Starting phenix.real_space_refine on Sat Mar 7 12:08:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ey6_31321/03_2026/7ey6_31321.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ey6_31321/03_2026/7ey6_31321.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ey6_31321/03_2026/7ey6_31321.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ey6_31321/03_2026/7ey6_31321.map" model { file = "/net/cci-nas-00/data/ceres_data/7ey6_31321/03_2026/7ey6_31321.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ey6_31321/03_2026/7ey6_31321.cif" } resolution = 4.3 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 ------------------------------------------------------------------------------- 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= 0.013 sd= 2.048 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 204 5.16 5 C 27756 2.51 5 N 7428 2.21 5 O 8640 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 168 residue(s): 0.05s 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: 44028 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3669 Classifications: {'peptide': 469} Link IDs: {'PTRANS': 22, 'TRANS': 446} Chain breaks: 1 Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L Time building chain proxies: 5.38, per 1000 atoms: 0.12 Number of scatterers: 44028 At special positions: 0 Unit cell: (189.23, 189.23, 118.11, 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 204 16.00 O 8640 8.00 N 7428 7.00 C 27756 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: 3.67 Conformation dependent library (CDL) restraints added in 1.9 seconds 11160 Ramachandran restraints generated. 5580 Oldfield, 0 Emsley, 5580 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10512 Finding SS restraints... Secondary structure from input PDB file: 204 helices and 60 sheets defined 51.8% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.52 Creating SS restraints... Processing helix chain 'A' and resid 6 through 10 removed outlier: 3.851A pdb=" N ALA A 9 " --> pdb=" O THR A 6 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU A 10 " --> pdb=" O GLY A 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 6 through 10' Processing helix chain 'A' and resid 12 through 39 removed outlier: 3.647A pdb=" N ASP A 23 " --> pdb=" O ARG A 19 " (cutoff:3.500A) Proline residue: A 26 - end of helix Processing helix chain 'A' and resid 40 through 43 removed outlier: 3.696A pdb=" N PHE A 43 " --> pdb=" O PRO A 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 40 through 43' Processing helix chain 'A' and resid 60 through 78 Processing helix chain 'A' and resid 91 through 96 Processing helix chain 'A' and resid 99 through 124 removed outlier: 3.717A pdb=" N LEU A 103 " --> pdb=" O ASP A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 140 Processing helix chain 'A' and resid 191 through 202 removed outlier: 3.521A pdb=" N GLN A 201 " --> pdb=" O ALA A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 272 removed outlier: 4.016A pdb=" N GLU A 271 " --> pdb=" O SER A 267 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N TYR A 272 " --> pdb=" O TYR A 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 267 through 272' Processing helix chain 'A' and resid 272 through 295 removed outlier: 3.599A pdb=" N LYS A 295 " --> pdb=" O MET A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 314 removed outlier: 4.268A pdb=" N LEU A 311 " --> pdb=" O GLN A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 357 Processing helix chain 'A' and resid 372 through 385 removed outlier: 4.086A pdb=" N TYR A 376 " --> pdb=" O GLU A 372 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER A 379 " --> pdb=" O ARG A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 396 removed outlier: 3.609A pdb=" N ILE A 391 " --> pdb=" O GLY A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 412 removed outlier: 3.523A pdb=" N GLN A 409 " --> pdb=" O LEU A 405 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA A 410 " --> pdb=" O LYS A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 451 Processing helix chain 'A' and resid 462 through 474 removed outlier: 4.163A pdb=" N ILE A 474 " --> pdb=" O ILE A 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 10 removed outlier: 3.852A pdb=" N ALA B 9 " --> pdb=" O THR B 6 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU B 10 " --> pdb=" O GLY B 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 6 through 10' Processing helix chain 'B' and resid 12 through 39 removed outlier: 3.646A pdb=" N ASP B 23 " --> pdb=" O ARG B 19 " (cutoff:3.500A) Proline residue: B 26 - end of helix Processing helix chain 'B' and resid 40 through 43 removed outlier: 3.696A pdb=" N PHE B 43 " --> pdb=" O PRO B 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 40 through 43' Processing helix chain 'B' and resid 60 through 78 Processing helix chain 'B' and resid 91 through 96 Processing helix chain 'B' and resid 99 through 124 removed outlier: 3.716A pdb=" N LEU B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 140 Processing helix chain 'B' and resid 191 through 202 removed outlier: 3.520A pdb=" N GLN B 201 " --> pdb=" O ALA B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 272 removed outlier: 4.018A pdb=" N GLU B 271 " --> pdb=" O SER B 267 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N TYR B 272 " --> pdb=" O TYR B 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 267 through 272' Processing helix chain 'B' and resid 272 through 295 removed outlier: 3.599A pdb=" N LYS B 295 " --> pdb=" O MET B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 314 removed outlier: 4.269A pdb=" N LEU B 311 " --> pdb=" O GLN B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 357 Processing helix chain 'B' and resid 372 through 385 removed outlier: 4.086A pdb=" N TYR B 376 " --> pdb=" O GLU B 372 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER B 379 " --> pdb=" O ARG B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 396 removed outlier: 3.609A pdb=" N ILE B 391 " --> pdb=" O GLY B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 412 removed outlier: 3.523A pdb=" N GLN B 409 " --> pdb=" O LEU B 405 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA B 410 " --> pdb=" O LYS B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 451 Processing helix chain 'B' and resid 462 through 474 removed outlier: 4.161A pdb=" N ILE B 474 " --> pdb=" O ILE B 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 10 removed outlier: 3.851A pdb=" N ALA C 9 " --> pdb=" O THR C 6 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU C 10 " --> pdb=" O GLY C 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 6 through 10' Processing helix chain 'C' and resid 12 through 39 removed outlier: 3.646A pdb=" N ASP C 23 " --> pdb=" O ARG C 19 " (cutoff:3.500A) Proline residue: C 26 - end of helix Processing helix chain 'C' and resid 40 through 43 removed outlier: 3.696A pdb=" N PHE C 43 " --> pdb=" O PRO C 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 40 through 43' Processing helix chain 'C' and resid 60 through 78 Processing helix chain 'C' and resid 91 through 96 Processing helix chain 'C' and resid 99 through 124 removed outlier: 3.717A pdb=" N LEU C 103 " --> pdb=" O ASP C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 140 Processing helix chain 'C' and resid 191 through 202 removed outlier: 3.521A pdb=" N GLN C 201 " --> pdb=" O ALA C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 272 removed outlier: 4.015A pdb=" N GLU C 271 " --> pdb=" O SER C 267 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N TYR C 272 " --> pdb=" O TYR C 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 267 through 272' Processing helix chain 'C' and resid 272 through 295 removed outlier: 3.600A pdb=" N LYS C 295 " --> pdb=" O MET C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 314 removed outlier: 4.268A pdb=" N LEU C 311 " --> pdb=" O GLN C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 357 Processing helix chain 'C' and resid 372 through 385 removed outlier: 4.086A pdb=" N TYR C 376 " --> pdb=" O GLU C 372 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER C 379 " --> pdb=" O ARG C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 396 removed outlier: 3.609A pdb=" N ILE C 391 " --> pdb=" O GLY C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 412 removed outlier: 3.523A pdb=" N GLN C 409 " --> pdb=" O LEU C 405 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA C 410 " --> pdb=" O LYS C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 451 Processing helix chain 'C' and resid 462 through 474 removed outlier: 4.162A pdb=" N ILE C 474 " --> pdb=" O ILE C 470 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 10 removed outlier: 3.852A pdb=" N ALA D 9 " --> pdb=" O THR D 6 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU D 10 " --> pdb=" O GLY D 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 6 through 10' Processing helix chain 'D' and resid 12 through 39 removed outlier: 3.646A pdb=" N ASP D 23 " --> pdb=" O ARG D 19 " (cutoff:3.500A) Proline residue: D 26 - end of helix Processing helix chain 'D' and resid 40 through 43 removed outlier: 3.697A pdb=" N PHE D 43 " --> pdb=" O PRO D 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 40 through 43' Processing helix chain 'D' and resid 60 through 78 Processing helix chain 'D' and resid 91 through 96 Processing helix chain 'D' and resid 99 through 124 removed outlier: 3.717A pdb=" N LEU D 103 " --> pdb=" O ASP D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 140 Processing helix chain 'D' and resid 191 through 202 removed outlier: 3.522A pdb=" N GLN D 201 " --> pdb=" O ALA D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 272 removed outlier: 4.016A pdb=" N GLU D 271 " --> pdb=" O SER D 267 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N TYR D 272 " --> pdb=" O TYR D 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 267 through 272' Processing helix chain 'D' and resid 272 through 295 removed outlier: 3.600A pdb=" N LYS D 295 " --> pdb=" O MET D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 314 removed outlier: 4.269A pdb=" N LEU D 311 " --> pdb=" O GLN D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 357 Processing helix chain 'D' and resid 372 through 385 removed outlier: 4.086A pdb=" N TYR D 376 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER D 379 " --> pdb=" O ARG D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 396 removed outlier: 3.610A pdb=" N ILE D 391 " --> pdb=" O GLY D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 412 removed outlier: 3.522A pdb=" N GLN D 409 " --> pdb=" O LEU D 405 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA D 410 " --> pdb=" O LYS D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 440 through 451 Processing helix chain 'D' and resid 462 through 474 removed outlier: 4.163A pdb=" N ILE D 474 " --> pdb=" O ILE D 470 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 10 removed outlier: 3.851A pdb=" N ALA E 9 " --> pdb=" O THR E 6 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU E 10 " --> pdb=" O GLY E 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 6 through 10' Processing helix chain 'E' and resid 12 through 39 removed outlier: 3.646A pdb=" N ASP E 23 " --> pdb=" O ARG E 19 " (cutoff:3.500A) Proline residue: E 26 - end of helix Processing helix chain 'E' and resid 40 through 43 removed outlier: 3.695A pdb=" N PHE E 43 " --> pdb=" O PRO E 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 40 through 43' Processing helix chain 'E' and resid 60 through 78 Processing helix chain 'E' and resid 91 through 96 Processing helix chain 'E' and resid 99 through 124 removed outlier: 3.717A pdb=" N LEU E 103 " --> pdb=" O ASP E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 140 Processing helix chain 'E' and resid 191 through 202 removed outlier: 3.520A pdb=" N GLN E 201 " --> pdb=" O ALA E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 272 removed outlier: 4.015A pdb=" N GLU E 271 " --> pdb=" O SER E 267 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N TYR E 272 " --> pdb=" O TYR E 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 267 through 272' Processing helix chain 'E' and resid 272 through 295 removed outlier: 3.600A pdb=" N LYS E 295 " --> pdb=" O MET E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 314 removed outlier: 4.269A pdb=" N LEU E 311 " --> pdb=" O GLN E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 357 Processing helix chain 'E' and resid 372 through 385 removed outlier: 4.085A pdb=" N TYR E 376 " --> pdb=" O GLU E 372 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER E 379 " --> pdb=" O ARG E 375 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 396 removed outlier: 3.609A pdb=" N ILE E 391 " --> pdb=" O GLY E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 412 removed outlier: 3.524A pdb=" N GLN E 409 " --> pdb=" O LEU E 405 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA E 410 " --> pdb=" O LYS E 406 " (cutoff:3.500A) Processing helix chain 'E' and resid 440 through 451 Processing helix chain 'E' and resid 462 through 474 removed outlier: 4.162A pdb=" N ILE E 474 " --> pdb=" O ILE E 470 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 10 removed outlier: 3.852A pdb=" N ALA F 9 " --> pdb=" O THR F 6 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU F 10 " --> pdb=" O GLY F 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 6 through 10' Processing helix chain 'F' and resid 12 through 39 removed outlier: 3.647A pdb=" N ASP F 23 " --> pdb=" O ARG F 19 " (cutoff:3.500A) Proline residue: F 26 - end of helix Processing helix chain 'F' and resid 40 through 43 removed outlier: 3.696A pdb=" N PHE F 43 " --> pdb=" O PRO F 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 40 through 43' Processing helix chain 'F' and resid 60 through 78 Processing helix chain 'F' and resid 91 through 96 Processing helix chain 'F' and resid 99 through 124 removed outlier: 3.716A pdb=" N LEU F 103 " --> pdb=" O ASP F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 140 Processing helix chain 'F' and resid 191 through 202 removed outlier: 3.521A pdb=" N GLN F 201 " --> pdb=" O ALA F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 272 removed outlier: 4.017A pdb=" N GLU F 271 " --> pdb=" O SER F 267 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N TYR F 272 " --> pdb=" O TYR F 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 267 through 272' Processing helix chain 'F' and resid 272 through 295 removed outlier: 3.600A pdb=" N LYS F 295 " --> pdb=" O MET F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 314 removed outlier: 4.269A pdb=" N LEU F 311 " --> pdb=" O GLN F 307 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 357 Processing helix chain 'F' and resid 372 through 385 removed outlier: 4.086A pdb=" N TYR F 376 " --> pdb=" O GLU F 372 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER F 379 " --> pdb=" O ARG F 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 387 through 396 removed outlier: 3.608A pdb=" N ILE F 391 " --> pdb=" O GLY F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 412 removed outlier: 3.523A pdb=" N GLN F 409 " --> pdb=" O LEU F 405 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA F 410 " --> pdb=" O LYS F 406 " (cutoff:3.500A) Processing helix chain 'F' and resid 440 through 451 Processing helix chain 'F' and resid 462 through 474 removed outlier: 4.163A pdb=" N ILE F 474 " --> pdb=" O ILE F 470 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 10 removed outlier: 3.851A pdb=" N ALA G 9 " --> pdb=" O THR G 6 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU G 10 " --> pdb=" O GLY G 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 6 through 10' Processing helix chain 'G' and resid 12 through 39 removed outlier: 3.647A pdb=" N ASP G 23 " --> pdb=" O ARG G 19 " (cutoff:3.500A) Proline residue: G 26 - end of helix Processing helix chain 'G' and resid 40 through 43 removed outlier: 3.695A pdb=" N PHE G 43 " --> pdb=" O PRO G 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 40 through 43' Processing helix chain 'G' and resid 60 through 78 Processing helix chain 'G' and resid 91 through 96 Processing helix chain 'G' and resid 99 through 124 removed outlier: 3.717A pdb=" N LEU G 103 " --> pdb=" O ASP G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 140 Processing helix chain 'G' and resid 191 through 202 removed outlier: 3.521A pdb=" N GLN G 201 " --> pdb=" O ALA G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 267 through 272 removed outlier: 4.016A pdb=" N GLU G 271 " --> pdb=" O SER G 267 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N TYR G 272 " --> pdb=" O TYR G 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 267 through 272' Processing helix chain 'G' and resid 272 through 295 removed outlier: 3.600A pdb=" N LYS G 295 " --> pdb=" O MET G 291 " (cutoff:3.500A) Processing helix chain 'G' and resid 307 through 314 removed outlier: 4.269A pdb=" N LEU G 311 " --> pdb=" O GLN G 307 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 357 Processing helix chain 'G' and resid 372 through 385 removed outlier: 4.086A pdb=" N TYR G 376 " --> pdb=" O GLU G 372 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER G 379 " --> pdb=" O ARG G 375 " (cutoff:3.500A) Processing helix chain 'G' and resid 387 through 396 removed outlier: 3.609A pdb=" N ILE G 391 " --> pdb=" O GLY G 387 " (cutoff:3.500A) Processing helix chain 'G' and resid 396 through 412 removed outlier: 3.522A pdb=" N GLN G 409 " --> pdb=" O LEU G 405 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA G 410 " --> pdb=" O LYS G 406 " (cutoff:3.500A) Processing helix chain 'G' and resid 440 through 451 Processing helix chain 'G' and resid 462 through 474 removed outlier: 4.163A pdb=" N ILE G 474 " --> pdb=" O ILE G 470 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 10 removed outlier: 3.851A pdb=" N ALA H 9 " --> pdb=" O THR H 6 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU H 10 " --> pdb=" O GLY H 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 6 through 10' Processing helix chain 'H' and resid 12 through 39 removed outlier: 3.648A pdb=" N ASP H 23 " --> pdb=" O ARG H 19 " (cutoff:3.500A) Proline residue: H 26 - end of helix Processing helix chain 'H' and resid 40 through 43 removed outlier: 3.696A pdb=" N PHE H 43 " --> pdb=" O PRO H 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 40 through 43' Processing helix chain 'H' and resid 60 through 78 Processing helix chain 'H' and resid 91 through 96 Processing helix chain 'H' and resid 99 through 124 removed outlier: 3.716A pdb=" N LEU H 103 " --> pdb=" O ASP H 99 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 140 Processing helix chain 'H' and resid 191 through 202 removed outlier: 3.521A pdb=" N GLN H 201 " --> pdb=" O ALA H 197 " (cutoff:3.500A) Processing helix chain 'H' and resid 267 through 272 removed outlier: 4.016A pdb=" N GLU H 271 " --> pdb=" O SER H 267 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N TYR H 272 " --> pdb=" O TYR H 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 267 through 272' Processing helix chain 'H' and resid 272 through 295 removed outlier: 3.600A pdb=" N LYS H 295 " --> pdb=" O MET H 291 " (cutoff:3.500A) Processing helix chain 'H' and resid 307 through 314 removed outlier: 4.269A pdb=" N LEU H 311 " --> pdb=" O GLN H 307 " (cutoff:3.500A) Processing helix chain 'H' and resid 335 through 357 Processing helix chain 'H' and resid 372 through 385 removed outlier: 4.086A pdb=" N TYR H 376 " --> pdb=" O GLU H 372 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER H 379 " --> pdb=" O ARG H 375 " (cutoff:3.500A) Processing helix chain 'H' and resid 387 through 396 removed outlier: 3.610A pdb=" N ILE H 391 " --> pdb=" O GLY H 387 " (cutoff:3.500A) Processing helix chain 'H' and resid 396 through 412 removed outlier: 3.523A pdb=" N GLN H 409 " --> pdb=" O LEU H 405 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA H 410 " --> pdb=" O LYS H 406 " (cutoff:3.500A) Processing helix chain 'H' and resid 440 through 451 Processing helix chain 'H' and resid 462 through 474 removed outlier: 4.162A pdb=" N ILE H 474 " --> pdb=" O ILE H 470 " (cutoff:3.500A) Processing helix chain 'I' and resid 6 through 10 removed outlier: 3.852A pdb=" N ALA I 9 " --> pdb=" O THR I 6 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU I 10 " --> pdb=" O GLY I 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 6 through 10' Processing helix chain 'I' and resid 12 through 39 removed outlier: 3.646A pdb=" N ASP I 23 " --> pdb=" O ARG I 19 " (cutoff:3.500A) Proline residue: I 26 - end of helix Processing helix chain 'I' and resid 40 through 43 removed outlier: 3.696A pdb=" N PHE I 43 " --> pdb=" O PRO I 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 40 through 43' Processing helix chain 'I' and resid 60 through 78 Processing helix chain 'I' and resid 91 through 96 Processing helix chain 'I' and resid 99 through 124 removed outlier: 3.716A pdb=" N LEU I 103 " --> pdb=" O ASP I 99 " (cutoff:3.500A) Processing helix chain 'I' and resid 125 through 140 Processing helix chain 'I' and resid 191 through 202 removed outlier: 3.521A pdb=" N GLN I 201 " --> pdb=" O ALA I 197 " (cutoff:3.500A) Processing helix chain 'I' and resid 267 through 272 removed outlier: 4.016A pdb=" N GLU I 271 " --> pdb=" O SER I 267 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N TYR I 272 " --> pdb=" O TYR I 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 267 through 272' Processing helix chain 'I' and resid 272 through 295 removed outlier: 3.600A pdb=" N LYS I 295 " --> pdb=" O MET I 291 " (cutoff:3.500A) Processing helix chain 'I' and resid 307 through 314 removed outlier: 4.269A pdb=" N LEU I 311 " --> pdb=" O GLN I 307 " (cutoff:3.500A) Processing helix chain 'I' and resid 335 through 357 Processing helix chain 'I' and resid 372 through 385 removed outlier: 4.085A pdb=" N TYR I 376 " --> pdb=" O GLU I 372 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER I 379 " --> pdb=" O ARG I 375 " (cutoff:3.500A) Processing helix chain 'I' and resid 387 through 396 removed outlier: 3.609A pdb=" N ILE I 391 " --> pdb=" O GLY I 387 " (cutoff:3.500A) Processing helix chain 'I' and resid 396 through 412 removed outlier: 3.523A pdb=" N GLN I 409 " --> pdb=" O LEU I 405 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA I 410 " --> pdb=" O LYS I 406 " (cutoff:3.500A) Processing helix chain 'I' and resid 440 through 451 Processing helix chain 'I' and resid 462 through 474 removed outlier: 4.163A pdb=" N ILE I 474 " --> pdb=" O ILE I 470 " (cutoff:3.500A) Processing helix chain 'J' and resid 6 through 10 removed outlier: 3.851A pdb=" N ALA J 9 " --> pdb=" O THR J 6 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU J 10 " --> pdb=" O GLY J 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 6 through 10' Processing helix chain 'J' and resid 12 through 39 removed outlier: 3.646A pdb=" N ASP J 23 " --> pdb=" O ARG J 19 " (cutoff:3.500A) Proline residue: J 26 - end of helix Processing helix chain 'J' and resid 40 through 43 removed outlier: 3.696A pdb=" N PHE J 43 " --> pdb=" O PRO J 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 40 through 43' Processing helix chain 'J' and resid 60 through 78 Processing helix chain 'J' and resid 91 through 96 Processing helix chain 'J' and resid 99 through 124 removed outlier: 3.717A pdb=" N LEU J 103 " --> pdb=" O ASP J 99 " (cutoff:3.500A) Processing helix chain 'J' and resid 125 through 140 Processing helix chain 'J' and resid 191 through 202 removed outlier: 3.521A pdb=" N GLN J 201 " --> pdb=" O ALA J 197 " (cutoff:3.500A) Processing helix chain 'J' and resid 267 through 272 removed outlier: 4.016A pdb=" N GLU J 271 " --> pdb=" O SER J 267 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N TYR J 272 " --> pdb=" O TYR J 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 267 through 272' Processing helix chain 'J' and resid 272 through 295 removed outlier: 3.601A pdb=" N LYS J 295 " --> pdb=" O MET J 291 " (cutoff:3.500A) Processing helix chain 'J' and resid 307 through 314 removed outlier: 4.268A pdb=" N LEU J 311 " --> pdb=" O GLN J 307 " (cutoff:3.500A) Processing helix chain 'J' and resid 335 through 357 Processing helix chain 'J' and resid 372 through 385 removed outlier: 4.086A pdb=" N TYR J 376 " --> pdb=" O GLU J 372 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER J 379 " --> pdb=" O ARG J 375 " (cutoff:3.500A) Processing helix chain 'J' and resid 387 through 396 removed outlier: 3.609A pdb=" N ILE J 391 " --> pdb=" O GLY J 387 " (cutoff:3.500A) Processing helix chain 'J' and resid 396 through 412 removed outlier: 3.523A pdb=" N GLN J 409 " --> pdb=" O LEU J 405 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA J 410 " --> pdb=" O LYS J 406 " (cutoff:3.500A) Processing helix chain 'J' and resid 440 through 451 Processing helix chain 'J' and resid 462 through 474 removed outlier: 4.163A pdb=" N ILE J 474 " --> pdb=" O ILE J 470 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 10 removed outlier: 3.851A pdb=" N ALA K 9 " --> pdb=" O THR K 6 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU K 10 " --> pdb=" O GLY K 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 6 through 10' Processing helix chain 'K' and resid 12 through 39 removed outlier: 3.647A pdb=" N ASP K 23 " --> pdb=" O ARG K 19 " (cutoff:3.500A) Proline residue: K 26 - end of helix Processing helix chain 'K' and resid 40 through 43 removed outlier: 3.696A pdb=" N PHE K 43 " --> pdb=" O PRO K 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 40 through 43' Processing helix chain 'K' and resid 60 through 78 Processing helix chain 'K' and resid 91 through 96 Processing helix chain 'K' and resid 99 through 124 removed outlier: 3.717A pdb=" N LEU K 103 " --> pdb=" O ASP K 99 " (cutoff:3.500A) Processing helix chain 'K' and resid 125 through 140 Processing helix chain 'K' and resid 191 through 202 removed outlier: 3.521A pdb=" N GLN K 201 " --> pdb=" O ALA K 197 " (cutoff:3.500A) Processing helix chain 'K' and resid 267 through 272 removed outlier: 4.016A pdb=" N GLU K 271 " --> pdb=" O SER K 267 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N TYR K 272 " --> pdb=" O TYR K 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 267 through 272' Processing helix chain 'K' and resid 272 through 295 removed outlier: 3.600A pdb=" N LYS K 295 " --> pdb=" O MET K 291 " (cutoff:3.500A) Processing helix chain 'K' and resid 307 through 314 removed outlier: 4.269A pdb=" N LEU K 311 " --> pdb=" O GLN K 307 " (cutoff:3.500A) Processing helix chain 'K' and resid 335 through 357 Processing helix chain 'K' and resid 372 through 385 removed outlier: 4.086A pdb=" N TYR K 376 " --> pdb=" O GLU K 372 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER K 379 " --> pdb=" O ARG K 375 " (cutoff:3.500A) Processing helix chain 'K' and resid 387 through 396 removed outlier: 3.609A pdb=" N ILE K 391 " --> pdb=" O GLY K 387 " (cutoff:3.500A) Processing helix chain 'K' and resid 396 through 412 removed outlier: 3.522A pdb=" N GLN K 409 " --> pdb=" O LEU K 405 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA K 410 " --> pdb=" O LYS K 406 " (cutoff:3.500A) Processing helix chain 'K' and resid 440 through 451 Processing helix chain 'K' and resid 462 through 474 removed outlier: 4.162A pdb=" N ILE K 474 " --> pdb=" O ILE K 470 " (cutoff:3.500A) Processing helix chain 'L' and resid 6 through 10 removed outlier: 3.851A pdb=" N ALA L 9 " --> pdb=" O THR L 6 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU L 10 " --> pdb=" O GLY L 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 6 through 10' Processing helix chain 'L' and resid 12 through 39 removed outlier: 3.647A pdb=" N ASP L 23 " --> pdb=" O ARG L 19 " (cutoff:3.500A) Proline residue: L 26 - end of helix Processing helix chain 'L' and resid 40 through 43 removed outlier: 3.697A pdb=" N PHE L 43 " --> pdb=" O PRO L 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 40 through 43' Processing helix chain 'L' and resid 60 through 78 Processing helix chain 'L' and resid 91 through 96 Processing helix chain 'L' and resid 99 through 124 removed outlier: 3.716A pdb=" N LEU L 103 " --> pdb=" O ASP L 99 " (cutoff:3.500A) Processing helix chain 'L' and resid 125 through 140 Processing helix chain 'L' and resid 191 through 202 removed outlier: 3.519A pdb=" N GLN L 201 " --> pdb=" O ALA L 197 " (cutoff:3.500A) Processing helix chain 'L' and resid 267 through 272 removed outlier: 4.017A pdb=" N GLU L 271 " --> pdb=" O SER L 267 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N TYR L 272 " --> pdb=" O TYR L 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 267 through 272' Processing helix chain 'L' and resid 272 through 295 removed outlier: 3.600A pdb=" N LYS L 295 " --> pdb=" O MET L 291 " (cutoff:3.500A) Processing helix chain 'L' and resid 307 through 314 removed outlier: 4.268A pdb=" N LEU L 311 " --> pdb=" O GLN L 307 " (cutoff:3.500A) Processing helix chain 'L' and resid 335 through 357 Processing helix chain 'L' and resid 372 through 385 removed outlier: 4.086A pdb=" N TYR L 376 " --> pdb=" O GLU L 372 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER L 379 " --> pdb=" O ARG L 375 " (cutoff:3.500A) Processing helix chain 'L' and resid 387 through 396 removed outlier: 3.609A pdb=" N ILE L 391 " --> pdb=" O GLY L 387 " (cutoff:3.500A) Processing helix chain 'L' and resid 396 through 412 removed outlier: 3.524A pdb=" N GLN L 409 " --> pdb=" O LEU L 405 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA L 410 " --> pdb=" O LYS L 406 " (cutoff:3.500A) Processing helix chain 'L' and resid 440 through 451 Processing helix chain 'L' and resid 462 through 474 removed outlier: 4.162A pdb=" N ILE L 474 " --> pdb=" O ILE L 470 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 86 Processing sheet with id=AA2, first strand: chain 'A' and resid 159 through 162 removed outlier: 3.720A pdb=" N LYS A 159 " --> pdb=" O TYR A 146 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR A 146 " --> pdb=" O LYS A 159 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL A 143 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU A 145 " --> pdb=" O ILE A 252 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 166 through 169 removed outlier: 3.760A pdb=" N GLN A 178 " --> pdb=" O GLN A 169 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR A 215 " --> pdb=" O THR A 181 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 166 through 169 removed outlier: 3.760A pdb=" N GLN A 178 " --> pdb=" O GLN A 169 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR A 215 " --> pdb=" O THR A 181 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 298 through 300 Processing sheet with id=AA6, first strand: chain 'B' and resid 85 through 86 Processing sheet with id=AA7, first strand: chain 'B' and resid 159 through 162 removed outlier: 3.721A pdb=" N LYS B 159 " --> pdb=" O TYR B 146 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR B 146 " --> pdb=" O LYS B 159 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL B 143 " --> pdb=" O ILE B 254 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU B 145 " --> pdb=" O ILE B 252 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 166 through 169 removed outlier: 3.759A pdb=" N GLN B 178 " --> pdb=" O GLN B 169 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR B 215 " --> pdb=" O THR B 181 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 166 through 169 removed outlier: 3.759A pdb=" N GLN B 178 " --> pdb=" O GLN B 169 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR B 215 " --> pdb=" O THR B 181 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 298 through 300 Processing sheet with id=AB2, first strand: chain 'C' and resid 85 through 86 Processing sheet with id=AB3, first strand: chain 'C' and resid 159 through 162 removed outlier: 3.721A pdb=" N LYS C 159 " --> pdb=" O TYR C 146 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR C 146 " --> pdb=" O LYS C 159 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL C 143 " --> pdb=" O ILE C 254 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU C 145 " --> pdb=" O ILE C 252 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 166 through 169 removed outlier: 3.760A pdb=" N GLN C 178 " --> pdb=" O GLN C 169 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR C 215 " --> pdb=" O THR C 181 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 166 through 169 removed outlier: 3.760A pdb=" N GLN C 178 " --> pdb=" O GLN C 169 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR C 215 " --> pdb=" O THR C 181 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 298 through 300 Processing sheet with id=AB7, first strand: chain 'D' and resid 85 through 86 Processing sheet with id=AB8, first strand: chain 'D' and resid 159 through 162 removed outlier: 3.719A pdb=" N LYS D 159 " --> pdb=" O TYR D 146 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR D 146 " --> pdb=" O LYS D 159 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL D 143 " --> pdb=" O ILE D 254 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU D 145 " --> pdb=" O ILE D 252 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 166 through 169 removed outlier: 3.761A pdb=" N GLN D 178 " --> pdb=" O GLN D 169 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR D 215 " --> pdb=" O THR D 181 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 166 through 169 removed outlier: 3.761A pdb=" N GLN D 178 " --> pdb=" O GLN D 169 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR D 215 " --> pdb=" O THR D 181 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 298 through 300 Processing sheet with id=AC3, first strand: chain 'E' and resid 85 through 86 Processing sheet with id=AC4, first strand: chain 'E' and resid 159 through 162 removed outlier: 3.720A pdb=" N LYS E 159 " --> pdb=" O TYR E 146 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR E 146 " --> pdb=" O LYS E 159 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL E 143 " --> pdb=" O ILE E 254 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU E 145 " --> pdb=" O ILE E 252 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 166 through 169 removed outlier: 3.762A pdb=" N GLN E 178 " --> pdb=" O GLN E 169 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR E 215 " --> pdb=" O THR E 181 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 166 through 169 removed outlier: 3.762A pdb=" N GLN E 178 " --> pdb=" O GLN E 169 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR E 215 " --> pdb=" O THR E 181 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 298 through 300 Processing sheet with id=AC8, first strand: chain 'F' and resid 85 through 86 Processing sheet with id=AC9, first strand: chain 'F' and resid 159 through 162 removed outlier: 3.721A pdb=" N LYS F 159 " --> pdb=" O TYR F 146 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR F 146 " --> pdb=" O LYS F 159 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL F 143 " --> pdb=" O ILE F 254 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU F 145 " --> pdb=" O ILE F 252 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 166 through 169 removed outlier: 3.760A pdb=" N GLN F 178 " --> pdb=" O GLN F 169 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR F 215 " --> pdb=" O THR F 181 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 166 through 169 removed outlier: 3.760A pdb=" N GLN F 178 " --> pdb=" O GLN F 169 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR F 215 " --> pdb=" O THR F 181 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 298 through 300 Processing sheet with id=AD4, first strand: chain 'G' and resid 85 through 86 Processing sheet with id=AD5, first strand: chain 'G' and resid 159 through 162 removed outlier: 3.720A pdb=" N LYS G 159 " --> pdb=" O TYR G 146 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR G 146 " --> pdb=" O LYS G 159 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL G 143 " --> pdb=" O ILE G 254 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU G 145 " --> pdb=" O ILE G 252 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 166 through 169 removed outlier: 3.760A pdb=" N GLN G 178 " --> pdb=" O GLN G 169 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR G 215 " --> pdb=" O THR G 181 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 166 through 169 removed outlier: 3.760A pdb=" N GLN G 178 " --> pdb=" O GLN G 169 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR G 215 " --> pdb=" O THR G 181 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 298 through 300 Processing sheet with id=AD9, first strand: chain 'H' and resid 85 through 86 Processing sheet with id=AE1, first strand: chain 'H' and resid 159 through 162 removed outlier: 3.721A pdb=" N LYS H 159 " --> pdb=" O TYR H 146 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR H 146 " --> pdb=" O LYS H 159 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL H 143 " --> pdb=" O ILE H 254 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU H 145 " --> pdb=" O ILE H 252 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 166 through 169 removed outlier: 3.760A pdb=" N GLN H 178 " --> pdb=" O GLN H 169 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR H 215 " --> pdb=" O THR H 181 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 166 through 169 removed outlier: 3.760A pdb=" N GLN H 178 " --> pdb=" O GLN H 169 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR H 215 " --> pdb=" O THR H 181 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 298 through 300 Processing sheet with id=AE5, first strand: chain 'I' and resid 85 through 86 Processing sheet with id=AE6, first strand: chain 'I' and resid 159 through 162 removed outlier: 3.720A pdb=" N LYS I 159 " --> pdb=" O TYR I 146 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR I 146 " --> pdb=" O LYS I 159 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL I 143 " --> pdb=" O ILE I 254 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU I 145 " --> pdb=" O ILE I 252 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 166 through 169 removed outlier: 3.761A pdb=" N GLN I 178 " --> pdb=" O GLN I 169 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR I 215 " --> pdb=" O THR I 181 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 166 through 169 removed outlier: 3.761A pdb=" N GLN I 178 " --> pdb=" O GLN I 169 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR I 215 " --> pdb=" O THR I 181 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 298 through 300 Processing sheet with id=AF1, first strand: chain 'J' and resid 85 through 86 Processing sheet with id=AF2, first strand: chain 'J' and resid 159 through 162 removed outlier: 3.721A pdb=" N LYS J 159 " --> pdb=" O TYR J 146 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR J 146 " --> pdb=" O LYS J 159 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL J 143 " --> pdb=" O ILE J 254 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU J 145 " --> pdb=" O ILE J 252 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 166 through 169 removed outlier: 3.760A pdb=" N GLN J 178 " --> pdb=" O GLN J 169 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR J 215 " --> pdb=" O THR J 181 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'J' and resid 166 through 169 removed outlier: 3.760A pdb=" N GLN J 178 " --> pdb=" O GLN J 169 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR J 215 " --> pdb=" O THR J 181 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'J' and resid 298 through 300 Processing sheet with id=AF6, first strand: chain 'K' and resid 85 through 86 Processing sheet with id=AF7, first strand: chain 'K' and resid 159 through 162 removed outlier: 3.721A pdb=" N LYS K 159 " --> pdb=" O TYR K 146 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR K 146 " --> pdb=" O LYS K 159 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL K 143 " --> pdb=" O ILE K 254 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU K 145 " --> pdb=" O ILE K 252 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'K' and resid 166 through 169 removed outlier: 3.760A pdb=" N GLN K 178 " --> pdb=" O GLN K 169 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR K 215 " --> pdb=" O THR K 181 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'K' and resid 166 through 169 removed outlier: 3.760A pdb=" N GLN K 178 " --> pdb=" O GLN K 169 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR K 215 " --> pdb=" O THR K 181 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'K' and resid 298 through 300 Processing sheet with id=AG2, first strand: chain 'L' and resid 85 through 86 Processing sheet with id=AG3, first strand: chain 'L' and resid 159 through 162 removed outlier: 3.720A pdb=" N LYS L 159 " --> pdb=" O TYR L 146 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR L 146 " --> pdb=" O LYS L 159 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL L 143 " --> pdb=" O ILE L 254 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU L 145 " --> pdb=" O ILE L 252 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'L' and resid 166 through 169 removed outlier: 3.760A pdb=" N GLN L 178 " --> pdb=" O GLN L 169 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR L 215 " --> pdb=" O THR L 181 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 166 through 169 removed outlier: 3.760A pdb=" N GLN L 178 " --> pdb=" O GLN L 169 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR L 215 " --> pdb=" O THR L 181 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'L' and resid 298 through 300 2232 hydrogen bonds defined for protein. 6588 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: 9.86 Time building geometry restraints manager: 4.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 13494 1.33 - 1.46: 8674 1.46 - 1.58: 22196 1.58 - 1.71: 0 1.71 - 1.84: 372 Bond restraints: 44736 Sorted by residual: bond pdb=" CA THR I 56 " pdb=" C THR I 56 " ideal model delta sigma weight residual 1.528 1.480 0.048 1.08e-02 8.57e+03 1.94e+01 bond pdb=" CA THR B 56 " pdb=" C THR B 56 " ideal model delta sigma weight residual 1.528 1.480 0.047 1.08e-02 8.57e+03 1.93e+01 bond pdb=" CA THR H 56 " pdb=" C THR H 56 " ideal model delta sigma weight residual 1.528 1.480 0.047 1.08e-02 8.57e+03 1.93e+01 bond pdb=" CA THR J 56 " pdb=" C THR J 56 " ideal model delta sigma weight residual 1.528 1.480 0.047 1.08e-02 8.57e+03 1.90e+01 bond pdb=" CA THR C 56 " pdb=" C THR C 56 " ideal model delta sigma weight residual 1.528 1.481 0.047 1.08e-02 8.57e+03 1.89e+01 ... (remaining 44731 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.68: 56296 2.68 - 5.36: 3293 5.36 - 8.04: 735 8.04 - 10.73: 192 10.73 - 13.41: 72 Bond angle restraints: 60588 Sorted by residual: angle pdb=" N ASP D 208 " pdb=" CA ASP D 208 " pdb=" C ASP D 208 " ideal model delta sigma weight residual 111.36 124.14 -12.78 1.09e+00 8.42e-01 1.37e+02 angle pdb=" N ASP A 208 " pdb=" CA ASP A 208 " pdb=" C ASP A 208 " ideal model delta sigma weight residual 111.36 124.13 -12.77 1.09e+00 8.42e-01 1.37e+02 angle pdb=" N ASP B 208 " pdb=" CA ASP B 208 " pdb=" C ASP B 208 " ideal model delta sigma weight residual 111.36 124.13 -12.77 1.09e+00 8.42e-01 1.37e+02 angle pdb=" N ASP E 208 " pdb=" CA ASP E 208 " pdb=" C ASP E 208 " ideal model delta sigma weight residual 111.36 124.11 -12.75 1.09e+00 8.42e-01 1.37e+02 angle pdb=" N ASP J 208 " pdb=" CA ASP J 208 " pdb=" C ASP J 208 " ideal model delta sigma weight residual 111.36 124.10 -12.74 1.09e+00 8.42e-01 1.37e+02 ... (remaining 60583 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 23928 17.81 - 35.62: 2364 35.62 - 53.42: 829 53.42 - 71.23: 359 71.23 - 89.04: 84 Dihedral angle restraints: 27564 sinusoidal: 11184 harmonic: 16380 Sorted by residual: dihedral pdb=" C TYR K 37 " pdb=" N TYR K 37 " pdb=" CA TYR K 37 " pdb=" CB TYR K 37 " ideal model delta harmonic sigma weight residual -122.60 -137.73 15.13 0 2.50e+00 1.60e-01 3.66e+01 dihedral pdb=" C TYR I 37 " pdb=" N TYR I 37 " pdb=" CA TYR I 37 " pdb=" CB TYR I 37 " ideal model delta harmonic sigma weight residual -122.60 -137.70 15.10 0 2.50e+00 1.60e-01 3.65e+01 dihedral pdb=" C TYR F 37 " pdb=" N TYR F 37 " pdb=" CA TYR F 37 " pdb=" CB TYR F 37 " ideal model delta harmonic sigma weight residual -122.60 -137.70 15.10 0 2.50e+00 1.60e-01 3.65e+01 ... (remaining 27561 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.126: 5578 0.126 - 0.252: 1130 0.252 - 0.378: 96 0.378 - 0.504: 44 0.504 - 0.630: 28 Chirality restraints: 6876 Sorted by residual: chirality pdb=" CA TYR F 37 " pdb=" N TYR F 37 " pdb=" C TYR F 37 " pdb=" CB TYR F 37 " both_signs ideal model delta sigma weight residual False 2.51 1.88 0.63 2.00e-01 2.50e+01 9.91e+00 chirality pdb=" CA TYR K 37 " pdb=" N TYR K 37 " pdb=" C TYR K 37 " pdb=" CB TYR K 37 " both_signs ideal model delta sigma weight residual False 2.51 1.88 0.63 2.00e-01 2.50e+01 9.87e+00 chirality pdb=" CA TYR I 37 " pdb=" N TYR I 37 " pdb=" C TYR I 37 " pdb=" CB TYR I 37 " both_signs ideal model delta sigma weight residual False 2.51 1.88 0.63 2.00e-01 2.50e+01 9.83e+00 ... (remaining 6873 not shown) Planarity restraints: 7932 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU G 398 " -0.056 5.00e-02 4.00e+02 8.46e-02 1.14e+01 pdb=" N PRO G 399 " 0.146 5.00e-02 4.00e+02 pdb=" CA PRO G 399 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO G 399 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU J 398 " -0.056 5.00e-02 4.00e+02 8.45e-02 1.14e+01 pdb=" N PRO J 399 " 0.146 5.00e-02 4.00e+02 pdb=" CA PRO J 399 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO J 399 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 398 " 0.056 5.00e-02 4.00e+02 8.45e-02 1.14e+01 pdb=" N PRO D 399 " -0.146 5.00e-02 4.00e+02 pdb=" CA PRO D 399 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO D 399 " 0.047 5.00e-02 4.00e+02 ... (remaining 7929 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 1395 2.65 - 3.21: 44769 3.21 - 3.78: 70733 3.78 - 4.34: 93193 4.34 - 4.90: 143138 Nonbonded interactions: 353228 Sorted by model distance: nonbonded pdb=" O THR I 6 " pdb=" OG1 THR I 6 " model vdw 2.089 3.040 nonbonded pdb=" O THR H 6 " pdb=" OG1 THR H 6 " model vdw 2.089 3.040 nonbonded pdb=" O THR K 6 " pdb=" OG1 THR K 6 " model vdw 2.089 3.040 nonbonded pdb=" O THR F 6 " pdb=" OG1 THR F 6 " model vdw 2.089 3.040 nonbonded pdb=" O THR G 6 " pdb=" OG1 THR G 6 " model vdw 2.090 3.040 ... (remaining 353223 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: 0.13 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.10 max=1.00 mean=0.95 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.530 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: 0.050 Extract box with map and model: 0.630 Check model and map are aligned: 0.130 Set scattering table: 0.120 Process input model: 36.340 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 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 : 0.009 0.051 44736 Z= 0.684 Angle : 1.559 13.408 60588 Z= 1.053 Chirality : 0.108 0.630 6876 Planarity : 0.007 0.085 7932 Dihedral : 18.035 89.041 17052 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 20.76 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.02 % Favored : 93.76 % Rotamer: Outliers : 16.41 % Allowed : 11.87 % Favored : 71.72 % Cbeta Deviations : 1.14 % 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: -0.70 (0.11), residues: 5580 helix: 1.35 (0.10), residues: 2472 sheet: -0.88 (0.19), residues: 648 loop : -2.37 (0.11), residues: 2460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 266 TYR 0.018 0.002 TYR L 37 PHE 0.012 0.002 PHE H 319 TRP 0.013 0.002 TRP J 83 HIS 0.001 0.001 HIS I 216 Details of bonding type rmsd covalent geometry : bond 0.00941 (44736) covalent geometry : angle 1.55904 (60588) hydrogen bonds : bond 0.20484 ( 2160) hydrogen bonds : angle 7.55985 ( 6588) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11160 Ramachandran restraints generated. 5580 Oldfield, 0 Emsley, 5580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11160 Ramachandran restraints generated. 5580 Oldfield, 0 Emsley, 5580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2305 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 780 poor density : 1525 time to evaluate : 1.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ILE cc_start: 0.8854 (tp) cc_final: 0.8573 (pt) REVERT: A 58 TRP cc_start: 0.7793 (m100) cc_final: 0.7251 (m100) REVERT: A 91 TYR cc_start: 0.6758 (t80) cc_final: 0.6450 (t80) REVERT: A 137 LEU cc_start: 0.7764 (tp) cc_final: 0.7457 (tp) REVERT: A 151 GLU cc_start: 0.8626 (mm-30) cc_final: 0.8374 (tt0) REVERT: A 263 SER cc_start: 0.7481 (OUTLIER) cc_final: 0.7240 (m) REVERT: A 268 TYR cc_start: 0.7656 (t80) cc_final: 0.6665 (t80) REVERT: A 273 LEU cc_start: 0.7824 (tp) cc_final: 0.7439 (tt) REVERT: A 284 GLU cc_start: 0.8748 (tt0) cc_final: 0.8440 (tt0) REVERT: A 470 ILE cc_start: 0.6655 (mm) cc_final: 0.5913 (pt) REVERT: A 474 ILE cc_start: 0.4977 (OUTLIER) cc_final: 0.4553 (tp) REVERT: B 54 TYR cc_start: 0.6794 (m-10) cc_final: 0.6090 (m-10) REVERT: B 58 TRP cc_start: 0.8203 (m100) cc_final: 0.7833 (m100) REVERT: B 112 MET cc_start: 0.7974 (mtt) cc_final: 0.6367 (tpt) REVERT: B 114 GLU cc_start: 0.7049 (tp30) cc_final: 0.6747 (tp30) REVERT: B 124 ASN cc_start: 0.7506 (OUTLIER) cc_final: 0.4929 (m-40) REVERT: B 132 GLU cc_start: 0.8447 (mm-30) cc_final: 0.8238 (tp30) REVERT: B 193 ASP cc_start: 0.7414 (OUTLIER) cc_final: 0.7201 (p0) REVERT: B 222 ASP cc_start: 0.6236 (m-30) cc_final: 0.5922 (m-30) REVERT: B 352 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.9015 (mm) REVERT: B 353 SER cc_start: 0.9070 (OUTLIER) cc_final: 0.8812 (m) REVERT: B 368 ARG cc_start: 0.0842 (OUTLIER) cc_final: 0.0446 (mmm160) REVERT: B 389 TYR cc_start: 0.7459 (OUTLIER) cc_final: 0.6224 (t80) REVERT: B 392 LEU cc_start: 0.8914 (tp) cc_final: 0.8710 (mm) REVERT: B 412 GLN cc_start: 0.0446 (OUTLIER) cc_final: -0.0429 (pt0) REVERT: B 465 MET cc_start: 0.4105 (mtm) cc_final: 0.2788 (ttt) REVERT: C 91 TYR cc_start: 0.7001 (t80) cc_final: 0.6615 (t80) REVERT: C 235 MET cc_start: 0.7523 (mmm) cc_final: 0.6876 (ptt) REVERT: C 388 VAL cc_start: 0.7633 (m) cc_final: 0.7403 (p) REVERT: C 470 ILE cc_start: 0.6437 (mm) cc_final: 0.5663 (pt) REVERT: C 474 ILE cc_start: 0.4316 (OUTLIER) cc_final: 0.3873 (tp) REVERT: D 58 TRP cc_start: 0.8078 (m100) cc_final: 0.7859 (m100) REVERT: D 59 GLN cc_start: 0.8635 (pp30) cc_final: 0.8409 (pp30) REVERT: D 114 GLU cc_start: 0.7203 (tp30) cc_final: 0.6733 (tp30) REVERT: D 132 GLU cc_start: 0.8561 (mm-30) cc_final: 0.8329 (tp30) REVERT: D 156 ASN cc_start: 0.8393 (t0) cc_final: 0.8120 (m-40) REVERT: D 340 VAL cc_start: 0.8932 (m) cc_final: 0.8622 (t) REVERT: D 446 VAL cc_start: 0.4531 (OUTLIER) cc_final: 0.4298 (p) REVERT: D 465 MET cc_start: 0.3332 (mtm) cc_final: 0.2070 (ttt) REVERT: E 54 TYR cc_start: 0.6579 (m-10) cc_final: 0.6343 (m-10) REVERT: E 58 TRP cc_start: 0.7743 (m100) cc_final: 0.7181 (m100) REVERT: E 88 ILE cc_start: 0.5323 (OUTLIER) cc_final: 0.5009 (tp) REVERT: E 91 TYR cc_start: 0.6674 (t80) cc_final: 0.6467 (t80) REVERT: E 235 MET cc_start: 0.7739 (mmm) cc_final: 0.6943 (ptt) REVERT: E 263 SER cc_start: 0.7290 (OUTLIER) cc_final: 0.7047 (m) REVERT: E 268 TYR cc_start: 0.7685 (t80) cc_final: 0.6638 (t80) REVERT: E 273 LEU cc_start: 0.8195 (tp) cc_final: 0.7674 (tt) REVERT: E 470 ILE cc_start: 0.6932 (mm) cc_final: 0.6217 (pt) REVERT: E 474 ILE cc_start: 0.4801 (OUTLIER) cc_final: 0.4599 (tp) REVERT: F 58 TRP cc_start: 0.8290 (m100) cc_final: 0.7887 (m100) REVERT: F 84 MET cc_start: 0.5741 (ptt) cc_final: 0.5220 (ptt) REVERT: F 114 GLU cc_start: 0.7262 (tp30) cc_final: 0.6581 (tp30) REVERT: F 118 MET cc_start: 0.8275 (mtp) cc_final: 0.7712 (mtp) REVERT: F 124 ASN cc_start: 0.7648 (OUTLIER) cc_final: 0.5726 (m-40) REVERT: F 156 ASN cc_start: 0.8597 (t0) cc_final: 0.8082 (m110) REVERT: F 222 ASP cc_start: 0.6250 (m-30) cc_final: 0.6040 (m-30) REVERT: F 268 TYR cc_start: 0.8306 (t80) cc_final: 0.7953 (t80) REVERT: F 340 VAL cc_start: 0.8867 (m) cc_final: 0.8579 (t) REVERT: F 381 LEU cc_start: 0.7674 (mt) cc_final: 0.7436 (tp) REVERT: F 389 TYR cc_start: 0.7118 (OUTLIER) cc_final: 0.6356 (t80) REVERT: F 392 LEU cc_start: 0.8746 (tp) cc_final: 0.8411 (mm) REVERT: F 412 GLN cc_start: 0.0231 (OUTLIER) cc_final: -0.0342 (mm-40) REVERT: F 428 THR cc_start: 0.8420 (t) cc_final: 0.8120 (t) REVERT: F 446 VAL cc_start: 0.4250 (OUTLIER) cc_final: 0.3975 (p) REVERT: F 465 MET cc_start: 0.3738 (mtm) cc_final: 0.2160 (ttt) REVERT: G 39 ILE cc_start: 0.8859 (tp) cc_final: 0.8538 (pt) REVERT: G 58 TRP cc_start: 0.7790 (m100) cc_final: 0.7219 (m100) REVERT: G 91 TYR cc_start: 0.6661 (t80) cc_final: 0.6449 (t80) REVERT: G 137 LEU cc_start: 0.7717 (tp) cc_final: 0.7351 (tp) REVERT: G 151 GLU cc_start: 0.8614 (mm-30) cc_final: 0.8371 (tt0) REVERT: G 263 SER cc_start: 0.7465 (OUTLIER) cc_final: 0.7255 (m) REVERT: G 268 TYR cc_start: 0.7772 (t80) cc_final: 0.6742 (t80) REVERT: G 273 LEU cc_start: 0.7834 (tp) cc_final: 0.7427 (tt) REVERT: G 284 GLU cc_start: 0.8774 (tt0) cc_final: 0.8450 (tt0) REVERT: G 470 ILE cc_start: 0.6634 (mm) cc_final: 0.5913 (pt) REVERT: G 474 ILE cc_start: 0.4535 (OUTLIER) cc_final: 0.4292 (tp) REVERT: H 54 TYR cc_start: 0.6818 (m-10) cc_final: 0.6115 (m-10) REVERT: H 58 TRP cc_start: 0.8178 (m100) cc_final: 0.7796 (m100) REVERT: H 101 ASP cc_start: 0.6154 (t0) cc_final: 0.5783 (t70) REVERT: H 112 MET cc_start: 0.7979 (mtt) cc_final: 0.6372 (tpt) REVERT: H 114 GLU cc_start: 0.7056 (tp30) cc_final: 0.6732 (tp30) REVERT: H 124 ASN cc_start: 0.7499 (OUTLIER) cc_final: 0.4911 (m-40) REVERT: H 132 GLU cc_start: 0.8446 (mm-30) cc_final: 0.8231 (tp30) REVERT: H 193 ASP cc_start: 0.7424 (OUTLIER) cc_final: 0.7200 (p0) REVERT: H 222 ASP cc_start: 0.6292 (m-30) cc_final: 0.6032 (m-30) REVERT: H 352 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.9016 (mm) REVERT: H 353 SER cc_start: 0.8982 (OUTLIER) cc_final: 0.8686 (m) REVERT: H 368 ARG cc_start: 0.0879 (OUTLIER) cc_final: 0.0481 (mmm160) REVERT: H 389 TYR cc_start: 0.7456 (OUTLIER) cc_final: 0.6244 (t80) REVERT: H 392 LEU cc_start: 0.8909 (tp) cc_final: 0.8707 (mm) REVERT: H 412 GLN cc_start: 0.0334 (OUTLIER) cc_final: -0.0485 (pt0) REVERT: H 428 THR cc_start: 0.8308 (t) cc_final: 0.8099 (t) REVERT: H 449 TRP cc_start: 0.2726 (m-10) cc_final: 0.2514 (m-10) REVERT: H 465 MET cc_start: 0.4102 (mtm) cc_final: 0.2781 (ttt) REVERT: I 91 TYR cc_start: 0.6987 (t80) cc_final: 0.6569 (t80) REVERT: I 388 VAL cc_start: 0.7629 (m) cc_final: 0.7391 (p) REVERT: I 470 ILE cc_start: 0.6391 (mm) cc_final: 0.5633 (pt) REVERT: I 474 ILE cc_start: 0.4316 (OUTLIER) cc_final: 0.3849 (tp) REVERT: J 58 TRP cc_start: 0.8141 (m100) cc_final: 0.7904 (m100) REVERT: J 59 GLN cc_start: 0.8566 (pp30) cc_final: 0.8320 (pp30) REVERT: J 114 GLU cc_start: 0.7123 (tp30) cc_final: 0.6665 (tp30) REVERT: J 132 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8345 (tp30) REVERT: J 340 VAL cc_start: 0.8921 (m) cc_final: 0.8622 (t) REVERT: J 446 VAL cc_start: 0.3796 (OUTLIER) cc_final: 0.3522 (p) REVERT: J 465 MET cc_start: 0.3374 (mtm) cc_final: 0.2130 (ttt) REVERT: K 54 TYR cc_start: 0.6581 (m-10) cc_final: 0.6347 (m-10) REVERT: K 58 TRP cc_start: 0.7742 (m100) cc_final: 0.7193 (m100) REVERT: K 88 ILE cc_start: 0.5329 (OUTLIER) cc_final: 0.5029 (tp) REVERT: K 91 TYR cc_start: 0.6667 (t80) cc_final: 0.6448 (t80) REVERT: K 235 MET cc_start: 0.7734 (mmm) cc_final: 0.6940 (ptt) REVERT: K 263 SER cc_start: 0.7273 (OUTLIER) cc_final: 0.7034 (m) REVERT: K 268 TYR cc_start: 0.7691 (t80) cc_final: 0.6658 (t80) REVERT: K 273 LEU cc_start: 0.8177 (tp) cc_final: 0.7673 (tt) REVERT: K 470 ILE cc_start: 0.6919 (mm) cc_final: 0.6213 (pt) REVERT: K 474 ILE cc_start: 0.4809 (OUTLIER) cc_final: 0.4598 (tp) REVERT: L 58 TRP cc_start: 0.8286 (m100) cc_final: 0.7866 (m100) REVERT: L 84 MET cc_start: 0.5698 (ptt) cc_final: 0.5243 (ptt) REVERT: L 112 MET cc_start: 0.8043 (mtt) cc_final: 0.6040 (tpt) REVERT: L 114 GLU cc_start: 0.7237 (tp30) cc_final: 0.6613 (tp30) REVERT: L 118 MET cc_start: 0.8313 (mtp) cc_final: 0.7387 (mtp) REVERT: L 124 ASN cc_start: 0.7668 (OUTLIER) cc_final: 0.5567 (m-40) REVERT: L 156 ASN cc_start: 0.8599 (t0) cc_final: 0.8072 (m110) REVERT: L 222 ASP cc_start: 0.6052 (m-30) cc_final: 0.5794 (m-30) REVERT: L 268 TYR cc_start: 0.8367 (t80) cc_final: 0.7985 (t80) REVERT: L 340 VAL cc_start: 0.8868 (m) cc_final: 0.8533 (t) REVERT: L 381 LEU cc_start: 0.7700 (mt) cc_final: 0.7466 (tp) REVERT: L 389 TYR cc_start: 0.7070 (OUTLIER) cc_final: 0.6312 (t80) REVERT: L 392 LEU cc_start: 0.8754 (tp) cc_final: 0.8429 (mm) REVERT: L 412 GLN cc_start: 0.0469 (OUTLIER) cc_final: -0.0211 (pt0) REVERT: L 428 THR cc_start: 0.8555 (t) cc_final: 0.8320 (t) REVERT: L 446 VAL cc_start: 0.4305 (OUTLIER) cc_final: 0.4012 (p) REVERT: L 465 MET cc_start: 0.3659 (mtm) cc_final: 0.2111 (ttt) outliers start: 780 outliers final: 155 residues processed: 1990 average time/residue: 0.2670 time to fit residues: 876.4236 Evaluate side-chains 1005 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 814 time to evaluate : 1.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 394 optimal weight: 0.5980 chunk 430 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 265 optimal weight: 4.9990 chunk 523 optimal weight: 7.9990 chunk 497 optimal weight: 5.9990 chunk 414 optimal weight: 4.9990 chunk 310 optimal weight: 1.9990 chunk 488 optimal weight: 5.9990 chunk 366 optimal weight: 10.0000 chunk 223 optimal weight: 2.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN A 124 ASN B 55 GLN B 68 ASN B 169 GLN C 55 GLN C 124 ASN C 397 GLN D 55 GLN D 169 GLN ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 GLN ** E 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 ASN E 124 ASN E 407 GLN F 55 GLN ** F 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 55 GLN ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 124 ASN H 55 GLN H 68 ASN H 169 GLN I 55 GLN I 124 ASN I 397 GLN J 55 GLN ** J 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 169 GLN K 55 GLN K 68 ASN K 124 ASN K 407 GLN L 55 GLN ** L 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.144228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.134906 restraints weight = 98873.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.133733 restraints weight = 113996.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.132036 restraints weight = 116237.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.132664 restraints weight = 95500.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.132726 restraints weight = 75324.329| |-----------------------------------------------------------------------------| r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3808 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3808 r_free = 0.3808 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3710 r_free = 0.3710 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 633 | |-----------------------------------------------------------------------------| r_final: 0.3710 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.4376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 44736 Z= 0.186 Angle : 0.751 11.247 60588 Z= 0.389 Chirality : 0.046 0.148 6876 Planarity : 0.005 0.053 7932 Dihedral : 5.105 23.462 6204 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.08 % Allowed : 5.24 % Favored : 94.68 % 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: -0.52 (0.11), residues: 5580 helix: 1.02 (0.10), residues: 2508 sheet: -0.97 (0.19), residues: 576 loop : -1.65 (0.12), residues: 2496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 182 TYR 0.035 0.002 TYR I 91 PHE 0.034 0.002 PHE F 131 TRP 0.022 0.002 TRP L 83 HIS 0.004 0.001 HIS J 216 Details of bonding type rmsd covalent geometry : bond 0.00417 (44736) covalent geometry : angle 0.75148 (60588) hydrogen bonds : bond 0.04964 ( 2160) hydrogen bonds : angle 5.13639 ( 6588) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11160 Ramachandran restraints generated. 5580 Oldfield, 0 Emsley, 5580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11160 Ramachandran restraints generated. 5580 Oldfield, 0 Emsley, 5580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1018 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 1014 time to evaluate : 1.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 ASP cc_start: 0.7840 (t70) cc_final: 0.7614 (t0) REVERT: A 39 ILE cc_start: 0.8935 (tp) cc_final: 0.8423 (pt) REVERT: A 137 LEU cc_start: 0.7400 (tp) cc_final: 0.7132 (tp) REVERT: A 151 GLU cc_start: 0.8784 (mm-30) cc_final: 0.8462 (tm-30) REVERT: A 158 MET cc_start: 0.7578 (tpp) cc_final: 0.7231 (mmm) REVERT: A 209 GLU cc_start: 0.5227 (mp0) cc_final: 0.4852 (mm-30) REVERT: A 268 TYR cc_start: 0.7762 (t80) cc_final: 0.6586 (t80) REVERT: A 329 PHE cc_start: 0.8555 (m-80) cc_final: 0.8346 (m-80) REVERT: A 392 LEU cc_start: 0.8904 (tp) cc_final: 0.8678 (tp) REVERT: A 465 MET cc_start: 0.4813 (mpp) cc_final: 0.3722 (mpp) REVERT: B 112 MET cc_start: 0.7100 (mtt) cc_final: 0.6223 (tpt) REVERT: B 132 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8144 (tp30) REVERT: B 169 GLN cc_start: 0.7583 (OUTLIER) cc_final: 0.7334 (tm-30) REVERT: B 230 GLU cc_start: 0.7359 (mt-10) cc_final: 0.6990 (mt-10) REVERT: B 289 MET cc_start: 0.8102 (ttm) cc_final: 0.7816 (ttm) REVERT: B 395 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7609 (mt-10) REVERT: B 449 TRP cc_start: 0.2326 (m-10) cc_final: 0.2091 (m-10) REVERT: C 130 LEU cc_start: 0.8545 (mm) cc_final: 0.8274 (mm) REVERT: C 209 GLU cc_start: 0.5074 (mp0) cc_final: 0.4642 (mm-30) REVERT: C 396 LEU cc_start: 0.8548 (mt) cc_final: 0.8330 (tp) REVERT: C 441 LYS cc_start: 0.4372 (pttm) cc_final: 0.3884 (mmtt) REVERT: C 465 MET cc_start: 0.4375 (mpp) cc_final: 0.3774 (mmt) REVERT: D 132 GLU cc_start: 0.8684 (mm-30) cc_final: 0.8343 (tp30) REVERT: D 268 TYR cc_start: 0.8147 (t80) cc_final: 0.7863 (t80) REVERT: D 301 ASN cc_start: 0.8996 (t0) cc_final: 0.8778 (t0) REVERT: D 325 GLU cc_start: 0.8602 (pt0) cc_final: 0.8316 (pt0) REVERT: D 333 GLU cc_start: 0.8683 (mp0) cc_final: 0.7734 (mp0) REVERT: E 54 TYR cc_start: 0.7455 (m-10) cc_final: 0.7235 (m-10) REVERT: E 74 MET cc_start: 0.8194 (tpp) cc_final: 0.7292 (tpt) REVERT: E 88 ILE cc_start: 0.4687 (mt) cc_final: 0.4483 (tp) REVERT: E 112 MET cc_start: 0.8362 (mtt) cc_final: 0.8097 (mtm) REVERT: E 130 LEU cc_start: 0.8545 (mm) cc_final: 0.8187 (mm) REVERT: E 209 GLU cc_start: 0.5681 (mp0) cc_final: 0.5398 (mm-30) REVERT: E 222 ASP cc_start: 0.5728 (m-30) cc_final: 0.5422 (m-30) REVERT: E 268 TYR cc_start: 0.7285 (t80) cc_final: 0.6376 (t80) REVERT: E 357 MET cc_start: 0.7238 (tpp) cc_final: 0.7033 (tpt) REVERT: E 381 LEU cc_start: 0.7904 (tp) cc_final: 0.7285 (tp) REVERT: E 441 LYS cc_start: 0.4830 (pttm) cc_final: 0.4325 (mmtt) REVERT: E 469 ARG cc_start: 0.4883 (mtt180) cc_final: 0.4583 (mpt-90) REVERT: E 472 ASN cc_start: 0.5950 (m-40) cc_final: 0.5721 (m-40) REVERT: F 132 GLU cc_start: 0.7872 (tp30) cc_final: 0.7388 (tp30) REVERT: F 268 TYR cc_start: 0.8177 (t80) cc_final: 0.7718 (t80) REVERT: F 301 ASN cc_start: 0.8864 (t0) cc_final: 0.8568 (t0) REVERT: F 337 ASP cc_start: 0.7691 (m-30) cc_final: 0.7128 (m-30) REVERT: F 395 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7422 (mm-30) REVERT: G 23 ASP cc_start: 0.7902 (t70) cc_final: 0.7692 (t0) REVERT: G 39 ILE cc_start: 0.8950 (tp) cc_final: 0.8435 (pt) REVERT: G 112 MET cc_start: 0.7948 (mtt) cc_final: 0.7729 (mtm) REVERT: G 137 LEU cc_start: 0.7261 (tp) cc_final: 0.7005 (tp) REVERT: G 151 GLU cc_start: 0.8767 (mm-30) cc_final: 0.8444 (tm-30) REVERT: G 158 MET cc_start: 0.7545 (tpp) cc_final: 0.7183 (mmm) REVERT: G 209 GLU cc_start: 0.5194 (mp0) cc_final: 0.4806 (mm-30) REVERT: G 268 TYR cc_start: 0.7800 (t80) cc_final: 0.6603 (t80) REVERT: G 465 MET cc_start: 0.4794 (mpp) cc_final: 0.3826 (mpp) REVERT: H 112 MET cc_start: 0.7166 (mtt) cc_final: 0.6236 (tpt) REVERT: H 132 GLU cc_start: 0.8551 (mm-30) cc_final: 0.8144 (tp30) REVERT: H 222 ASP cc_start: 0.6741 (m-30) cc_final: 0.6477 (m-30) REVERT: H 230 GLU cc_start: 0.7346 (mt-10) cc_final: 0.6952 (mt-10) REVERT: H 353 SER cc_start: 0.8703 (p) cc_final: 0.8486 (m) REVERT: H 395 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7580 (mt-10) REVERT: I 112 MET cc_start: 0.7939 (mtt) cc_final: 0.7657 (mtt) REVERT: I 130 LEU cc_start: 0.8527 (mm) cc_final: 0.8262 (mm) REVERT: I 209 GLU cc_start: 0.5077 (mp0) cc_final: 0.4693 (mm-30) REVERT: I 441 LYS cc_start: 0.4351 (pttm) cc_final: 0.3952 (mmtt) REVERT: I 465 MET cc_start: 0.3873 (mpp) cc_final: 0.3258 (mmt) REVERT: J 79 PRO cc_start: 0.9049 (Cg_exo) cc_final: 0.8784 (Cg_endo) REVERT: J 132 GLU cc_start: 0.8690 (mm-30) cc_final: 0.8389 (tp30) REVERT: J 268 TYR cc_start: 0.8176 (t80) cc_final: 0.7927 (t80) REVERT: J 301 ASN cc_start: 0.8980 (t0) cc_final: 0.8742 (t0) REVERT: J 325 GLU cc_start: 0.8513 (pt0) cc_final: 0.8217 (pt0) REVERT: J 333 GLU cc_start: 0.8696 (mp0) cc_final: 0.7730 (mp0) REVERT: K 54 TYR cc_start: 0.7444 (m-10) cc_final: 0.7123 (m-10) REVERT: K 84 MET cc_start: 0.7431 (ptt) cc_final: 0.7201 (ptp) REVERT: K 112 MET cc_start: 0.8370 (mtt) cc_final: 0.8121 (mtm) REVERT: K 130 LEU cc_start: 0.8552 (mm) cc_final: 0.8177 (mm) REVERT: K 209 GLU cc_start: 0.5740 (mp0) cc_final: 0.5449 (mm-30) REVERT: K 222 ASP cc_start: 0.5573 (m-30) cc_final: 0.5226 (m-30) REVERT: K 268 TYR cc_start: 0.7266 (t80) cc_final: 0.6300 (t80) REVERT: K 357 MET cc_start: 0.7237 (tpp) cc_final: 0.6977 (tpp) REVERT: K 381 LEU cc_start: 0.7880 (tp) cc_final: 0.7364 (tp) REVERT: K 385 LEU cc_start: 0.7699 (mt) cc_final: 0.7493 (mt) REVERT: K 396 LEU cc_start: 0.9050 (tp) cc_final: 0.8848 (tp) REVERT: K 441 LYS cc_start: 0.4953 (pttm) cc_final: 0.4401 (mmmt) REVERT: K 469 ARG cc_start: 0.4900 (mtt180) cc_final: 0.4604 (mpt-90) REVERT: K 472 ASN cc_start: 0.5954 (m-40) cc_final: 0.5737 (m-40) REVERT: L 80 MET cc_start: 0.7281 (tpp) cc_final: 0.6993 (tpp) REVERT: L 112 MET cc_start: 0.7238 (mtt) cc_final: 0.5733 (tpt) REVERT: L 118 MET cc_start: 0.7094 (mtp) cc_final: 0.6143 (mtp) REVERT: L 204 GLU cc_start: 0.7350 (pm20) cc_final: 0.7122 (mm-30) REVERT: L 301 ASN cc_start: 0.8855 (t0) cc_final: 0.8556 (t0) REVERT: L 337 ASP cc_start: 0.7646 (m-30) cc_final: 0.7238 (m-30) REVERT: L 465 MET cc_start: 0.2941 (mtm) cc_final: 0.2717 (mtt) outliers start: 4 outliers final: 0 residues processed: 1018 average time/residue: 0.2640 time to fit residues: 445.5782 Evaluate side-chains 646 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 645 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 396 optimal weight: 3.9990 chunk 372 optimal weight: 6.9990 chunk 100 optimal weight: 7.9990 chunk 158 optimal weight: 0.0970 chunk 493 optimal weight: 0.7980 chunk 151 optimal weight: 4.9990 chunk 442 optimal weight: 3.9990 chunk 414 optimal weight: 0.0570 chunk 449 optimal weight: 9.9990 chunk 417 optimal weight: 0.9980 chunk 467 optimal weight: 7.9990 overall best weight: 1.1898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 ASN B 169 GLN B 283 GLN D 169 GLN E 68 ASN ** F 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 169 GLN F 335 GLN G 124 ASN J 169 GLN K 68 ASN L 169 GLN L 335 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.138731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.126672 restraints weight = 96141.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.126501 restraints weight = 92349.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 78)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.125883 restraints weight = 73891.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.126064 restraints weight = 68050.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.126271 restraints weight = 57846.122| |-----------------------------------------------------------------------------| r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3720 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3720 r_free = 0.3720 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 633 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3710 r_free = 0.3710 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 646 | |-----------------------------------------------------------------------------| r_final: 0.3710 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.5225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 44736 Z= 0.134 Angle : 0.638 7.906 60588 Z= 0.325 Chirality : 0.042 0.163 6876 Planarity : 0.004 0.048 7932 Dihedral : 4.603 24.016 6204 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.02 % Allowed : 4.69 % Favored : 95.29 % 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: -0.25 (0.11), residues: 5580 helix: 1.27 (0.10), residues: 2544 sheet: -0.76 (0.19), residues: 576 loop : -1.59 (0.12), residues: 2460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 170 TYR 0.044 0.002 TYR I 91 PHE 0.024 0.002 PHE H 354 TRP 0.041 0.002 TRP J 449 HIS 0.004 0.001 HIS D 216 Details of bonding type rmsd covalent geometry : bond 0.00297 (44736) covalent geometry : angle 0.63779 (60588) hydrogen bonds : bond 0.04130 ( 2160) hydrogen bonds : angle 4.72631 ( 6588) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11160 Ramachandran restraints generated. 5580 Oldfield, 0 Emsley, 5580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11160 Ramachandran restraints generated. 5580 Oldfield, 0 Emsley, 5580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 949 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 948 time to evaluate : 1.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 ASP cc_start: 0.8018 (t70) cc_final: 0.7799 (t0) REVERT: A 39 ILE cc_start: 0.8864 (tp) cc_final: 0.8580 (tt) REVERT: A 151 GLU cc_start: 0.8863 (mm-30) cc_final: 0.8394 (tm-30) REVERT: A 251 TYR cc_start: 0.7710 (m-10) cc_final: 0.7240 (m-10) REVERT: A 268 TYR cc_start: 0.7442 (t80) cc_final: 0.6694 (t80) REVERT: A 329 PHE cc_start: 0.8305 (m-80) cc_final: 0.7927 (m-80) REVERT: A 441 LYS cc_start: 0.4017 (pttm) cc_final: 0.3796 (mmtt) REVERT: B 41 SER cc_start: 0.7860 (p) cc_final: 0.7582 (p) REVERT: B 52 THR cc_start: 0.6547 (p) cc_final: 0.5968 (t) REVERT: B 106 VAL cc_start: 0.7483 (t) cc_final: 0.7139 (t) REVERT: B 112 MET cc_start: 0.7256 (mtt) cc_final: 0.6267 (tpt) REVERT: B 132 GLU cc_start: 0.8679 (mm-30) cc_final: 0.8430 (tp30) REVERT: B 134 LEU cc_start: 0.8973 (tt) cc_final: 0.8726 (tt) REVERT: B 204 GLU cc_start: 0.7482 (pm20) cc_final: 0.7062 (mm-30) REVERT: B 209 GLU cc_start: 0.7858 (mp0) cc_final: 0.7332 (mm-30) REVERT: B 325 GLU cc_start: 0.8699 (pt0) cc_final: 0.7728 (pt0) REVERT: C 58 TRP cc_start: 0.7803 (m100) cc_final: 0.7471 (m100) REVERT: C 130 LEU cc_start: 0.8822 (mm) cc_final: 0.8573 (mm) REVERT: C 134 LEU cc_start: 0.8321 (tt) cc_final: 0.7993 (tp) REVERT: C 251 TYR cc_start: 0.7599 (m-80) cc_final: 0.7309 (m-80) REVERT: C 284 GLU cc_start: 0.8530 (tt0) cc_final: 0.8235 (tp30) REVERT: C 329 PHE cc_start: 0.8412 (m-80) cc_final: 0.8206 (m-80) REVERT: C 441 LYS cc_start: 0.4116 (pttm) cc_final: 0.3742 (mmtt) REVERT: C 465 MET cc_start: 0.4056 (mpp) cc_final: 0.3450 (mmt) REVERT: D 132 GLU cc_start: 0.8607 (mm-30) cc_final: 0.8180 (tp30) REVERT: D 216 HIS cc_start: 0.7330 (t-90) cc_final: 0.6909 (t-170) REVERT: D 268 TYR cc_start: 0.8076 (t80) cc_final: 0.7875 (t80) REVERT: D 301 ASN cc_start: 0.8851 (t0) cc_final: 0.8534 (t0) REVERT: D 325 GLU cc_start: 0.8490 (pt0) cc_final: 0.8200 (pt0) REVERT: D 346 ASP cc_start: 0.8669 (m-30) cc_final: 0.8445 (m-30) REVERT: D 353 SER cc_start: 0.8381 (m) cc_final: 0.8134 (m) REVERT: E 112 MET cc_start: 0.8339 (mtt) cc_final: 0.8131 (mtm) REVERT: E 130 LEU cc_start: 0.8621 (mm) cc_final: 0.8346 (mm) REVERT: E 222 ASP cc_start: 0.5747 (m-30) cc_final: 0.5541 (m-30) REVERT: E 268 TYR cc_start: 0.7116 (t80) cc_final: 0.6626 (t80) REVERT: E 337 ASP cc_start: 0.8407 (m-30) cc_final: 0.8177 (m-30) REVERT: E 357 MET cc_start: 0.7573 (tpp) cc_final: 0.7362 (mmt) REVERT: E 381 LEU cc_start: 0.7475 (tp) cc_final: 0.7060 (tp) REVERT: E 441 LYS cc_start: 0.4764 (pttm) cc_final: 0.4313 (mmtt) REVERT: E 469 ARG cc_start: 0.5150 (mtt180) cc_final: 0.4713 (mpt-90) REVERT: F 47 SER cc_start: 0.7689 (m) cc_final: 0.7120 (p) REVERT: F 83 TRP cc_start: 0.6174 (p90) cc_final: 0.5972 (p90) REVERT: F 114 GLU cc_start: 0.7904 (tm-30) cc_final: 0.7463 (tp30) REVERT: F 118 MET cc_start: 0.8214 (mtp) cc_final: 0.8012 (mtp) REVERT: F 132 GLU cc_start: 0.7839 (tp30) cc_final: 0.7615 (tp30) REVERT: F 262 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7627 (mt-10) REVERT: F 268 TYR cc_start: 0.8153 (t80) cc_final: 0.7683 (t80) REVERT: F 301 ASN cc_start: 0.8849 (t0) cc_final: 0.8516 (t0) REVERT: F 337 ASP cc_start: 0.7295 (m-30) cc_final: 0.6913 (m-30) REVERT: G 23 ASP cc_start: 0.7985 (t70) cc_final: 0.7735 (t0) REVERT: G 39 ILE cc_start: 0.8866 (tp) cc_final: 0.8586 (tt) REVERT: G 151 GLU cc_start: 0.8847 (mm-30) cc_final: 0.8404 (tm-30) REVERT: G 196 LYS cc_start: 0.7356 (mtmm) cc_final: 0.6707 (tptt) REVERT: G 251 TYR cc_start: 0.7710 (m-10) cc_final: 0.7299 (m-10) REVERT: G 268 TYR cc_start: 0.7454 (t80) cc_final: 0.6607 (t80) REVERT: G 441 LYS cc_start: 0.4167 (pttm) cc_final: 0.3788 (mmtt) REVERT: H 41 SER cc_start: 0.7887 (p) cc_final: 0.7595 (p) REVERT: H 52 THR cc_start: 0.6551 (p) cc_final: 0.5995 (t) REVERT: H 106 VAL cc_start: 0.7503 (t) cc_final: 0.7169 (t) REVERT: H 112 MET cc_start: 0.7406 (mtt) cc_final: 0.6327 (tpt) REVERT: H 132 GLU cc_start: 0.8709 (mm-30) cc_final: 0.8451 (tp30) REVERT: H 134 LEU cc_start: 0.9021 (tt) cc_final: 0.8693 (tt) REVERT: H 209 GLU cc_start: 0.7883 (mp0) cc_final: 0.7564 (mm-30) REVERT: I 58 TRP cc_start: 0.7806 (m100) cc_final: 0.7490 (m100) REVERT: I 130 LEU cc_start: 0.8888 (mm) cc_final: 0.8614 (mm) REVERT: I 134 LEU cc_start: 0.8320 (tt) cc_final: 0.7961 (tp) REVERT: I 251 TYR cc_start: 0.7598 (m-80) cc_final: 0.7347 (m-80) REVERT: I 284 GLU cc_start: 0.8536 (tt0) cc_final: 0.8240 (tp30) REVERT: I 329 PHE cc_start: 0.8400 (m-80) cc_final: 0.8177 (m-80) REVERT: I 441 LYS cc_start: 0.4041 (pttm) cc_final: 0.3691 (mmtt) REVERT: I 465 MET cc_start: 0.3917 (mpp) cc_final: 0.3304 (mmt) REVERT: J 78 PHE cc_start: 0.7939 (m-80) cc_final: 0.7709 (m-80) REVERT: J 132 GLU cc_start: 0.8645 (mm-30) cc_final: 0.8235 (tp30) REVERT: J 301 ASN cc_start: 0.8833 (t0) cc_final: 0.8467 (t0) REVERT: J 325 GLU cc_start: 0.8223 (pt0) cc_final: 0.7991 (pt0) REVERT: J 402 ARG cc_start: 0.7971 (ttm170) cc_final: 0.7138 (ttm-80) REVERT: K 112 MET cc_start: 0.8345 (mtt) cc_final: 0.8111 (mtm) REVERT: K 130 LEU cc_start: 0.8635 (mm) cc_final: 0.8348 (mm) REVERT: K 268 TYR cc_start: 0.7188 (t80) cc_final: 0.6589 (t80) REVERT: K 357 MET cc_start: 0.7571 (tpp) cc_final: 0.7345 (mmt) REVERT: K 381 LEU cc_start: 0.7584 (tp) cc_final: 0.7147 (tp) REVERT: K 441 LYS cc_start: 0.4770 (pttm) cc_final: 0.4322 (mmtt) REVERT: K 469 ARG cc_start: 0.5161 (mtt180) cc_final: 0.4742 (mpt-90) REVERT: L 47 SER cc_start: 0.7664 (m) cc_final: 0.7115 (p) REVERT: L 112 MET cc_start: 0.7531 (mtt) cc_final: 0.5793 (tpt) REVERT: L 230 GLU cc_start: 0.7177 (mt-10) cc_final: 0.6750 (mt-10) REVERT: L 301 ASN cc_start: 0.8794 (t0) cc_final: 0.8533 (t0) REVERT: L 332 LEU cc_start: 0.8330 (mm) cc_final: 0.8046 (mm) REVERT: L 337 ASP cc_start: 0.7581 (m-30) cc_final: 0.7025 (m-30) REVERT: L 395 GLU cc_start: 0.8297 (mm-30) cc_final: 0.7751 (mm-30) outliers start: 1 outliers final: 0 residues processed: 949 average time/residue: 0.2696 time to fit residues: 425.6676 Evaluate side-chains 622 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 622 time to evaluate : 1.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 134 optimal weight: 3.9990 chunk 239 optimal weight: 10.0000 chunk 263 optimal weight: 0.9990 chunk 513 optimal weight: 4.9990 chunk 423 optimal weight: 0.6980 chunk 302 optimal weight: 0.9990 chunk 49 optimal weight: 0.0870 chunk 177 optimal weight: 2.9990 chunk 356 optimal weight: 7.9990 chunk 215 optimal weight: 8.9990 chunk 89 optimal weight: 8.9990 overall best weight: 1.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 ASN A 184 GLN A 216 HIS ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 335 GLN ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 ASN C 335 GLN C 407 GLN D 169 GLN E 178 GLN ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 169 GLN ** G 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 124 ASN G 184 GLN G 216 HIS G 335 GLN ** G 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 169 GLN ** I 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 407 GLN J 169 GLN K 32 GLN ** K 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 169 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.138930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.126888 restraints weight = 96044.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.126798 restraints weight = 90094.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.125868 restraints weight = 76118.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.126082 restraints weight = 68446.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.126128 restraints weight = 59963.739| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3716 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3716 r_free = 0.3716 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 646 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3713 r_free = 0.3713 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 664 | |-----------------------------------------------------------------------------| r_final: 0.3713 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.5764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 44736 Z= 0.129 Angle : 0.625 7.974 60588 Z= 0.319 Chirality : 0.042 0.165 6876 Planarity : 0.004 0.052 7932 Dihedral : 4.412 23.730 6204 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.11 % Allowed : 3.41 % Favored : 96.49 % 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: -0.15 (0.11), residues: 5580 helix: 1.37 (0.10), residues: 2568 sheet: -0.77 (0.19), residues: 636 loop : -1.60 (0.12), residues: 2376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 170 TYR 0.029 0.002 TYR B 126 PHE 0.027 0.002 PHE D 354 TRP 0.028 0.002 TRP G 58 HIS 0.005 0.001 HIS D 216 Details of bonding type rmsd covalent geometry : bond 0.00289 (44736) covalent geometry : angle 0.62537 (60588) hydrogen bonds : bond 0.03926 ( 2160) hydrogen bonds : angle 4.59098 ( 6588) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11160 Ramachandran restraints generated. 5580 Oldfield, 0 Emsley, 5580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11160 Ramachandran restraints generated. 5580 Oldfield, 0 Emsley, 5580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 909 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 904 time to evaluate : 2.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ILE cc_start: 0.8920 (tp) cc_final: 0.8651 (tt) REVERT: A 151 GLU cc_start: 0.8860 (mm-30) cc_final: 0.8354 (tm-30) REVERT: A 251 TYR cc_start: 0.7632 (m-10) cc_final: 0.7336 (m-10) REVERT: A 268 TYR cc_start: 0.7450 (t80) cc_final: 0.6807 (t80) REVERT: A 329 PHE cc_start: 0.8372 (m-80) cc_final: 0.8078 (m-80) REVERT: A 441 LYS cc_start: 0.4656 (pttm) cc_final: 0.4117 (mmtt) REVERT: A 465 MET cc_start: 0.3708 (mmt) cc_final: 0.3120 (mmt) REVERT: A 470 ILE cc_start: 0.5916 (mm) cc_final: 0.5678 (mm) REVERT: B 106 VAL cc_start: 0.7400 (t) cc_final: 0.7130 (t) REVERT: B 112 MET cc_start: 0.6849 (mtt) cc_final: 0.6202 (tpt) REVERT: B 132 GLU cc_start: 0.8711 (mm-30) cc_final: 0.8433 (tp30) REVERT: B 204 GLU cc_start: 0.7254 (pm20) cc_final: 0.6803 (mm-30) REVERT: B 222 ASP cc_start: 0.6786 (m-30) cc_final: 0.6150 (m-30) REVERT: B 291 MET cc_start: 0.7900 (mmp) cc_final: 0.7321 (mmt) REVERT: B 325 GLU cc_start: 0.8750 (pt0) cc_final: 0.7913 (pt0) REVERT: B 353 SER cc_start: 0.8629 (m) cc_final: 0.8226 (m) REVERT: B 395 GLU cc_start: 0.8312 (mt-10) cc_final: 0.7339 (mt-10) REVERT: C 58 TRP cc_start: 0.7757 (m100) cc_final: 0.7537 (m100) REVERT: C 130 LEU cc_start: 0.8763 (mm) cc_final: 0.8453 (mm) REVERT: C 251 TYR cc_start: 0.7477 (m-80) cc_final: 0.7168 (m-80) REVERT: C 441 LYS cc_start: 0.4229 (pttm) cc_final: 0.3954 (mmtt) REVERT: C 465 MET cc_start: 0.4250 (mpp) cc_final: 0.3579 (mmm) REVERT: C 470 ILE cc_start: 0.5809 (mm) cc_final: 0.5502 (mm) REVERT: D 37 TYR cc_start: 0.7543 (m-80) cc_final: 0.7297 (m-10) REVERT: D 118 MET cc_start: 0.7395 (mtt) cc_final: 0.5978 (mtt) REVERT: D 132 GLU cc_start: 0.8577 (mm-30) cc_final: 0.8274 (tp30) REVERT: D 216 HIS cc_start: 0.7192 (t-90) cc_final: 0.6725 (t-170) REVERT: D 291 MET cc_start: 0.7563 (mmp) cc_final: 0.6520 (ttt) REVERT: D 301 ASN cc_start: 0.8588 (t0) cc_final: 0.8325 (t0) REVERT: D 325 GLU cc_start: 0.8594 (pt0) cc_final: 0.8048 (pt0) REVERT: D 395 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7408 (mt-10) REVERT: E 268 TYR cc_start: 0.7129 (t80) cc_final: 0.6843 (t80) REVERT: E 279 LEU cc_start: 0.9110 (tp) cc_final: 0.8880 (tt) REVERT: E 381 LEU cc_start: 0.7646 (tp) cc_final: 0.7277 (tp) REVERT: E 441 LYS cc_start: 0.4858 (pttm) cc_final: 0.4384 (mmtt) REVERT: E 469 ARG cc_start: 0.4912 (mtt180) cc_final: 0.4637 (mpt-90) REVERT: F 37 TYR cc_start: 0.7251 (m-80) cc_final: 0.6939 (m-10) REVERT: F 47 SER cc_start: 0.7686 (m) cc_final: 0.7107 (p) REVERT: F 114 GLU cc_start: 0.8116 (tm-30) cc_final: 0.7530 (tm-30) REVERT: F 121 ILE cc_start: 0.8064 (mm) cc_final: 0.7654 (mm) REVERT: F 169 GLN cc_start: 0.8165 (OUTLIER) cc_final: 0.7703 (pp30) REVERT: F 235 MET cc_start: 0.7372 (ptp) cc_final: 0.7132 (ptt) REVERT: F 268 TYR cc_start: 0.8100 (t80) cc_final: 0.7686 (t80) REVERT: F 301 ASN cc_start: 0.8894 (t0) cc_final: 0.8566 (t0) REVERT: F 337 ASP cc_start: 0.7598 (m-30) cc_final: 0.6789 (m-30) REVERT: F 395 GLU cc_start: 0.8001 (mt-10) cc_final: 0.6702 (mt-10) REVERT: G 39 ILE cc_start: 0.8908 (tp) cc_final: 0.8601 (tt) REVERT: G 112 MET cc_start: 0.8322 (mtm) cc_final: 0.8119 (mtm) REVERT: G 151 GLU cc_start: 0.8859 (mm-30) cc_final: 0.8350 (tm-30) REVERT: G 196 LYS cc_start: 0.7551 (mtmm) cc_final: 0.6843 (tptt) REVERT: G 268 TYR cc_start: 0.7459 (t80) cc_final: 0.6823 (t80) REVERT: G 441 LYS cc_start: 0.4483 (pttm) cc_final: 0.3952 (mmtt) REVERT: G 470 ILE cc_start: 0.5826 (mm) cc_final: 0.5604 (mm) REVERT: H 106 VAL cc_start: 0.7378 (t) cc_final: 0.7073 (t) REVERT: H 112 MET cc_start: 0.7233 (mtt) cc_final: 0.6197 (tpt) REVERT: H 132 GLU cc_start: 0.8748 (mm-30) cc_final: 0.8506 (tp30) REVERT: H 144 LEU cc_start: 0.8993 (tp) cc_final: 0.8706 (tt) REVERT: H 352 LEU cc_start: 0.9035 (mm) cc_final: 0.8397 (mt) REVERT: I 80 MET cc_start: 0.7555 (mpp) cc_final: 0.7243 (mpp) REVERT: I 441 LYS cc_start: 0.4352 (pttm) cc_final: 0.4049 (mmtt) REVERT: I 465 MET cc_start: 0.3330 (mpp) cc_final: 0.2672 (mmm) REVERT: J 37 TYR cc_start: 0.7551 (m-80) cc_final: 0.7302 (m-10) REVERT: J 132 GLU cc_start: 0.8688 (mm-30) cc_final: 0.8423 (tp30) REVERT: J 256 MET cc_start: 0.7042 (tmm) cc_final: 0.6758 (tpp) REVERT: J 291 MET cc_start: 0.7573 (mmp) cc_final: 0.6507 (ttt) REVERT: J 301 ASN cc_start: 0.8593 (t0) cc_final: 0.8356 (t0) REVERT: J 395 GLU cc_start: 0.7741 (mt-10) cc_final: 0.6887 (mt-10) REVERT: J 472 ASN cc_start: 0.7223 (t0) cc_final: 0.6872 (p0) REVERT: K 441 LYS cc_start: 0.4992 (pttm) cc_final: 0.4295 (mmtt) REVERT: K 469 ARG cc_start: 0.4933 (mtt180) cc_final: 0.4684 (mpt-90) REVERT: L 37 TYR cc_start: 0.7319 (m-80) cc_final: 0.7001 (m-10) REVERT: L 47 SER cc_start: 0.7597 (m) cc_final: 0.7174 (p) REVERT: L 112 MET cc_start: 0.7587 (mtt) cc_final: 0.5867 (tpt) REVERT: L 132 GLU cc_start: 0.7867 (tp30) cc_final: 0.7663 (tp30) REVERT: L 169 GLN cc_start: 0.8157 (OUTLIER) cc_final: 0.7674 (pp30) REVERT: L 230 GLU cc_start: 0.7066 (mt-10) cc_final: 0.6814 (mt-10) REVERT: L 268 TYR cc_start: 0.7495 (t80) cc_final: 0.7098 (t80) REVERT: L 337 ASP cc_start: 0.7677 (m-30) cc_final: 0.6867 (m-30) REVERT: L 395 GLU cc_start: 0.8353 (mm-30) cc_final: 0.7648 (mt-10) outliers start: 5 outliers final: 0 residues processed: 909 average time/residue: 0.2532 time to fit residues: 385.1041 Evaluate side-chains 625 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 623 time to evaluate : 1.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 548 optimal weight: 20.0000 chunk 93 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 516 optimal weight: 5.9990 chunk 372 optimal weight: 0.0870 chunk 485 optimal weight: 6.9990 chunk 403 optimal weight: 2.9990 chunk 184 optimal weight: 5.9990 chunk 271 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 299 optimal weight: 7.9990 overall best weight: 2.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 124 ASN A 178 GLN A 184 GLN ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 GLN ** E 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 216 HIS ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 216 HIS F 283 GLN G 32 GLN G 124 ASN G 178 GLN G 184 GLN ** G 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 68 ASN J 363 GLN K 178 GLN ** K 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.135944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.121926 restraints weight = 96651.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.121870 restraints weight = 96948.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.122622 restraints weight = 78634.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.123045 restraints weight = 60139.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.123029 restraints weight = 59007.579| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3667 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3667 r_free = 0.3667 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 664 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3664 r_free = 0.3664 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 673 | |-----------------------------------------------------------------------------| r_final: 0.3664 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.6044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 44736 Z= 0.151 Angle : 0.634 7.412 60588 Z= 0.323 Chirality : 0.042 0.155 6876 Planarity : 0.004 0.046 7932 Dihedral : 4.366 23.275 6204 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.02 % Allowed : 2.95 % Favored : 97.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.11), residues: 5580 helix: 1.11 (0.10), residues: 2628 sheet: -0.78 (0.20), residues: 636 loop : -1.55 (0.13), residues: 2316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 64 TYR 0.049 0.002 TYR I 91 PHE 0.027 0.002 PHE H 354 TRP 0.021 0.002 TRP J 83 HIS 0.009 0.002 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00349 (44736) covalent geometry : angle 0.63434 (60588) hydrogen bonds : bond 0.04021 ( 2160) hydrogen bonds : angle 4.60411 ( 6588) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11160 Ramachandran restraints generated. 5580 Oldfield, 0 Emsley, 5580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11160 Ramachandran restraints generated. 5580 Oldfield, 0 Emsley, 5580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 874 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 873 time to evaluate : 1.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ILE cc_start: 0.9066 (tp) cc_final: 0.8776 (tt) REVERT: A 151 GLU cc_start: 0.8926 (mm-30) cc_final: 0.8462 (tt0) REVERT: A 268 TYR cc_start: 0.7486 (t80) cc_final: 0.7093 (t80) REVERT: A 357 MET cc_start: 0.6938 (tpt) cc_final: 0.6483 (tpp) REVERT: A 441 LYS cc_start: 0.4613 (pttm) cc_final: 0.4094 (mmtt) REVERT: A 470 ILE cc_start: 0.6050 (mm) cc_final: 0.5799 (mm) REVERT: B 112 MET cc_start: 0.6749 (mtt) cc_final: 0.5920 (tpt) REVERT: B 132 GLU cc_start: 0.8774 (mm-30) cc_final: 0.8473 (tp30) REVERT: B 204 GLU cc_start: 0.7399 (pm20) cc_final: 0.7024 (mm-30) REVERT: B 291 MET cc_start: 0.8192 (mmp) cc_final: 0.7588 (mmt) REVERT: B 325 GLU cc_start: 0.8844 (pt0) cc_final: 0.7908 (pt0) REVERT: B 395 GLU cc_start: 0.7916 (mt-10) cc_final: 0.6864 (mt-10) REVERT: B 397 GLN cc_start: 0.7257 (mm-40) cc_final: 0.6990 (mm-40) REVERT: C 58 TRP cc_start: 0.7996 (m100) cc_final: 0.6909 (m100) REVERT: C 337 ASP cc_start: 0.8544 (m-30) cc_final: 0.8326 (m-30) REVERT: C 441 LYS cc_start: 0.4093 (pttm) cc_final: 0.3830 (mmtt) REVERT: C 470 ILE cc_start: 0.5918 (mm) cc_final: 0.5527 (mm) REVERT: D 132 GLU cc_start: 0.8624 (mm-30) cc_final: 0.8320 (tp30) REVERT: D 216 HIS cc_start: 0.7451 (t-90) cc_final: 0.6819 (t-170) REVERT: D 291 MET cc_start: 0.7938 (mmp) cc_final: 0.6794 (ttt) REVERT: D 301 ASN cc_start: 0.8809 (t0) cc_final: 0.8570 (t0) REVERT: D 325 GLU cc_start: 0.8810 (pt0) cc_final: 0.8139 (pt0) REVERT: D 353 SER cc_start: 0.8113 (m) cc_final: 0.7648 (t) REVERT: D 376 TYR cc_start: 0.7247 (t80) cc_final: 0.6821 (t80) REVERT: E 130 LEU cc_start: 0.8553 (mm) cc_final: 0.8256 (mm) REVERT: E 230 GLU cc_start: 0.7604 (pm20) cc_final: 0.7391 (pm20) REVERT: E 279 LEU cc_start: 0.9239 (tp) cc_final: 0.8928 (tt) REVERT: E 441 LYS cc_start: 0.4552 (pttm) cc_final: 0.4264 (mmtt) REVERT: E 469 ARG cc_start: 0.4807 (mtt180) cc_final: 0.4576 (mpt-90) REVERT: E 470 ILE cc_start: 0.6366 (mm) cc_final: 0.5950 (mm) REVERT: F 37 TYR cc_start: 0.7432 (m-80) cc_final: 0.7110 (m-10) REVERT: F 47 SER cc_start: 0.7295 (m) cc_final: 0.6646 (p) REVERT: F 268 TYR cc_start: 0.8257 (t80) cc_final: 0.7726 (t80) REVERT: F 269 ILE cc_start: 0.8803 (mm) cc_final: 0.8442 (mm) REVERT: F 337 ASP cc_start: 0.7591 (m-30) cc_final: 0.6895 (m-30) REVERT: G 39 ILE cc_start: 0.9006 (tp) cc_final: 0.8723 (tt) REVERT: G 151 GLU cc_start: 0.8853 (mm-30) cc_final: 0.8427 (tt0) REVERT: G 196 LYS cc_start: 0.7514 (mtmm) cc_final: 0.6710 (tptt) REVERT: G 268 TYR cc_start: 0.7505 (t80) cc_final: 0.7085 (t80) REVERT: G 441 LYS cc_start: 0.4598 (pttm) cc_final: 0.4066 (mmtt) REVERT: G 470 ILE cc_start: 0.6069 (mm) cc_final: 0.5845 (mm) REVERT: H 112 MET cc_start: 0.6858 (mtt) cc_final: 0.6055 (tpt) REVERT: H 118 MET cc_start: 0.7511 (mtt) cc_final: 0.6602 (mtt) REVERT: H 132 GLU cc_start: 0.8784 (mm-30) cc_final: 0.8476 (tp30) REVERT: H 218 TYR cc_start: 0.5545 (p90) cc_final: 0.5341 (p90) REVERT: I 58 TRP cc_start: 0.7155 (m100) cc_final: 0.6947 (m100) REVERT: I 80 MET cc_start: 0.7780 (mpp) cc_final: 0.7281 (mpp) REVERT: I 112 MET cc_start: 0.7985 (mtm) cc_final: 0.7694 (mtm) REVERT: I 441 LYS cc_start: 0.4264 (pttm) cc_final: 0.4009 (mmtt) REVERT: J 37 TYR cc_start: 0.7576 (m-80) cc_final: 0.7316 (m-10) REVERT: J 78 PHE cc_start: 0.8113 (m-10) cc_final: 0.7909 (m-10) REVERT: J 132 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8338 (tp30) REVERT: J 267 SER cc_start: 0.8132 (p) cc_final: 0.7743 (p) REVERT: J 291 MET cc_start: 0.7968 (mmp) cc_final: 0.6780 (ttt) REVERT: J 301 ASN cc_start: 0.8790 (t0) cc_final: 0.8548 (t0) REVERT: J 325 GLU cc_start: 0.8383 (pt0) cc_final: 0.7937 (pt0) REVERT: J 353 SER cc_start: 0.8044 (m) cc_final: 0.7507 (t) REVERT: J 376 TYR cc_start: 0.7157 (t80) cc_final: 0.6574 (t80) REVERT: K 130 LEU cc_start: 0.8611 (mm) cc_final: 0.8319 (mm) REVERT: K 351 ARG cc_start: 0.7286 (ttp-110) cc_final: 0.6980 (ttm110) REVERT: K 398 LEU cc_start: 0.8789 (mm) cc_final: 0.8566 (mm) REVERT: K 441 LYS cc_start: 0.4817 (pttm) cc_final: 0.4348 (mmtt) REVERT: K 469 ARG cc_start: 0.4826 (mtt180) cc_final: 0.4592 (mpt-90) REVERT: K 470 ILE cc_start: 0.6302 (mm) cc_final: 0.5981 (mm) REVERT: L 37 TYR cc_start: 0.7474 (m-80) cc_final: 0.7116 (m-10) REVERT: L 47 SER cc_start: 0.7315 (m) cc_final: 0.6732 (p) REVERT: L 112 MET cc_start: 0.7634 (mtt) cc_final: 0.5869 (tpt) REVERT: L 114 GLU cc_start: 0.8136 (tm-30) cc_final: 0.7919 (tm-30) REVERT: L 230 GLU cc_start: 0.7150 (mt-10) cc_final: 0.6824 (mt-10) REVERT: L 337 ASP cc_start: 0.7708 (m-30) cc_final: 0.6967 (m-30) REVERT: L 395 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7547 (mt-10) outliers start: 1 outliers final: 0 residues processed: 874 average time/residue: 0.2532 time to fit residues: 370.7492 Evaluate side-chains 600 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 600 time to evaluate : 1.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 464 optimal weight: 9.9990 chunk 75 optimal weight: 0.0980 chunk 176 optimal weight: 6.9990 chunk 42 optimal weight: 9.9990 chunk 498 optimal weight: 0.9990 chunk 318 optimal weight: 7.9990 chunk 340 optimal weight: 7.9990 chunk 116 optimal weight: 5.9990 chunk 68 optimal weight: 8.9990 chunk 369 optimal weight: 0.8980 chunk 534 optimal weight: 8.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 ASN A 124 ASN A 184 GLN ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 HIS ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 ASN D 281 ASN ** E 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 ASN E 178 GLN E 184 GLN ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 169 GLN F 184 GLN G 68 ASN G 124 ASN G 184 GLN ** G 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 GLN H 169 GLN ** I 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 281 ASN J 472 ASN K 32 GLN K 68 ASN K 184 GLN K 216 HIS ** K 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 169 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.133073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.118850 restraints weight = 97629.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.119182 restraints weight = 85308.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.119522 restraints weight = 67054.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.119539 restraints weight = 58699.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.119627 restraints weight = 50168.784| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3620 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3620 r_free = 0.3620 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 673 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3618 r_free = 0.3618 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 696 | |-----------------------------------------------------------------------------| r_final: 0.3618 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.6373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 44736 Z= 0.178 Angle : 0.667 7.564 60588 Z= 0.343 Chirality : 0.043 0.163 6876 Planarity : 0.004 0.046 7932 Dihedral : 4.539 23.896 6204 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 0.04 % Allowed : 2.99 % Favored : 96.97 % 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: -0.44 (0.11), residues: 5580 helix: 0.93 (0.10), residues: 2640 sheet: -0.89 (0.20), residues: 648 loop : -1.56 (0.13), residues: 2292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 64 TYR 0.035 0.002 TYR I 91 PHE 0.027 0.002 PHE F 354 TRP 0.057 0.002 TRP J 449 HIS 0.011 0.003 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00408 (44736) covalent geometry : angle 0.66703 (60588) hydrogen bonds : bond 0.04225 ( 2160) hydrogen bonds : angle 4.69042 ( 6588) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11160 Ramachandran restraints generated. 5580 Oldfield, 0 Emsley, 5580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11160 Ramachandran restraints generated. 5580 Oldfield, 0 Emsley, 5580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 807 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 805 time to evaluate : 1.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ILE cc_start: 0.9030 (tp) cc_final: 0.8759 (tt) REVERT: A 54 TYR cc_start: 0.7743 (m-10) cc_final: 0.7531 (m-10) REVERT: A 68 ASN cc_start: 0.8874 (t0) cc_final: 0.8638 (t0) REVERT: A 137 LEU cc_start: 0.7774 (tp) cc_final: 0.7459 (tt) REVERT: A 151 GLU cc_start: 0.8945 (mm-30) cc_final: 0.8424 (tt0) REVERT: A 268 TYR cc_start: 0.7686 (t80) cc_final: 0.7349 (t80) REVERT: A 273 LEU cc_start: 0.8316 (tp) cc_final: 0.7853 (tp) REVERT: A 441 LYS cc_start: 0.4747 (pttm) cc_final: 0.4072 (mmtt) REVERT: B 112 MET cc_start: 0.6386 (mtt) cc_final: 0.5897 (tpt) REVERT: B 132 GLU cc_start: 0.8867 (mm-30) cc_final: 0.8600 (tp30) REVERT: B 204 GLU cc_start: 0.7545 (pm20) cc_final: 0.7160 (mm-30) REVERT: B 291 MET cc_start: 0.8169 (mmp) cc_final: 0.7576 (mmm) REVERT: B 325 GLU cc_start: 0.8858 (pt0) cc_final: 0.8054 (pt0) REVERT: B 397 GLN cc_start: 0.7237 (mm-40) cc_final: 0.6759 (mm-40) REVERT: C 130 LEU cc_start: 0.8838 (mm) cc_final: 0.8462 (mm) REVERT: C 146 TYR cc_start: 0.7030 (t80) cc_final: 0.6646 (t80) REVERT: C 381 LEU cc_start: 0.7863 (tp) cc_final: 0.7570 (tp) REVERT: C 465 MET cc_start: 0.3278 (mpp) cc_final: 0.2980 (mpp) REVERT: D 132 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8385 (tp30) REVERT: D 268 TYR cc_start: 0.8022 (t80) cc_final: 0.7661 (t80) REVERT: D 291 MET cc_start: 0.7917 (mmp) cc_final: 0.6911 (ttt) REVERT: D 301 ASN cc_start: 0.8780 (t0) cc_final: 0.8557 (t0) REVERT: D 325 GLU cc_start: 0.8675 (pt0) cc_final: 0.8020 (pt0) REVERT: D 333 GLU cc_start: 0.8551 (mp0) cc_final: 0.7591 (mp0) REVERT: D 353 SER cc_start: 0.8208 (m) cc_final: 0.7724 (t) REVERT: D 376 TYR cc_start: 0.6949 (t80) cc_final: 0.6609 (t80) REVERT: D 395 GLU cc_start: 0.8361 (mt-10) cc_final: 0.7807 (mt-10) REVERT: E 230 GLU cc_start: 0.7831 (pm20) cc_final: 0.7618 (pm20) REVERT: E 357 MET cc_start: 0.7158 (tpt) cc_final: 0.6738 (tpt) REVERT: F 37 TYR cc_start: 0.7600 (m-80) cc_final: 0.7379 (m-10) REVERT: F 53 ASP cc_start: 0.8555 (p0) cc_final: 0.7525 (p0) REVERT: F 112 MET cc_start: 0.6136 (mtm) cc_final: 0.5288 (tpp) REVERT: F 132 GLU cc_start: 0.7750 (tp30) cc_final: 0.7227 (tp30) REVERT: F 155 TYR cc_start: 0.7721 (p90) cc_final: 0.7490 (p90) REVERT: F 216 HIS cc_start: 0.7394 (t-90) cc_final: 0.7071 (t-170) REVERT: F 235 MET cc_start: 0.7299 (ptp) cc_final: 0.6997 (ptt) REVERT: F 260 ASP cc_start: 0.6113 (p0) cc_final: 0.5818 (p0) REVERT: F 357 MET cc_start: 0.7500 (tmm) cc_final: 0.6552 (tmm) REVERT: G 39 ILE cc_start: 0.9012 (tp) cc_final: 0.8682 (tt) REVERT: G 151 GLU cc_start: 0.8922 (mm-30) cc_final: 0.8456 (tt0) REVERT: G 196 LYS cc_start: 0.7724 (mtmm) cc_final: 0.6844 (tptt) REVERT: G 268 TYR cc_start: 0.7730 (t80) cc_final: 0.7247 (t80) REVERT: G 273 LEU cc_start: 0.8273 (tp) cc_final: 0.7831 (tp) REVERT: G 441 LYS cc_start: 0.4626 (pttm) cc_final: 0.4049 (mmtt) REVERT: H 83 TRP cc_start: 0.5664 (p90) cc_final: 0.5259 (p90) REVERT: H 112 MET cc_start: 0.6891 (mtt) cc_final: 0.6064 (tpt) REVERT: H 132 GLU cc_start: 0.8851 (mm-30) cc_final: 0.8578 (tp30) REVERT: H 325 GLU cc_start: 0.8702 (pt0) cc_final: 0.7895 (pt0) REVERT: I 58 TRP cc_start: 0.7358 (m100) cc_final: 0.6968 (m100) REVERT: I 80 MET cc_start: 0.7707 (mpp) cc_final: 0.7229 (mpp) REVERT: I 146 TYR cc_start: 0.7118 (t80) cc_final: 0.6865 (t80) REVERT: I 381 LEU cc_start: 0.7685 (tp) cc_final: 0.7465 (tp) REVERT: I 465 MET cc_start: 0.3129 (mpp) cc_final: 0.2763 (mpp) REVERT: J 37 TYR cc_start: 0.7622 (m-80) cc_final: 0.7379 (m-10) REVERT: J 291 MET cc_start: 0.7909 (mmp) cc_final: 0.6821 (ttt) REVERT: J 301 ASN cc_start: 0.8763 (t0) cc_final: 0.8490 (t0) REVERT: J 325 GLU cc_start: 0.8365 (pt0) cc_final: 0.7977 (pt0) REVERT: J 376 TYR cc_start: 0.7225 (t80) cc_final: 0.6618 (t80) REVERT: J 472 ASN cc_start: 0.7555 (t0) cc_final: 0.6837 (m-40) REVERT: K 259 LEU cc_start: 0.8068 (mt) cc_final: 0.7858 (mp) REVERT: K 441 LYS cc_start: 0.4842 (pttm) cc_final: 0.4533 (mmtt) REVERT: L 37 TYR cc_start: 0.7630 (m-80) cc_final: 0.7345 (m-10) REVERT: L 53 ASP cc_start: 0.8583 (p0) cc_final: 0.7442 (p0) REVERT: L 112 MET cc_start: 0.7799 (mtt) cc_final: 0.5941 (tpt) REVERT: L 260 ASP cc_start: 0.5745 (p0) cc_final: 0.5444 (p0) REVERT: L 325 GLU cc_start: 0.7733 (pt0) cc_final: 0.7441 (pt0) REVERT: L 337 ASP cc_start: 0.7477 (m-30) cc_final: 0.6946 (m-30) REVERT: L 395 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7481 (mt-10) outliers start: 2 outliers final: 0 residues processed: 807 average time/residue: 0.2589 time to fit residues: 352.2839 Evaluate side-chains 575 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 575 time to evaluate : 1.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 112 optimal weight: 9.9990 chunk 67 optimal weight: 1.9990 chunk 170 optimal weight: 5.9990 chunk 210 optimal weight: 1.9990 chunk 225 optimal weight: 0.0670 chunk 211 optimal weight: 1.9990 chunk 173 optimal weight: 4.9990 chunk 392 optimal weight: 1.9990 chunk 469 optimal weight: 0.5980 chunk 404 optimal weight: 2.9990 chunk 84 optimal weight: 9.9990 overall best weight: 1.3324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 ASN A 178 GLN A 184 GLN ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 ASN D 281 ASN E 32 GLN E 81 GLN E 175 ASN E 184 GLN ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 124 ASN G 178 GLN G 184 GLN ** G 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 68 ASN K 184 GLN ** K 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.136012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.122133 restraints weight = 96438.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.122667 restraints weight = 90324.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.122535 restraints weight = 59835.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.122523 restraints weight = 52599.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.122541 restraints weight = 47654.321| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3659 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3659 r_free = 0.3659 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 696 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3657 r_free = 0.3657 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 701 | |-----------------------------------------------------------------------------| r_final: 0.3657 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.6637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 44736 Z= 0.131 Angle : 0.626 9.929 60588 Z= 0.319 Chirality : 0.042 0.190 6876 Planarity : 0.004 0.057 7932 Dihedral : 4.337 22.232 6204 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % 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: -0.36 (0.11), residues: 5580 helix: 1.15 (0.10), residues: 2568 sheet: -0.93 (0.20), residues: 648 loop : -1.61 (0.12), residues: 2364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 64 TYR 0.027 0.002 TYR I 91 PHE 0.028 0.001 PHE D 354 TRP 0.043 0.002 TRP J 449 HIS 0.007 0.002 HIS K 216 Details of bonding type rmsd covalent geometry : bond 0.00299 (44736) covalent geometry : angle 0.62586 (60588) hydrogen bonds : bond 0.03843 ( 2160) hydrogen bonds : angle 4.56045 ( 6588) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11160 Ramachandran restraints generated. 5580 Oldfield, 0 Emsley, 5580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11160 Ramachandran restraints generated. 5580 Oldfield, 0 Emsley, 5580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 827 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 827 time to evaluate : 1.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ILE cc_start: 0.8777 (tp) cc_final: 0.8518 (tt) REVERT: A 151 GLU cc_start: 0.8957 (mm-30) cc_final: 0.8431 (tt0) REVERT: A 273 LEU cc_start: 0.8287 (tp) cc_final: 0.7852 (tp) REVERT: A 441 LYS cc_start: 0.4867 (pttm) cc_final: 0.4215 (mmtt) REVERT: A 465 MET cc_start: 0.4176 (mmt) cc_final: 0.3553 (mmt) REVERT: B 112 MET cc_start: 0.6919 (mtt) cc_final: 0.5936 (tpt) REVERT: B 114 GLU cc_start: 0.8101 (tm-30) cc_final: 0.7618 (tm-30) REVERT: B 132 GLU cc_start: 0.8865 (mm-30) cc_final: 0.8610 (tp30) REVERT: B 204 GLU cc_start: 0.7452 (pm20) cc_final: 0.7065 (mm-30) REVERT: B 291 MET cc_start: 0.8106 (mmp) cc_final: 0.7395 (mmt) REVERT: B 325 GLU cc_start: 0.8877 (pt0) cc_final: 0.8017 (pt0) REVERT: B 397 GLN cc_start: 0.7456 (mm-40) cc_final: 0.7033 (mm-40) REVERT: C 58 TRP cc_start: 0.7685 (m100) cc_final: 0.6818 (m100) REVERT: C 80 MET cc_start: 0.7737 (mpp) cc_final: 0.7474 (mpp) REVERT: C 130 LEU cc_start: 0.8755 (mm) cc_final: 0.8530 (mm) REVERT: C 279 LEU cc_start: 0.8957 (tp) cc_final: 0.8685 (tt) REVERT: C 470 ILE cc_start: 0.5597 (mm) cc_final: 0.5309 (mm) REVERT: D 132 GLU cc_start: 0.8557 (mm-30) cc_final: 0.8351 (tp30) REVERT: D 291 MET cc_start: 0.7697 (mmp) cc_final: 0.6839 (ttt) REVERT: D 301 ASN cc_start: 0.8864 (t0) cc_final: 0.8637 (t0) REVERT: D 333 GLU cc_start: 0.8509 (mp0) cc_final: 0.7456 (mp0) REVERT: D 353 SER cc_start: 0.8084 (m) cc_final: 0.7509 (t) REVERT: D 376 TYR cc_start: 0.7044 (t80) cc_final: 0.6506 (t80) REVERT: D 395 GLU cc_start: 0.8296 (mt-10) cc_final: 0.7503 (mt-10) REVERT: E 68 ASN cc_start: 0.8849 (t0) cc_final: 0.8431 (t0) REVERT: E 230 GLU cc_start: 0.7831 (pm20) cc_final: 0.7590 (pm20) REVERT: E 279 LEU cc_start: 0.9179 (tp) cc_final: 0.8832 (tt) REVERT: E 470 ILE cc_start: 0.5835 (mm) cc_final: 0.5388 (mm) REVERT: F 37 TYR cc_start: 0.7389 (m-80) cc_final: 0.7084 (m-10) REVERT: F 53 ASP cc_start: 0.8775 (p0) cc_final: 0.7929 (p0) REVERT: F 112 MET cc_start: 0.6029 (mtm) cc_final: 0.5264 (tpp) REVERT: F 132 GLU cc_start: 0.7815 (tp30) cc_final: 0.7549 (tp30) REVERT: F 216 HIS cc_start: 0.7174 (t-90) cc_final: 0.6799 (t-170) REVERT: F 260 ASP cc_start: 0.5763 (p0) cc_final: 0.5473 (p0) REVERT: F 269 ILE cc_start: 0.8757 (mm) cc_final: 0.8356 (mm) REVERT: G 39 ILE cc_start: 0.8837 (tp) cc_final: 0.8485 (tt) REVERT: G 151 GLU cc_start: 0.8988 (mm-30) cc_final: 0.8496 (tt0) REVERT: G 196 LYS cc_start: 0.7733 (mtmm) cc_final: 0.6728 (tptt) REVERT: G 273 LEU cc_start: 0.8258 (tp) cc_final: 0.7803 (tp) REVERT: G 279 LEU cc_start: 0.9241 (tp) cc_final: 0.9032 (tt) REVERT: G 441 LYS cc_start: 0.4835 (pttm) cc_final: 0.4176 (mmtt) REVERT: G 465 MET cc_start: 0.4105 (mmt) cc_final: 0.3296 (mmm) REVERT: G 470 ILE cc_start: 0.5759 (mm) cc_final: 0.5558 (mm) REVERT: H 112 MET cc_start: 0.7158 (mtt) cc_final: 0.6316 (tpt) REVERT: H 132 GLU cc_start: 0.8859 (mm-30) cc_final: 0.8576 (tp30) REVERT: H 325 GLU cc_start: 0.8790 (pt0) cc_final: 0.7801 (pt0) REVERT: H 408 LEU cc_start: 0.7827 (mp) cc_final: 0.6692 (tp) REVERT: I 58 TRP cc_start: 0.7346 (m100) cc_final: 0.6957 (m100) REVERT: I 80 MET cc_start: 0.7894 (mpp) cc_final: 0.7250 (mpp) REVERT: I 465 MET cc_start: 0.2609 (mpp) cc_final: 0.2388 (mpp) REVERT: J 37 TYR cc_start: 0.7560 (m-80) cc_final: 0.7294 (m-10) REVERT: J 270 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7654 (mt-10) REVERT: J 291 MET cc_start: 0.7756 (mmp) cc_final: 0.6911 (ttt) REVERT: J 301 ASN cc_start: 0.8850 (t0) cc_final: 0.8636 (t0) REVERT: J 333 GLU cc_start: 0.8454 (mp0) cc_final: 0.7437 (mp0) REVERT: J 376 TYR cc_start: 0.7237 (t80) cc_final: 0.6505 (t80) REVERT: K 137 LEU cc_start: 0.7861 (tt) cc_final: 0.7572 (tp) REVERT: K 470 ILE cc_start: 0.6040 (mm) cc_final: 0.5693 (mm) REVERT: L 37 TYR cc_start: 0.7440 (m-80) cc_final: 0.7135 (m-10) REVERT: L 53 ASP cc_start: 0.8735 (p0) cc_final: 0.7777 (p0) REVERT: L 112 MET cc_start: 0.7750 (mtt) cc_final: 0.5961 (tpt) REVERT: L 114 GLU cc_start: 0.8201 (tm-30) cc_final: 0.7909 (tp30) REVERT: L 132 GLU cc_start: 0.8019 (tp30) cc_final: 0.7536 (tp30) REVERT: L 260 ASP cc_start: 0.5599 (p0) cc_final: 0.5299 (p0) REVERT: L 268 TYR cc_start: 0.7723 (t80) cc_final: 0.7361 (t80) REVERT: L 289 MET cc_start: 0.8080 (ttm) cc_final: 0.7855 (ttm) REVERT: L 291 MET cc_start: 0.8063 (mmm) cc_final: 0.7290 (mmm) REVERT: L 337 ASP cc_start: 0.7290 (m-30) cc_final: 0.6888 (m-30) REVERT: L 395 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7350 (mt-10) outliers start: 0 outliers final: 0 residues processed: 827 average time/residue: 0.2561 time to fit residues: 357.3475 Evaluate side-chains 573 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 573 time to evaluate : 1.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 315 optimal weight: 0.9980 chunk 396 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 497 optimal weight: 8.9990 chunk 384 optimal weight: 6.9990 chunk 214 optimal weight: 0.9990 chunk 76 optimal weight: 8.9990 chunk 3 optimal weight: 0.5980 chunk 191 optimal weight: 6.9990 chunk 398 optimal weight: 1.9990 chunk 439 optimal weight: 7.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 ASN A 136 GLN A 184 GLN ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 68 ASN D 281 ASN E 68 ASN E 178 GLN E 184 GLN ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 216 HIS G 68 ASN G 124 ASN G 136 GLN G 184 GLN ** G 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 GLN ** H 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 397 GLN ** I 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 472 ASN K 32 GLN K 184 GLN ** K 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.135922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.121892 restraints weight = 96321.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.121644 restraints weight = 79142.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.121640 restraints weight = 67305.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.122029 restraints weight = 53491.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.122025 restraints weight = 44885.205| |-----------------------------------------------------------------------------| r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3650 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3650 r_free = 0.3650 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 701 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3648 r_free = 0.3648 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 721 | |-----------------------------------------------------------------------------| r_final: 0.3648 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.6846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 44736 Z= 0.138 Angle : 0.642 9.669 60588 Z= 0.327 Chirality : 0.043 0.291 6876 Planarity : 0.004 0.043 7932 Dihedral : 4.305 21.527 6204 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.02 % Allowed : 1.41 % Favored : 98.57 % 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: -0.40 (0.11), residues: 5580 helix: 1.01 (0.10), residues: 2640 sheet: -0.89 (0.20), residues: 648 loop : -1.60 (0.13), residues: 2292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG J 444 TYR 0.022 0.002 TYR J 54 PHE 0.019 0.001 PHE D 354 TRP 0.038 0.002 TRP J 449 HIS 0.008 0.002 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00315 (44736) covalent geometry : angle 0.64163 (60588) hydrogen bonds : bond 0.03832 ( 2160) hydrogen bonds : angle 4.52999 ( 6588) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11160 Ramachandran restraints generated. 5580 Oldfield, 0 Emsley, 5580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11160 Ramachandran restraints generated. 5580 Oldfield, 0 Emsley, 5580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 755 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 754 time to evaluate : 1.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ILE cc_start: 0.8965 (tp) cc_final: 0.8527 (tt) REVERT: A 146 TYR cc_start: 0.6958 (t80) cc_final: 0.6702 (t80) REVERT: A 151 GLU cc_start: 0.8952 (mm-30) cc_final: 0.8399 (tt0) REVERT: A 273 LEU cc_start: 0.8271 (tp) cc_final: 0.7793 (tp) REVERT: A 289 MET cc_start: 0.7421 (ttm) cc_final: 0.7220 (ttm) REVERT: A 441 LYS cc_start: 0.4561 (pttm) cc_final: 0.4040 (mmtt) REVERT: A 465 MET cc_start: 0.4070 (mmt) cc_final: 0.3518 (mmt) REVERT: B 112 MET cc_start: 0.6716 (mtt) cc_final: 0.5999 (tpt) REVERT: B 132 GLU cc_start: 0.8846 (mm-30) cc_final: 0.8594 (tp30) REVERT: B 204 GLU cc_start: 0.7479 (pm20) cc_final: 0.7073 (mm-30) REVERT: B 291 MET cc_start: 0.7735 (mmp) cc_final: 0.7001 (mmt) REVERT: B 301 ASN cc_start: 0.8906 (t0) cc_final: 0.8513 (t0) REVERT: B 325 GLU cc_start: 0.8858 (pt0) cc_final: 0.8141 (pt0) REVERT: B 395 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7421 (mt-10) REVERT: C 58 TRP cc_start: 0.7800 (m100) cc_final: 0.7054 (m100) REVERT: C 80 MET cc_start: 0.7850 (mpp) cc_final: 0.7575 (mpp) REVERT: C 130 LEU cc_start: 0.8850 (mm) cc_final: 0.8536 (mm) REVERT: C 134 LEU cc_start: 0.8589 (tt) cc_final: 0.8332 (tp) REVERT: C 146 TYR cc_start: 0.7090 (t80) cc_final: 0.6823 (t80) REVERT: C 470 ILE cc_start: 0.5499 (mm) cc_final: 0.5206 (mm) REVERT: D 132 GLU cc_start: 0.8565 (mm-30) cc_final: 0.8351 (tp30) REVERT: D 291 MET cc_start: 0.7666 (mmp) cc_final: 0.6770 (ttt) REVERT: D 376 TYR cc_start: 0.7010 (t80) cc_final: 0.6455 (t80) REVERT: D 395 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7346 (mt-10) REVERT: E 61 VAL cc_start: 0.8806 (t) cc_final: 0.8180 (t) REVERT: E 74 MET cc_start: 0.8410 (tpp) cc_final: 0.7500 (tpp) REVERT: E 230 GLU cc_start: 0.7899 (pm20) cc_final: 0.7649 (pm20) REVERT: E 279 LEU cc_start: 0.9171 (tp) cc_final: 0.8806 (tt) REVERT: E 470 ILE cc_start: 0.5627 (mm) cc_final: 0.5314 (mm) REVERT: F 37 TYR cc_start: 0.7337 (m-80) cc_final: 0.7039 (m-10) REVERT: F 53 ASP cc_start: 0.8682 (p0) cc_final: 0.7698 (p0) REVERT: F 112 MET cc_start: 0.6001 (mtm) cc_final: 0.5598 (tpt) REVERT: F 132 GLU cc_start: 0.7896 (tp30) cc_final: 0.7478 (tp30) REVERT: F 235 MET cc_start: 0.7217 (ptp) cc_final: 0.6541 (ptt) REVERT: F 260 ASP cc_start: 0.5897 (p0) cc_final: 0.5531 (p0) REVERT: F 395 GLU cc_start: 0.7969 (mt-10) cc_final: 0.6521 (mt-10) REVERT: F 455 MET cc_start: 0.3885 (tpp) cc_final: 0.3540 (tpt) REVERT: G 39 ILE cc_start: 0.8911 (tp) cc_final: 0.8523 (tt) REVERT: G 151 GLU cc_start: 0.8971 (mm-30) cc_final: 0.8533 (tt0) REVERT: G 196 LYS cc_start: 0.7749 (mtmm) cc_final: 0.6702 (tptt) REVERT: G 273 LEU cc_start: 0.8238 (tp) cc_final: 0.7767 (tp) REVERT: G 279 LEU cc_start: 0.9198 (tp) cc_final: 0.8972 (tt) REVERT: G 441 LYS cc_start: 0.4653 (pttm) cc_final: 0.4097 (mmtt) REVERT: G 465 MET cc_start: 0.4072 (mmt) cc_final: 0.3281 (mmm) REVERT: H 112 MET cc_start: 0.7122 (mtt) cc_final: 0.6264 (tpt) REVERT: H 132 GLU cc_start: 0.8860 (mm-30) cc_final: 0.8572 (tp30) REVERT: H 199 GLU cc_start: 0.5906 (mt-10) cc_final: 0.5531 (mt-10) REVERT: H 270 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7645 (mt-10) REVERT: H 301 ASN cc_start: 0.8875 (t0) cc_final: 0.8449 (t0) REVERT: H 408 LEU cc_start: 0.7837 (mp) cc_final: 0.6681 (tp) REVERT: I 58 TRP cc_start: 0.7202 (m100) cc_final: 0.6735 (m100) REVERT: I 80 MET cc_start: 0.7678 (mpp) cc_final: 0.7167 (mpp) REVERT: J 37 TYR cc_start: 0.7568 (m-80) cc_final: 0.7302 (m-10) REVERT: J 270 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7873 (mt-10) REVERT: J 291 MET cc_start: 0.7712 (mmp) cc_final: 0.6794 (ttt) REVERT: J 301 ASN cc_start: 0.8746 (t0) cc_final: 0.8441 (t0) REVERT: J 376 TYR cc_start: 0.7171 (t80) cc_final: 0.6304 (t80) REVERT: J 395 GLU cc_start: 0.7785 (mt-10) cc_final: 0.6815 (mt-10) REVERT: K 74 MET cc_start: 0.8430 (tpp) cc_final: 0.7460 (tpp) REVERT: K 351 ARG cc_start: 0.6478 (ttp-110) cc_final: 0.6031 (ttp-170) REVERT: K 470 ILE cc_start: 0.5847 (mm) cc_final: 0.5514 (mm) REVERT: L 37 TYR cc_start: 0.7461 (m-80) cc_final: 0.7204 (m-10) REVERT: L 53 ASP cc_start: 0.8704 (p0) cc_final: 0.7762 (p0) REVERT: L 112 MET cc_start: 0.7613 (mtt) cc_final: 0.5883 (tpt) REVERT: L 114 GLU cc_start: 0.8117 (tm-30) cc_final: 0.7891 (tp30) REVERT: L 132 GLU cc_start: 0.8146 (tp30) cc_final: 0.7638 (tp30) REVERT: L 291 MET cc_start: 0.7971 (mmm) cc_final: 0.7271 (mmm) REVERT: L 337 ASP cc_start: 0.7500 (m-30) cc_final: 0.7070 (m-30) REVERT: L 455 MET cc_start: 0.3978 (tpp) cc_final: 0.3621 (tpt) outliers start: 1 outliers final: 0 residues processed: 755 average time/residue: 0.2498 time to fit residues: 323.4640 Evaluate side-chains 553 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 553 time to evaluate : 1.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 357 optimal weight: 10.0000 chunk 70 optimal weight: 0.9990 chunk 323 optimal weight: 0.7980 chunk 508 optimal weight: 5.9990 chunk 253 optimal weight: 0.7980 chunk 514 optimal weight: 6.9990 chunk 250 optimal weight: 10.0000 chunk 426 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 390 optimal weight: 1.9990 chunk 336 optimal weight: 0.2980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 ASN A 175 ASN A 178 GLN A 184 GLN A 335 GLN ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 HIS D 281 ASN E 81 GLN E 184 GLN E 335 GLN ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 124 ASN G 178 GLN G 184 GLN ** G 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 184 GLN ** K 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 216 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.137724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.123881 restraints weight = 95954.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.124586 restraints weight = 78640.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.124684 restraints weight = 54646.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.124554 restraints weight = 45918.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.124592 restraints weight = 45120.322| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3689 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3689 r_free = 0.3689 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 721 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3687 r_free = 0.3687 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 728 | |-----------------------------------------------------------------------------| r_final: 0.3687 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.7071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 44736 Z= 0.125 Angle : 0.640 11.772 60588 Z= 0.323 Chirality : 0.042 0.196 6876 Planarity : 0.004 0.046 7932 Dihedral : 4.174 21.413 6204 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % 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: -0.31 (0.11), residues: 5580 helix: 1.26 (0.10), residues: 2568 sheet: -0.74 (0.18), residues: 768 loop : -1.77 (0.13), residues: 2244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 258 TYR 0.041 0.001 TYR I 91 PHE 0.018 0.001 PHE D 354 TRP 0.048 0.002 TRP J 449 HIS 0.007 0.002 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00279 (44736) covalent geometry : angle 0.63967 (60588) hydrogen bonds : bond 0.03663 ( 2160) hydrogen bonds : angle 4.49978 ( 6588) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11160 Ramachandran restraints generated. 5580 Oldfield, 0 Emsley, 5580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11160 Ramachandran restraints generated. 5580 Oldfield, 0 Emsley, 5580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 786 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 786 time to evaluate : 1.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ILE cc_start: 0.8823 (tp) cc_final: 0.8479 (tt) REVERT: A 146 TYR cc_start: 0.7019 (t80) cc_final: 0.6735 (t80) REVERT: A 151 GLU cc_start: 0.8929 (mm-30) cc_final: 0.8394 (tt0) REVERT: A 273 LEU cc_start: 0.8280 (tp) cc_final: 0.7797 (tp) REVERT: A 441 LYS cc_start: 0.4824 (pttm) cc_final: 0.4250 (mmmt) REVERT: A 465 MET cc_start: 0.4455 (mmt) cc_final: 0.3710 (mmm) REVERT: B 112 MET cc_start: 0.6595 (mtt) cc_final: 0.5999 (tpt) REVERT: B 132 GLU cc_start: 0.8805 (mm-30) cc_final: 0.8559 (tp30) REVERT: B 235 MET cc_start: 0.7513 (ptp) cc_final: 0.7300 (ptt) REVERT: B 270 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7423 (mt-10) REVERT: B 301 ASN cc_start: 0.8859 (t0) cc_final: 0.8496 (t0) REVERT: B 325 GLU cc_start: 0.8892 (pt0) cc_final: 0.8395 (pt0) REVERT: B 395 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7125 (mt-10) REVERT: C 130 LEU cc_start: 0.8818 (mm) cc_final: 0.8414 (mm) REVERT: C 146 TYR cc_start: 0.7307 (t80) cc_final: 0.6881 (t80) REVERT: C 231 GLU cc_start: 0.6798 (pt0) cc_final: 0.6496 (pp20) REVERT: C 470 ILE cc_start: 0.5393 (mm) cc_final: 0.4940 (tt) REVERT: D 132 GLU cc_start: 0.8628 (mm-30) cc_final: 0.8415 (tp30) REVERT: D 179 MET cc_start: 0.7249 (ptt) cc_final: 0.6949 (ptt) REVERT: D 268 TYR cc_start: 0.8042 (t80) cc_final: 0.7704 (t80) REVERT: D 291 MET cc_start: 0.7578 (mmp) cc_final: 0.6671 (ttt) REVERT: D 301 ASN cc_start: 0.8721 (t0) cc_final: 0.8449 (t0) REVERT: D 376 TYR cc_start: 0.7047 (t80) cc_final: 0.6501 (t80) REVERT: D 395 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7395 (mt-10) REVERT: E 61 VAL cc_start: 0.8969 (t) cc_final: 0.8539 (t) REVERT: E 64 ARG cc_start: 0.7566 (ttp-110) cc_final: 0.7256 (ttp-110) REVERT: E 74 MET cc_start: 0.8386 (tpp) cc_final: 0.7605 (tpp) REVERT: E 230 GLU cc_start: 0.7858 (pm20) cc_final: 0.7650 (pm20) REVERT: E 279 LEU cc_start: 0.9129 (tp) cc_final: 0.8890 (tt) REVERT: E 430 LEU cc_start: 0.6114 (tp) cc_final: 0.5662 (tt) REVERT: E 469 ARG cc_start: 0.4666 (mtt180) cc_final: 0.4330 (mpt-90) REVERT: E 470 ILE cc_start: 0.5448 (mm) cc_final: 0.5149 (mm) REVERT: F 37 TYR cc_start: 0.7241 (m-80) cc_final: 0.6998 (m-10) REVERT: F 53 ASP cc_start: 0.8638 (p0) cc_final: 0.7462 (p0) REVERT: F 112 MET cc_start: 0.5888 (mtm) cc_final: 0.5580 (tpt) REVERT: F 260 ASP cc_start: 0.5336 (p0) cc_final: 0.5041 (p0) REVERT: F 289 MET cc_start: 0.7888 (ttm) cc_final: 0.7652 (ttm) REVERT: F 291 MET cc_start: 0.7200 (mmm) cc_final: 0.6822 (mmm) REVERT: F 395 GLU cc_start: 0.7902 (mt-10) cc_final: 0.6465 (mt-10) REVERT: F 472 ASN cc_start: 0.5952 (m-40) cc_final: 0.5667 (p0) REVERT: G 39 ILE cc_start: 0.8854 (tp) cc_final: 0.8498 (tt) REVERT: G 80 MET cc_start: 0.7315 (mpp) cc_final: 0.7071 (mpp) REVERT: G 151 GLU cc_start: 0.8858 (mm-30) cc_final: 0.8484 (tt0) REVERT: G 196 LYS cc_start: 0.7621 (mtmm) cc_final: 0.6626 (tptt) REVERT: G 273 LEU cc_start: 0.8280 (tp) cc_final: 0.7816 (tp) REVERT: G 279 LEU cc_start: 0.9157 (tp) cc_final: 0.8947 (tt) REVERT: G 337 ASP cc_start: 0.8220 (m-30) cc_final: 0.7958 (m-30) REVERT: G 441 LYS cc_start: 0.4828 (pttm) cc_final: 0.4165 (mmmt) REVERT: G 465 MET cc_start: 0.4383 (mmt) cc_final: 0.3658 (mmm) REVERT: H 112 MET cc_start: 0.7113 (mtt) cc_final: 0.6375 (tpt) REVERT: H 132 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8543 (tp30) REVERT: H 199 GLU cc_start: 0.6112 (mt-10) cc_final: 0.5713 (mt-10) REVERT: H 235 MET cc_start: 0.7489 (ptp) cc_final: 0.7266 (ptt) REVERT: H 270 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7619 (mt-10) REVERT: H 301 ASN cc_start: 0.8848 (t0) cc_final: 0.8454 (t0) REVERT: H 395 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7015 (mt-10) REVERT: H 408 LEU cc_start: 0.7833 (mp) cc_final: 0.6691 (tp) REVERT: I 58 TRP cc_start: 0.7127 (m100) cc_final: 0.6855 (m100) REVERT: I 80 MET cc_start: 0.7623 (mpp) cc_final: 0.7130 (mpp) REVERT: I 231 GLU cc_start: 0.6880 (pt0) cc_final: 0.6515 (pp20) REVERT: I 329 PHE cc_start: 0.8401 (m-80) cc_final: 0.8150 (m-10) REVERT: J 37 TYR cc_start: 0.7422 (m-80) cc_final: 0.7167 (m-10) REVERT: J 216 HIS cc_start: 0.7249 (t70) cc_final: 0.6689 (t-90) REVERT: J 291 MET cc_start: 0.7649 (mmp) cc_final: 0.6642 (ttt) REVERT: J 325 GLU cc_start: 0.8574 (pp20) cc_final: 0.8056 (pp20) REVERT: J 376 TYR cc_start: 0.7093 (t80) cc_final: 0.6312 (t80) REVERT: J 395 GLU cc_start: 0.7784 (mt-10) cc_final: 0.6840 (mt-10) REVERT: K 74 MET cc_start: 0.8409 (tpp) cc_final: 0.7962 (tpp) REVERT: K 230 GLU cc_start: 0.7999 (mp0) cc_final: 0.7608 (mp0) REVERT: K 470 ILE cc_start: 0.5426 (mm) cc_final: 0.5087 (mm) REVERT: L 37 TYR cc_start: 0.7325 (m-80) cc_final: 0.7017 (m-10) REVERT: L 53 ASP cc_start: 0.8627 (p0) cc_final: 0.7407 (p0) REVERT: L 112 MET cc_start: 0.7604 (mtt) cc_final: 0.5979 (tpt) REVERT: L 114 GLU cc_start: 0.8082 (tm-30) cc_final: 0.7828 (tp30) REVERT: L 132 GLU cc_start: 0.7999 (tp30) cc_final: 0.7606 (tp30) REVERT: L 270 GLU cc_start: 0.7468 (mt-10) cc_final: 0.7160 (mt-10) REVERT: L 291 MET cc_start: 0.7857 (mmm) cc_final: 0.7278 (ttt) REVERT: L 455 MET cc_start: 0.4163 (tpp) cc_final: 0.3835 (tpt) outliers start: 0 outliers final: 0 residues processed: 786 average time/residue: 0.2477 time to fit residues: 332.7089 Evaluate side-chains 562 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 562 time to evaluate : 1.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 407 optimal weight: 0.9990 chunk 244 optimal weight: 5.9990 chunk 527 optimal weight: 10.0000 chunk 354 optimal weight: 0.9980 chunk 438 optimal weight: 9.9990 chunk 264 optimal weight: 1.9990 chunk 439 optimal weight: 0.9990 chunk 250 optimal weight: 7.9990 chunk 508 optimal weight: 0.9980 chunk 519 optimal weight: 3.9990 chunk 230 optimal weight: 4.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 ASN A 184 GLN ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 175 ASN D 68 ASN E 178 GLN E 184 GLN ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 169 GLN ** F 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 124 ASN G 184 GLN ** G 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 472 ASN K 32 GLN K 184 GLN ** K 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 169 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.136881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.122790 restraints weight = 96691.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.122710 restraints weight = 80489.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.122874 restraints weight = 67646.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.123211 restraints weight = 54124.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.123233 restraints weight = 45058.062| |-----------------------------------------------------------------------------| r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3671 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3671 r_free = 0.3671 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 728 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3670 r_free = 0.3670 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 740 | |-----------------------------------------------------------------------------| r_final: 0.3670 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.7210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 44736 Z= 0.130 Angle : 0.641 10.747 60588 Z= 0.325 Chirality : 0.042 0.179 6876 Planarity : 0.004 0.057 7932 Dihedral : 4.149 20.740 6204 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 0.06 % Allowed : 0.38 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.11), residues: 5580 helix: 1.08 (0.10), residues: 2640 sheet: -0.71 (0.18), residues: 768 loop : -1.77 (0.13), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 258 TYR 0.039 0.002 TYR I 91 PHE 0.020 0.001 PHE A 173 TRP 0.048 0.002 TRP J 449 HIS 0.008 0.003 HIS L 216 Details of bonding type rmsd covalent geometry : bond 0.00295 (44736) covalent geometry : angle 0.64116 (60588) hydrogen bonds : bond 0.03715 ( 2160) hydrogen bonds : angle 4.47262 ( 6588) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11160 Ramachandran restraints generated. 5580 Oldfield, 0 Emsley, 5580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11160 Ramachandran restraints generated. 5580 Oldfield, 0 Emsley, 5580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 717 time to evaluate : 1.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ILE cc_start: 0.8816 (tp) cc_final: 0.8479 (tt) REVERT: A 146 TYR cc_start: 0.7276 (t80) cc_final: 0.6834 (t80) REVERT: A 151 GLU cc_start: 0.8884 (mm-30) cc_final: 0.8336 (tt0) REVERT: A 273 LEU cc_start: 0.8318 (tp) cc_final: 0.7888 (tp) REVERT: A 441 LYS cc_start: 0.4677 (pttm) cc_final: 0.4158 (mmmt) REVERT: A 465 MET cc_start: 0.4405 (mmt) cc_final: 0.3658 (mmm) REVERT: B 112 MET cc_start: 0.6586 (mtt) cc_final: 0.5992 (tpt) REVERT: B 132 GLU cc_start: 0.8805 (mm-30) cc_final: 0.8528 (tp30) REVERT: B 199 GLU cc_start: 0.6133 (mt-10) cc_final: 0.5815 (mt-10) REVERT: B 208 ASP cc_start: 0.7506 (p0) cc_final: 0.7096 (p0) REVERT: B 209 GLU cc_start: 0.8238 (mp0) cc_final: 0.7869 (mp0) REVERT: B 235 MET cc_start: 0.7458 (ptp) cc_final: 0.7197 (ptt) REVERT: B 270 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7547 (mt-10) REVERT: B 291 MET cc_start: 0.7650 (mmp) cc_final: 0.7399 (ttt) REVERT: B 325 GLU cc_start: 0.8886 (pt0) cc_final: 0.8282 (pt0) REVERT: B 376 TYR cc_start: 0.6678 (t80) cc_final: 0.6408 (t80) REVERT: C 80 MET cc_start: 0.7961 (mpp) cc_final: 0.7653 (mpp) REVERT: C 146 TYR cc_start: 0.7312 (t80) cc_final: 0.6956 (t80) REVERT: C 231 GLU cc_start: 0.6859 (pt0) cc_final: 0.6513 (pp20) REVERT: C 470 ILE cc_start: 0.5365 (mm) cc_final: 0.4891 (tt) REVERT: D 216 HIS cc_start: 0.7374 (t-90) cc_final: 0.7030 (t-90) REVERT: D 268 TYR cc_start: 0.7982 (t80) cc_final: 0.7738 (t80) REVERT: D 270 GLU cc_start: 0.8296 (mt-10) cc_final: 0.8010 (mt-10) REVERT: D 291 MET cc_start: 0.7601 (mmp) cc_final: 0.6676 (ttt) REVERT: D 376 TYR cc_start: 0.6912 (t80) cc_final: 0.6421 (t80) REVERT: D 395 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7398 (mt-10) REVERT: E 61 VAL cc_start: 0.8839 (t) cc_final: 0.8480 (t) REVERT: E 74 MET cc_start: 0.8402 (tpp) cc_final: 0.7547 (tpp) REVERT: E 230 GLU cc_start: 0.7918 (pm20) cc_final: 0.7685 (pm20) REVERT: E 430 LEU cc_start: 0.6368 (tp) cc_final: 0.5940 (tt) REVERT: E 465 MET cc_start: 0.4123 (mpp) cc_final: 0.2998 (mpp) REVERT: E 469 ARG cc_start: 0.4626 (mtt180) cc_final: 0.4290 (mpt-90) REVERT: E 470 ILE cc_start: 0.5234 (mm) cc_final: 0.4988 (mm) REVERT: F 37 TYR cc_start: 0.7234 (m-80) cc_final: 0.6822 (m-10) REVERT: F 53 ASP cc_start: 0.8639 (p0) cc_final: 0.7435 (p0) REVERT: F 112 MET cc_start: 0.6013 (mtm) cc_final: 0.5646 (tpt) REVERT: F 260 ASP cc_start: 0.5197 (p0) cc_final: 0.4857 (p0) REVERT: F 289 MET cc_start: 0.7962 (ttm) cc_final: 0.7722 (ttm) REVERT: F 291 MET cc_start: 0.7330 (mmm) cc_final: 0.6671 (ttt) REVERT: F 381 LEU cc_start: 0.7561 (pp) cc_final: 0.7356 (pp) REVERT: F 395 GLU cc_start: 0.7829 (mt-10) cc_final: 0.6656 (mt-10) REVERT: F 472 ASN cc_start: 0.5976 (m-40) cc_final: 0.5672 (p0) REVERT: G 39 ILE cc_start: 0.8919 (tp) cc_final: 0.8557 (tt) REVERT: G 80 MET cc_start: 0.7331 (mpp) cc_final: 0.7070 (mpp) REVERT: G 151 GLU cc_start: 0.8865 (mm-30) cc_final: 0.8437 (tt0) REVERT: G 196 LYS cc_start: 0.7639 (mtmm) cc_final: 0.6655 (tptt) REVERT: G 273 LEU cc_start: 0.8309 (tp) cc_final: 0.7845 (tp) REVERT: G 279 LEU cc_start: 0.9182 (tp) cc_final: 0.8867 (tt) REVERT: G 337 ASP cc_start: 0.8209 (m-30) cc_final: 0.7835 (m-30) REVERT: G 441 LYS cc_start: 0.4833 (pttm) cc_final: 0.4197 (mmmt) REVERT: G 465 MET cc_start: 0.4452 (mmt) cc_final: 0.4095 (mmt) REVERT: H 112 MET cc_start: 0.7171 (mtt) cc_final: 0.6390 (tpt) REVERT: H 132 GLU cc_start: 0.8836 (mm-30) cc_final: 0.8582 (tp30) REVERT: H 199 GLU cc_start: 0.6171 (mt-10) cc_final: 0.5703 (mt-10) REVERT: H 235 MET cc_start: 0.7440 (ptp) cc_final: 0.7192 (ptt) REVERT: H 270 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7611 (mt-10) REVERT: H 408 LEU cc_start: 0.7804 (mp) cc_final: 0.6662 (tp) REVERT: I 80 MET cc_start: 0.7775 (mpp) cc_final: 0.7309 (mpp) REVERT: I 231 GLU cc_start: 0.6870 (pt0) cc_final: 0.6529 (pp20) REVERT: I 329 PHE cc_start: 0.8361 (m-80) cc_final: 0.8112 (m-80) REVERT: J 37 TYR cc_start: 0.7384 (m-80) cc_final: 0.7152 (m-10) REVERT: J 53 ASP cc_start: 0.8385 (p0) cc_final: 0.7865 (p0) REVERT: J 291 MET cc_start: 0.7661 (mmp) cc_final: 0.6705 (ttt) REVERT: J 325 GLU cc_start: 0.8758 (pp20) cc_final: 0.8111 (pp20) REVERT: J 376 TYR cc_start: 0.6956 (t80) cc_final: 0.6210 (t80) REVERT: J 395 GLU cc_start: 0.7830 (mt-10) cc_final: 0.6877 (mt-10) REVERT: J 472 ASN cc_start: 0.7383 (OUTLIER) cc_final: 0.6937 (p0) REVERT: K 74 MET cc_start: 0.8333 (tpp) cc_final: 0.7444 (tpp) REVERT: K 80 MET cc_start: 0.7221 (mpp) cc_final: 0.6926 (mpp) REVERT: K 465 MET cc_start: 0.4088 (mpp) cc_final: 0.3365 (mpp) REVERT: K 470 ILE cc_start: 0.5333 (mm) cc_final: 0.5091 (mm) REVERT: L 37 TYR cc_start: 0.7209 (m-80) cc_final: 0.6905 (m-10) REVERT: L 53 ASP cc_start: 0.8551 (p0) cc_final: 0.7387 (p0) REVERT: L 112 MET cc_start: 0.7403 (mtt) cc_final: 0.5936 (tpt) REVERT: L 114 GLU cc_start: 0.8119 (tm-30) cc_final: 0.7841 (tp30) REVERT: L 132 GLU cc_start: 0.7933 (tp30) cc_final: 0.7449 (tp30) REVERT: L 260 ASP cc_start: 0.5224 (p0) cc_final: 0.4887 (p0) REVERT: L 270 GLU cc_start: 0.7449 (mt-10) cc_final: 0.7168 (mt-10) REVERT: L 291 MET cc_start: 0.7927 (mmm) cc_final: 0.7340 (mmm) REVERT: L 346 ASP cc_start: 0.8980 (m-30) cc_final: 0.7918 (t70) outliers start: 3 outliers final: 0 residues processed: 719 average time/residue: 0.2356 time to fit residues: 292.6958 Evaluate side-chains 538 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 537 time to evaluate : 1.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 348 optimal weight: 7.9990 chunk 506 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 544 optimal weight: 6.9990 chunk 534 optimal weight: 0.0980 chunk 419 optimal weight: 0.8980 chunk 487 optimal weight: 1.9990 chunk 361 optimal weight: 0.9990 chunk 170 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 ASN A 178 GLN A 184 GLN ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 184 GLN ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 124 ASN G 178 GLN G 184 GLN ** G 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 335 GLN ** J 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 184 GLN ** K 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 68 ASN ** L 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.137714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.123580 restraints weight = 96503.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.124063 restraints weight = 80943.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.123564 restraints weight = 61467.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.123918 restraints weight = 55954.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.124049 restraints weight = 46870.084| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3684 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3684 r_free = 0.3684 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 740 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3683 r_free = 0.3683 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 750 | |-----------------------------------------------------------------------------| r_final: 0.3683 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.7363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 44736 Z= 0.126 Angle : 0.639 10.715 60588 Z= 0.323 Chirality : 0.042 0.164 6876 Planarity : 0.004 0.053 7932 Dihedral : 4.098 20.162 6204 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % 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: -0.38 (0.11), residues: 5580 helix: 1.09 (0.10), residues: 2640 sheet: -0.68 (0.18), residues: 768 loop : -1.79 (0.13), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 258 TYR 0.037 0.001 TYR I 91 PHE 0.018 0.001 PHE E 354 TRP 0.047 0.001 TRP J 449 HIS 0.006 0.002 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00283 (44736) covalent geometry : angle 0.63905 (60588) hydrogen bonds : bond 0.03636 ( 2160) hydrogen bonds : angle 4.42737 ( 6588) =============================================================================== Job complete usr+sys time: 8754.03 seconds wall clock time: 151 minutes 44.55 seconds (9104.55 seconds total)