angle : 0.663 9.179 21996 Z= 0.329 Chirality : 0.048 0.147 2586 Planarity : 0.004 0.044 2856 Dihedral : 4.839 21.901 2226 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 5.35 % Allowed : 20.82 % Favored : 73.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.17), residues: 2094 helix: -2.80 (0.24), residues: 258 sheet: 0.39 (0.20), residues: 684 loop : -1.08 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 456 TYR 0.007 0.001 TYR A 302 PHE 0.010 0.001 PHE E 451 TRP 0.011 0.002 TRP F 222 HIS 0.004 0.001 HIS D 441 Details of bonding type rmsd covalent geometry : bond 0.00380 (16212) covalent geometry : angle 0.66317 (21996) hydrogen bonds : bond 0.03623 ( 552) hydrogen bonds : angle 6.71985 ( 1404) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 224 time to evaluate : 0.401 Fit side-chains REVERT: A 208 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7520 (mm-30) REVERT: A 209 ARG cc_start: 0.5856 (OUTLIER) cc_final: 0.4529 (ttt90) REVERT: A 271 TYR cc_start: 0.8486 (m-80) cc_final: 0.8263 (m-10) REVERT: A 278 GLN cc_start: 0.8107 (OUTLIER) cc_final: 0.7037 (mp10) REVERT: A 294 THR cc_start: 0.8520 (m) cc_final: 0.8144 (t) REVERT: A 376 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7388 (tm-30) REVERT: A 417 GLN cc_start: 0.8697 (tt0) cc_final: 0.8414 (tt0) REVERT: A 456 ARG cc_start: 0.7483 (mtm110) cc_final: 0.6476 (mmm160) REVERT: A 482 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.7588 (ttt90) REVERT: A 505 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8604 (mm) REVERT: B 174 ASN cc_start: 0.8270 (m-40) cc_final: 0.7693 (p0) REVERT: B 278 GLN cc_start: 0.8673 (mm-40) cc_final: 0.8248 (mp10) REVERT: B 312 LYS cc_start: 0.8152 (tttt) cc_final: 0.7615 (ttpt) REVERT: B 409 GLN cc_start: 0.8979 (mm-40) cc_final: 0.8476 (mt0) REVERT: B 411 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7736 (tt) REVERT: B 425 LYS cc_start: 0.8130 (tttm) cc_final: 0.7474 (mttm) REVERT: B 456 ARG cc_start: 0.7239 (mtt180) cc_final: 0.6931 (mtt180) REVERT: C 209 ARG cc_start: 0.6452 (OUTLIER) cc_final: 0.4638 (ttt90) REVERT: C 233 ILE cc_start: 0.5157 (OUTLIER) cc_final: 0.4730 (mp) REVERT: C 271 TYR cc_start: 0.8449 (m-80) cc_final: 0.8177 (m-10) REVERT: C 278 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.7835 (mp10) REVERT: C 284 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8114 (mtmm) REVERT: C 297 SER cc_start: 0.8699 (m) cc_final: 0.8402 (t) REVERT: C 347 LYS cc_start: 0.7541 (pttt) cc_final: 0.6854 (tptp) REVERT: C 425 LYS cc_start: 0.8137 (tttm) cc_final: 0.7474 (mttm) REVERT: D 169 ASP cc_start: 0.8650 (p0) cc_final: 0.8308 (p0) REVERT: D 209 ARG cc_start: 0.6410 (OUTLIER) cc_final: 0.4868 (ttt90) REVERT: D 271 TYR cc_start: 0.8440 (m-80) cc_final: 0.8090 (m-10) REVERT: D 278 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.7154 (mp10) REVERT: D 294 THR cc_start: 0.8481 (m) cc_final: 0.8072 (t) REVERT: D 312 LYS cc_start: 0.8187 (OUTLIER) cc_final: 0.7595 (ttpt) REVERT: D 409 GLN cc_start: 0.9103 (mt0) cc_final: 0.8868 (mt0) REVERT: D 456 ARG cc_start: 0.7489 (mtm110) cc_final: 0.6426 (mmm160) REVERT: D 501 LEU cc_start: 0.8923 (tp) cc_final: 0.8529 (tm) REVERT: E 174 ASN cc_start: 0.8231 (m-40) cc_final: 0.7654 (p0) REVERT: E 209 ARG cc_start: 0.6804 (OUTLIER) cc_final: 0.4991 (ttt180) REVERT: E 278 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.7053 (mp10) REVERT: E 286 GLU cc_start: 0.8031 (tt0) cc_final: 0.7713 (tt0) REVERT: E 312 LYS cc_start: 0.8183 (tttp) cc_final: 0.7712 (ttpt) REVERT: E 402 SER cc_start: 0.9108 (OUTLIER) cc_final: 0.8831 (p) REVERT: E 409 GLN cc_start: 0.8962 (mm-40) cc_final: 0.8315 (mt0) REVERT: E 411 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7610 (tt) REVERT: E 456 ARG cc_start: 0.7085 (mtt180) cc_final: 0.6088 (mmt180) REVERT: F 206 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8605 (tp) REVERT: F 233 ILE cc_start: 0.5088 (OUTLIER) cc_final: 0.4665 (mp) REVERT: F 271 TYR cc_start: 0.8470 (m-80) cc_final: 0.8204 (m-10) REVERT: F 278 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.7627 (mp10) REVERT: F 294 THR cc_start: 0.8423 (m) cc_final: 0.8061 (t) REVERT: F 297 SER cc_start: 0.8497 (m) cc_final: 0.8074 (t) REVERT: F 347 LYS cc_start: 0.7529 (pttt) cc_final: 0.6845 (tptp) outliers start: 94 outliers final: 48 residues processed: 286 average time/residue: 0.5390 time to fit residues: 170.3309 Evaluate side-chains 283 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 214 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 209 ARG Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 376 GLU Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 443 GLU Chi-restraints excluded: chain A residue 482 ARG Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 209 ARG Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 278 GLN Chi-restraints excluded: chain C residue 284 LYS Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain D residue 278 GLN Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 312 LYS Chi-restraints excluded: chain D residue 354 ASN Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 443 GLU Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 209 ARG Chi-restraints excluded: chain E residue 278 GLN Chi-restraints excluded: chain E residue 297 SER Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 402 SER Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 412 ILE Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 443 GLU Chi-restraints excluded: chain F residue 162 MET Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 206 LEU Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 278 GLN Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 354 ASN Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 452 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 22 optimal weight: 1.9990 chunk 173 optimal weight: 0.0020 chunk 81 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 195 optimal weight: 0.9980 chunk 78 optimal weight: 7.9990 chunk 176 optimal weight: 3.9990 chunk 124 optimal weight: 7.9990 chunk 123 optimal weight: 0.9990 chunk 133 optimal weight: 0.6980 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 440 GLN ** D 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 417 GLN ** F 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.140972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.110889 restraints weight = 20573.287| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 3.13 r_work: 0.3257 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.4218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16212 Z= 0.152 Angle : 0.675 10.145 21996 Z= 0.333 Chirality : 0.048 0.147 2586 Planarity : 0.004 0.044 2856 Dihedral : 4.814 21.751 2226 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 4.61 % Allowed : 21.79 % Favored : 73.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.17), residues: 2094 helix: -2.81 (0.24), residues: 258 sheet: 0.39 (0.20), residues: 684 loop : -1.05 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 442 TYR 0.007 0.001 TYR D 302 PHE 0.011 0.001 PHE E 451 TRP 0.012 0.002 TRP F 222 HIS 0.004 0.001 HIS D 441 Details of bonding type rmsd covalent geometry : bond 0.00364 (16212) covalent geometry : angle 0.67509 (21996) hydrogen bonds : bond 0.03537 ( 552) hydrogen bonds : angle 6.66512 ( 1404) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 222 time to evaluate : 0.413 Fit side-chains REVERT: A 208 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7557 (mm-30) REVERT: A 209 ARG cc_start: 0.5890 (OUTLIER) cc_final: 0.4572 (ttt90) REVERT: A 271 TYR cc_start: 0.8524 (m-80) cc_final: 0.8307 (m-10) REVERT: A 278 GLN cc_start: 0.8151 (OUTLIER) cc_final: 0.7083 (mp10) REVERT: A 294 THR cc_start: 0.8531 (m) cc_final: 0.8133 (t) REVERT: A 376 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7415 (tm-30) REVERT: A 417 GLN cc_start: 0.8722 (tt0) cc_final: 0.8466 (tt0) REVERT: A 456 ARG cc_start: 0.7556 (mtm110) cc_final: 0.6549 (mmm160) REVERT: A 482 ARG cc_start: 0.8137 (OUTLIER) cc_final: 0.7602 (ttt90) REVERT: A 501 LEU cc_start: 0.9007 (tp) cc_final: 0.8651 (tm) REVERT: B 174 ASN cc_start: 0.8268 (m-40) cc_final: 0.7727 (p0) REVERT: B 259 SER cc_start: 0.8127 (m) cc_final: 0.7671 (p) REVERT: B 278 GLN cc_start: 0.8693 (mm-40) cc_final: 0.8273 (mp10) REVERT: B 312 LYS cc_start: 0.8185 (tttt) cc_final: 0.7673 (ttpt) REVERT: B 409 GLN cc_start: 0.9004 (mm-40) cc_final: 0.8527 (mt0) REVERT: B 411 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7787 (tt) REVERT: B 425 LYS cc_start: 0.8159 (tttm) cc_final: 0.7547 (mttm) REVERT: B 456 ARG cc_start: 0.7316 (mtt180) cc_final: 0.7033 (mtt180) REVERT: C 209 ARG cc_start: 0.6503 (OUTLIER) cc_final: 0.4662 (ttt90) REVERT: C 233 ILE cc_start: 0.5163 (OUTLIER) cc_final: 0.4725 (mp) REVERT: C 278 GLN cc_start: 0.8371 (OUTLIER) cc_final: 0.7886 (mp10) REVERT: C 284 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8207 (mtmm) REVERT: C 297 SER cc_start: 0.8727 (m) cc_final: 0.8438 (t) REVERT: C 347 LYS cc_start: 0.7562 (pttt) cc_final: 0.6905 (tptp) REVERT: C 425 LYS cc_start: 0.8107 (tttm) cc_final: 0.7553 (mttm) REVERT: D 169 ASP cc_start: 0.8630 (p0) cc_final: 0.8299 (p0) REVERT: D 209 ARG cc_start: 0.6346 (OUTLIER) cc_final: 0.4767 (ttt90) REVERT: D 271 TYR cc_start: 0.8476 (m-80) cc_final: 0.8210 (m-10) REVERT: D 278 GLN cc_start: 0.8158 (OUTLIER) cc_final: 0.7178 (mp10) REVERT: D 294 THR cc_start: 0.8551 (m) cc_final: 0.8145 (t) REVERT: D 297 SER cc_start: 0.8568 (m) cc_final: 0.8136 (t) REVERT: D 312 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.7672 (ttpt) REVERT: D 456 ARG cc_start: 0.7508 (mtm110) cc_final: 0.6439 (mmt180) REVERT: D 501 LEU cc_start: 0.8959 (tp) cc_final: 0.8604 (tm) REVERT: E 174 ASN cc_start: 0.8200 (m-40) cc_final: 0.7669 (p0) REVERT: E 209 ARG cc_start: 0.6858 (OUTLIER) cc_final: 0.5013 (ttt180) REVERT: E 259 SER cc_start: 0.7985 (m) cc_final: 0.7561 (p) REVERT: E 278 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.7092 (mp10) REVERT: E 286 GLU cc_start: 0.8027 (tt0) cc_final: 0.7714 (tt0) REVERT: E 312 LYS cc_start: 0.8227 (tttp) cc_final: 0.7773 (ttpt) REVERT: E 402 SER cc_start: 0.9139 (OUTLIER) cc_final: 0.8862 (p) REVERT: E 409 GLN cc_start: 0.8987 (mm-40) cc_final: 0.8364 (mt0) REVERT: E 411 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7657 (tt) REVERT: E 456 ARG cc_start: 0.7124 (mtt180) cc_final: 0.6830 (mtt180) REVERT: F 233 ILE cc_start: 0.5093 (OUTLIER) cc_final: 0.4660 (mp) REVERT: F 271 TYR cc_start: 0.8519 (m-80) cc_final: 0.8267 (m-10) REVERT: F 278 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.7662 (mp10) REVERT: F 294 THR cc_start: 0.8471 (m) cc_final: 0.8136 (t) REVERT: F 297 SER cc_start: 0.8625 (m) cc_final: 0.8195 (t) REVERT: F 347 LYS cc_start: 0.7518 (pttt) cc_final: 0.6829 (tptm) outliers start: 81 outliers final: 48 residues processed: 277 average time/residue: 0.5278 time to fit residues: 161.8809 Evaluate side-chains 279 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 212 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 209 ARG Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 376 GLU Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 443 GLU Chi-restraints excluded: chain A residue 482 ARG Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 209 ARG Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 278 GLN Chi-restraints excluded: chain C residue 284 LYS Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain D residue 278 GLN Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 312 LYS Chi-restraints excluded: chain D residue 354 ASN Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 443 GLU Chi-restraints excluded: chain D residue 502 GLU Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 209 ARG Chi-restraints excluded: chain E residue 278 GLN Chi-restraints excluded: chain E residue 297 SER Chi-restraints excluded: chain E residue 359 LEU Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 402 SER Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 412 ILE Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 443 GLU Chi-restraints excluded: chain F residue 162 MET Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 278 GLN Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 354 ASN Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 452 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 131 optimal weight: 1.9990 chunk 129 optimal weight: 0.3980 chunk 169 optimal weight: 0.9980 chunk 135 optimal weight: 8.9990 chunk 105 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 chunk 142 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 417 GLN ** F 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.140905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.111043 restraints weight = 20669.853| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 3.15 r_work: 0.3253 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.4261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16212 Z= 0.150 Angle : 0.674 9.879 21996 Z= 0.333 Chirality : 0.048 0.147 2586 Planarity : 0.004 0.050 2856 Dihedral : 4.802 21.646 2226 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 4.32 % Allowed : 22.75 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.17), residues: 2094 helix: -2.87 (0.24), residues: 258 sheet: 0.39 (0.20), residues: 684 loop : -1.03 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 442 TYR 0.008 0.001 TYR D 302 PHE 0.011 0.001 PHE E 451 TRP 0.012 0.002 TRP F 222 HIS 0.004 0.001 HIS D 441 Details of bonding type rmsd covalent geometry : bond 0.00359 (16212) covalent geometry : angle 0.67360 (21996) hydrogen bonds : bond 0.03504 ( 552) hydrogen bonds : angle 6.69406 ( 1404) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 222 time to evaluate : 0.620 Fit side-chains REVERT: A 208 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7524 (mm-30) REVERT: A 209 ARG cc_start: 0.5874 (OUTLIER) cc_final: 0.4546 (ttt90) REVERT: A 271 TYR cc_start: 0.8484 (m-80) cc_final: 0.8257 (m-10) REVERT: A 278 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.7091 (mp10) REVERT: A 294 THR cc_start: 0.8459 (m) cc_final: 0.8045 (t) REVERT: A 376 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7364 (tm-30) REVERT: A 417 GLN cc_start: 0.8713 (tt0) cc_final: 0.8462 (tt0) REVERT: A 456 ARG cc_start: 0.7498 (mtm110) cc_final: 0.6550 (mmm160) REVERT: A 482 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.7530 (ttt90) REVERT: A 501 LEU cc_start: 0.8925 (tp) cc_final: 0.8462 (tm) REVERT: B 174 ASN cc_start: 0.8227 (m-40) cc_final: 0.7694 (p0) REVERT: B 259 SER cc_start: 0.8088 (m) cc_final: 0.7630 (p) REVERT: B 278 GLN cc_start: 0.8678 (mm-40) cc_final: 0.8247 (mp10) REVERT: B 294 THR cc_start: 0.8132 (m) cc_final: 0.7678 (t) REVERT: B 312 LYS cc_start: 0.8147 (tttt) cc_final: 0.7617 (ttpt) REVERT: B 409 GLN cc_start: 0.8983 (mm-40) cc_final: 0.8487 (mt0) REVERT: B 411 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7704 (tt) REVERT: B 425 LYS cc_start: 0.8196 (tttm) cc_final: 0.7490 (mttm) REVERT: B 456 ARG cc_start: 0.7269 (mtt180) cc_final: 0.6982 (mtt180) REVERT: C 209 ARG cc_start: 0.6513 (OUTLIER) cc_final: 0.4677 (ttt90) REVERT: C 233 ILE cc_start: 0.5127 (OUTLIER) cc_final: 0.4692 (mp) REVERT: C 278 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.7849 (mp10) REVERT: C 284 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8154 (mtmm) REVERT: C 297 SER cc_start: 0.8702 (m) cc_final: 0.8410 (t) REVERT: C 347 LYS cc_start: 0.7562 (pttt) cc_final: 0.6885 (tptp) REVERT: C 425 LYS cc_start: 0.8072 (tttm) cc_final: 0.7508 (mttm) REVERT: C 502 GLU cc_start: 0.8812 (tt0) cc_final: 0.8297 (tp30) REVERT: D 169 ASP cc_start: 0.8639 (p0) cc_final: 0.8298 (p0) REVERT: D 209 ARG cc_start: 0.6312 (OUTLIER) cc_final: 0.4732 (ttt90) REVERT: D 271 TYR cc_start: 0.8453 (m-80) cc_final: 0.8201 (m-10) REVERT: D 278 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.7163 (mp10) REVERT: D 294 THR cc_start: 0.8512 (m) cc_final: 0.8094 (t) REVERT: D 297 SER cc_start: 0.8536 (m) cc_final: 0.8095 (t) REVERT: D 456 ARG cc_start: 0.7464 (mtm110) cc_final: 0.6504 (mmm160) REVERT: D 501 LEU cc_start: 0.8564 (tp) cc_final: 0.8265 (tm) REVERT: D 505 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8572 (mm) REVERT: E 174 ASN cc_start: 0.8178 (m-40) cc_final: 0.7645 (p0) REVERT: E 209 ARG cc_start: 0.6848 (OUTLIER) cc_final: 0.5002 (ttt180) REVERT: E 259 SER cc_start: 0.8034 (m) cc_final: 0.7634 (p) REVERT: E 278 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7064 (mp10) REVERT: E 286 GLU cc_start: 0.8034 (tt0) cc_final: 0.7714 (tt0) REVERT: E 402 SER cc_start: 0.9121 (OUTLIER) cc_final: 0.8841 (p) REVERT: E 409 GLN cc_start: 0.8967 (mm-40) cc_final: 0.8476 (mt0) REVERT: E 411 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7581 (tt) REVERT: E 456 ARG cc_start: 0.7067 (mtt180) cc_final: 0.6767 (mtt180) REVERT: F 233 ILE cc_start: 0.5071 (OUTLIER) cc_final: 0.4616 (mp) REVERT: F 271 TYR cc_start: 0.8473 (m-80) cc_final: 0.8206 (m-10) REVERT: F 278 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.7651 (mp10) REVERT: F 294 THR cc_start: 0.8412 (m) cc_final: 0.8057 (t) REVERT: F 297 SER cc_start: 0.8582 (m) cc_final: 0.8148 (t) REVERT: F 347 LYS cc_start: 0.7518 (pttt) cc_final: 0.6829 (tptp) outliers start: 76 outliers final: 47 residues processed: 269 average time/residue: 0.5457 time to fit residues: 162.2389 Evaluate side-chains 283 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 217 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 209 ARG Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 376 GLU Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 443 GLU Chi-restraints excluded: chain A residue 482 ARG Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 209 ARG Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 278 GLN Chi-restraints excluded: chain C residue 284 LYS Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain D residue 278 GLN Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 354 ASN Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 443 GLU Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 209 ARG Chi-restraints excluded: chain E residue 278 GLN Chi-restraints excluded: chain E residue 297 SER Chi-restraints excluded: chain E residue 359 LEU Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 402 SER Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 412 ILE Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 443 GLU Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 278 GLN Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 354 ASN Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 452 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 89 optimal weight: 0.6980 chunk 46 optimal weight: 0.0870 chunk 181 optimal weight: 0.9980 chunk 96 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 165 optimal weight: 0.9980 chunk 28 optimal weight: 0.0870 chunk 121 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 overall best weight: 0.5136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 417 GLN ** F 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.142386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.112397 restraints weight = 20538.529| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 3.16 r_work: 0.3274 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.4329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16212 Z= 0.131 Angle : 0.661 9.988 21996 Z= 0.325 Chirality : 0.047 0.143 2586 Planarity : 0.004 0.055 2856 Dihedral : 4.672 21.405 2226 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 4.10 % Allowed : 23.09 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.18), residues: 2094 helix: -2.79 (0.25), residues: 258 sheet: 0.42 (0.20), residues: 684 loop : -0.97 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 442 TYR 0.008 0.001 TYR D 302 PHE 0.010 0.001 PHE E 451 TRP 0.013 0.002 TRP F 222 HIS 0.004 0.001 HIS D 441 Details of bonding type rmsd covalent geometry : bond 0.00311 (16212) covalent geometry : angle 0.66093 (21996) hydrogen bonds : bond 0.03371 ( 552) hydrogen bonds : angle 6.56312 ( 1404) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4620.63 seconds wall clock time: 79 minutes 28.04 seconds (4768.04 seconds total)