Starting phenix.real_space_refine on Sat Mar 7 01:48:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6qxm_4669/03_2026/6qxm_4669.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qxm_4669/03_2026/6qxm_4669.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6qxm_4669/03_2026/6qxm_4669.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qxm_4669/03_2026/6qxm_4669.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6qxm_4669/03_2026/6qxm_4669.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qxm_4669/03_2026/6qxm_4669.map" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.016 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 168 5.16 5 C 23532 2.51 5 N 6264 2.21 5 O 7200 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 288 residue(s): 0.04s 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: 37164 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3097 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 19, 'TRANS': 372} Chain breaks: 2 Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L Time building chain proxies: 3.68, per 1000 atoms: 0.10 Number of scatterers: 37164 At special positions: 0 Unit cell: (188.24, 188.24, 111.28, 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 168 16.00 O 7200 8.00 N 6264 7.00 C 23532 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.92 Conformation dependent library (CDL) restraints added in 1.8 seconds 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8808 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 48 sheets defined 41.9% alpha, 16.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'A' and resid 13 through 21 removed outlier: 3.648A pdb=" N TYR A 17 " --> pdb=" O ALA A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 36 removed outlier: 3.570A pdb=" N ARG A 30 " --> pdb=" O PRO A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 78 removed outlier: 3.740A pdb=" N ARG A 64 " --> pdb=" O ALA A 60 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN A 67 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU A 75 " --> pdb=" O SER A 71 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE A 78 " --> pdb=" O MET A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 124 removed outlier: 3.522A pdb=" N VAL A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE A 117 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N MET A 118 " --> pdb=" O GLU A 114 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU A 122 " --> pdb=" O MET A 118 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER A 123 " --> pdb=" O ASN A 119 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN A 124 " --> pdb=" O TYR A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 138 removed outlier: 4.226A pdb=" N THR A 129 " --> pdb=" O SER A 125 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE A 131 " --> pdb=" O ARG A 127 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU A 132 " --> pdb=" O VAL A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 199 removed outlier: 3.777A pdb=" N VAL A 198 " --> pdb=" O ILE A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 295 removed outlier: 4.395A pdb=" N ALA A 285 " --> pdb=" O ASN A 281 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE A 292 " --> pdb=" O LYS A 288 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS A 295 " --> pdb=" O MET A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 313 removed outlier: 3.793A pdb=" N LEU A 311 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LYS A 313 " --> pdb=" O ARG A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 356 removed outlier: 3.503A pdb=" N THR A 339 " --> pdb=" O GLN A 335 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A 340 " --> pdb=" O ALA A 336 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA A 341 " --> pdb=" O ASP A 337 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE A 354 " --> pdb=" O ALA A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 386 removed outlier: 4.070A pdb=" N TYR A 376 " --> pdb=" O GLU A 372 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY A 386 " --> pdb=" O GLU A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 392 Processing helix chain 'A' and resid 396 through 407 removed outlier: 3.714A pdb=" N VAL A 401 " --> pdb=" O GLN A 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 21 Processing helix chain 'B' and resid 24 through 36 removed outlier: 3.570A pdb=" N ARG B 30 " --> pdb=" O PRO B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 78 removed outlier: 3.740A pdb=" N ARG B 64 " --> pdb=" O ALA B 60 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN B 67 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU B 75 " --> pdb=" O SER B 71 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE B 78 " --> pdb=" O MET B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 124 removed outlier: 3.523A pdb=" N VAL B 113 " --> pdb=" O GLY B 109 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE B 117 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N MET B 118 " --> pdb=" O GLU B 114 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU B 122 " --> pdb=" O MET B 118 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER B 123 " --> pdb=" O ASN B 119 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN B 124 " --> pdb=" O TYR B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 138 removed outlier: 4.226A pdb=" N THR B 129 " --> pdb=" O SER B 125 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE B 131 " --> pdb=" O ARG B 127 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU B 132 " --> pdb=" O VAL B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 199 removed outlier: 3.777A pdb=" N VAL B 198 " --> pdb=" O ILE B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 295 removed outlier: 4.395A pdb=" N ALA B 285 " --> pdb=" O ASN B 281 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS B 295 " --> pdb=" O MET B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 313 removed outlier: 3.793A pdb=" N LEU B 311 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LYS B 313 " --> pdb=" O ARG B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 356 removed outlier: 3.503A pdb=" N THR B 339 " --> pdb=" O GLN B 335 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL B 340 " --> pdb=" O ALA B 336 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ALA B 341 " --> pdb=" O ASP B 337 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE B 354 " --> pdb=" O ALA B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 386 removed outlier: 4.069A pdb=" N TYR B 376 " --> pdb=" O GLU B 372 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY B 386 " --> pdb=" O GLU B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 392 Processing helix chain 'B' and resid 396 through 407 removed outlier: 3.716A pdb=" N VAL B 401 " --> pdb=" O GLN B 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 21 Processing helix chain 'C' and resid 24 through 36 removed outlier: 3.569A pdb=" N ARG C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 78 removed outlier: 3.740A pdb=" N ARG C 64 " --> pdb=" O ALA C 60 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN C 67 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU C 75 " --> pdb=" O SER C 71 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE C 78 " --> pdb=" O MET C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 124 removed outlier: 3.522A pdb=" N VAL C 113 " --> pdb=" O GLY C 109 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE C 117 " --> pdb=" O VAL C 113 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N MET C 118 " --> pdb=" O GLU C 114 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU C 122 " --> pdb=" O MET C 118 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER C 123 " --> pdb=" O ASN C 119 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN C 124 " --> pdb=" O TYR C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 138 removed outlier: 4.226A pdb=" N THR C 129 " --> pdb=" O SER C 125 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE C 131 " --> pdb=" O ARG C 127 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU C 132 " --> pdb=" O VAL C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 199 removed outlier: 3.777A pdb=" N VAL C 198 " --> pdb=" O ILE C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 295 removed outlier: 4.396A pdb=" N ALA C 285 " --> pdb=" O ASN C 281 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE C 292 " --> pdb=" O LYS C 288 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS C 295 " --> pdb=" O MET C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 313 removed outlier: 3.793A pdb=" N LEU C 311 " --> pdb=" O GLN C 307 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LYS C 313 " --> pdb=" O ARG C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 356 removed outlier: 3.503A pdb=" N THR C 339 " --> pdb=" O GLN C 335 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL C 340 " --> pdb=" O ALA C 336 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA C 341 " --> pdb=" O ASP C 337 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE C 354 " --> pdb=" O ALA C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 386 removed outlier: 4.070A pdb=" N TYR C 376 " --> pdb=" O GLU C 372 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY C 386 " --> pdb=" O GLU C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 392 Processing helix chain 'C' and resid 396 through 407 removed outlier: 3.715A pdb=" N VAL C 401 " --> pdb=" O GLN C 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 21 Processing helix chain 'D' and resid 24 through 36 removed outlier: 3.569A pdb=" N ARG D 30 " --> pdb=" O PRO D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 78 removed outlier: 3.740A pdb=" N ARG D 64 " --> pdb=" O ALA D 60 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN D 67 " --> pdb=" O ALA D 63 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU D 75 " --> pdb=" O SER D 71 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE D 78 " --> pdb=" O MET D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 124 removed outlier: 3.522A pdb=" N VAL D 113 " --> pdb=" O GLY D 109 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE D 117 " --> pdb=" O VAL D 113 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N MET D 118 " --> pdb=" O GLU D 114 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU D 122 " --> pdb=" O MET D 118 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER D 123 " --> pdb=" O ASN D 119 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN D 124 " --> pdb=" O TYR D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 138 removed outlier: 4.226A pdb=" N THR D 129 " --> pdb=" O SER D 125 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE D 131 " --> pdb=" O ARG D 127 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU D 132 " --> pdb=" O VAL D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 199 removed outlier: 3.777A pdb=" N VAL D 198 " --> pdb=" O ILE D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 295 removed outlier: 4.396A pdb=" N ALA D 285 " --> pdb=" O ASN D 281 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE D 292 " --> pdb=" O LYS D 288 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS D 295 " --> pdb=" O MET D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 313 removed outlier: 3.792A pdb=" N LEU D 311 " --> pdb=" O GLN D 307 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LYS D 313 " --> pdb=" O ARG D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 356 removed outlier: 3.503A pdb=" N THR D 339 " --> pdb=" O GLN D 335 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL D 340 " --> pdb=" O ALA D 336 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA D 341 " --> pdb=" O ASP D 337 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE D 354 " --> pdb=" O ALA D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 386 removed outlier: 4.070A pdb=" N TYR D 376 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY D 386 " --> pdb=" O GLU D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 392 Processing helix chain 'D' and resid 396 through 407 removed outlier: 3.715A pdb=" N VAL D 401 " --> pdb=" O GLN D 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 21 Processing helix chain 'E' and resid 24 through 36 removed outlier: 3.569A pdb=" N ARG E 30 " --> pdb=" O PRO E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 78 removed outlier: 3.740A pdb=" N ARG E 64 " --> pdb=" O ALA E 60 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN E 67 " --> pdb=" O ALA E 63 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU E 75 " --> pdb=" O SER E 71 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE E 78 " --> pdb=" O MET E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 124 removed outlier: 3.522A pdb=" N VAL E 113 " --> pdb=" O GLY E 109 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE E 117 " --> pdb=" O VAL E 113 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N MET E 118 " --> pdb=" O GLU E 114 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU E 122 " --> pdb=" O MET E 118 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER E 123 " --> pdb=" O ASN E 119 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN E 124 " --> pdb=" O TYR E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 138 removed outlier: 4.226A pdb=" N THR E 129 " --> pdb=" O SER E 125 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE E 131 " --> pdb=" O ARG E 127 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLU E 132 " --> pdb=" O VAL E 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 199 removed outlier: 3.777A pdb=" N VAL E 198 " --> pdb=" O ILE E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 295 removed outlier: 4.395A pdb=" N ALA E 285 " --> pdb=" O ASN E 281 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE E 292 " --> pdb=" O LYS E 288 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS E 295 " --> pdb=" O MET E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 313 removed outlier: 3.793A pdb=" N LEU E 311 " --> pdb=" O GLN E 307 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LYS E 313 " --> pdb=" O ARG E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 356 removed outlier: 3.504A pdb=" N THR E 339 " --> pdb=" O GLN E 335 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL E 340 " --> pdb=" O ALA E 336 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA E 341 " --> pdb=" O ASP E 337 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE E 354 " --> pdb=" O ALA E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 372 through 386 removed outlier: 4.070A pdb=" N TYR E 376 " --> pdb=" O GLU E 372 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY E 386 " --> pdb=" O GLU E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 392 Processing helix chain 'E' and resid 396 through 407 removed outlier: 3.715A pdb=" N VAL E 401 " --> pdb=" O GLN E 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 21 Processing helix chain 'F' and resid 24 through 36 removed outlier: 3.569A pdb=" N ARG F 30 " --> pdb=" O PRO F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 78 removed outlier: 3.740A pdb=" N ARG F 64 " --> pdb=" O ALA F 60 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN F 67 " --> pdb=" O ALA F 63 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU F 75 " --> pdb=" O SER F 71 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE F 78 " --> pdb=" O MET F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 124 removed outlier: 3.522A pdb=" N VAL F 113 " --> pdb=" O GLY F 109 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE F 117 " --> pdb=" O VAL F 113 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N MET F 118 " --> pdb=" O GLU F 114 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU F 122 " --> pdb=" O MET F 118 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER F 123 " --> pdb=" O ASN F 119 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN F 124 " --> pdb=" O TYR F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 138 removed outlier: 4.226A pdb=" N THR F 129 " --> pdb=" O SER F 125 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE F 131 " --> pdb=" O ARG F 127 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLU F 132 " --> pdb=" O VAL F 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 199 removed outlier: 3.777A pdb=" N VAL F 198 " --> pdb=" O ILE F 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 272 through 295 removed outlier: 4.395A pdb=" N ALA F 285 " --> pdb=" O ASN F 281 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE F 292 " --> pdb=" O LYS F 288 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS F 295 " --> pdb=" O MET F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 313 removed outlier: 3.793A pdb=" N LEU F 311 " --> pdb=" O GLN F 307 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LYS F 313 " --> pdb=" O ARG F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 356 removed outlier: 3.504A pdb=" N THR F 339 " --> pdb=" O GLN F 335 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL F 340 " --> pdb=" O ALA F 336 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ALA F 341 " --> pdb=" O ASP F 337 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE F 354 " --> pdb=" O ALA F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 386 removed outlier: 4.070A pdb=" N TYR F 376 " --> pdb=" O GLU F 372 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY F 386 " --> pdb=" O GLU F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 387 through 392 Processing helix chain 'F' and resid 396 through 407 removed outlier: 3.715A pdb=" N VAL F 401 " --> pdb=" O GLN F 397 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 21 Processing helix chain 'G' and resid 24 through 36 removed outlier: 3.570A pdb=" N ARG G 30 " --> pdb=" O PRO G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 78 removed outlier: 3.740A pdb=" N ARG G 64 " --> pdb=" O ALA G 60 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN G 67 " --> pdb=" O ALA G 63 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU G 75 " --> pdb=" O SER G 71 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE G 78 " --> pdb=" O MET G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 124 removed outlier: 3.521A pdb=" N VAL G 113 " --> pdb=" O GLY G 109 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE G 117 " --> pdb=" O VAL G 113 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N MET G 118 " --> pdb=" O GLU G 114 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU G 122 " --> pdb=" O MET G 118 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER G 123 " --> pdb=" O ASN G 119 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN G 124 " --> pdb=" O TYR G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 138 removed outlier: 4.227A pdb=" N THR G 129 " --> pdb=" O SER G 125 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE G 131 " --> pdb=" O ARG G 127 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU G 132 " --> pdb=" O VAL G 128 " (cutoff:3.500A) Processing helix chain 'G' and resid 194 through 199 removed outlier: 3.777A pdb=" N VAL G 198 " --> pdb=" O ILE G 194 " (cutoff:3.500A) Processing helix chain 'G' and resid 272 through 295 removed outlier: 4.396A pdb=" N ALA G 285 " --> pdb=" O ASN G 281 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE G 292 " --> pdb=" O LYS G 288 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS G 295 " --> pdb=" O MET G 291 " (cutoff:3.500A) Processing helix chain 'G' and resid 307 through 313 removed outlier: 3.793A pdb=" N LEU G 311 " --> pdb=" O GLN G 307 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LYS G 313 " --> pdb=" O ARG G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 356 removed outlier: 3.503A pdb=" N THR G 339 " --> pdb=" O GLN G 335 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL G 340 " --> pdb=" O ALA G 336 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA G 341 " --> pdb=" O ASP G 337 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE G 354 " --> pdb=" O ALA G 350 " (cutoff:3.500A) Processing helix chain 'G' and resid 372 through 386 removed outlier: 4.070A pdb=" N TYR G 376 " --> pdb=" O GLU G 372 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY G 386 " --> pdb=" O GLU G 382 " (cutoff:3.500A) Processing helix chain 'G' and resid 387 through 392 Processing helix chain 'G' and resid 396 through 407 removed outlier: 3.716A pdb=" N VAL G 401 " --> pdb=" O GLN G 397 " (cutoff:3.500A) Processing helix chain 'H' and resid 14 through 21 Processing helix chain 'H' and resid 24 through 36 removed outlier: 3.569A pdb=" N ARG H 30 " --> pdb=" O PRO H 26 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 78 removed outlier: 3.740A pdb=" N ARG H 64 " --> pdb=" O ALA H 60 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN H 67 " --> pdb=" O ALA H 63 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU H 75 " --> pdb=" O SER H 71 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE H 78 " --> pdb=" O MET H 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 124 removed outlier: 3.522A pdb=" N VAL H 113 " --> pdb=" O GLY H 109 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE H 117 " --> pdb=" O VAL H 113 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N MET H 118 " --> pdb=" O GLU H 114 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU H 122 " --> pdb=" O MET H 118 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER H 123 " --> pdb=" O ASN H 119 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN H 124 " --> pdb=" O TYR H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 138 removed outlier: 4.226A pdb=" N THR H 129 " --> pdb=" O SER H 125 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE H 131 " --> pdb=" O ARG H 127 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLU H 132 " --> pdb=" O VAL H 128 " (cutoff:3.500A) Processing helix chain 'H' and resid 194 through 199 removed outlier: 3.777A pdb=" N VAL H 198 " --> pdb=" O ILE H 194 " (cutoff:3.500A) Processing helix chain 'H' and resid 272 through 295 removed outlier: 4.395A pdb=" N ALA H 285 " --> pdb=" O ASN H 281 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE H 292 " --> pdb=" O LYS H 288 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS H 295 " --> pdb=" O MET H 291 " (cutoff:3.500A) Processing helix chain 'H' and resid 307 through 313 removed outlier: 3.794A pdb=" N LEU H 311 " --> pdb=" O GLN H 307 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LYS H 313 " --> pdb=" O ARG H 309 " (cutoff:3.500A) Processing helix chain 'H' and resid 335 through 356 removed outlier: 3.503A pdb=" N THR H 339 " --> pdb=" O GLN H 335 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL H 340 " --> pdb=" O ALA H 336 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA H 341 " --> pdb=" O ASP H 337 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE H 354 " --> pdb=" O ALA H 350 " (cutoff:3.500A) Processing helix chain 'H' and resid 372 through 386 removed outlier: 4.070A pdb=" N TYR H 376 " --> pdb=" O GLU H 372 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY H 386 " --> pdb=" O GLU H 382 " (cutoff:3.500A) Processing helix chain 'H' and resid 387 through 392 Processing helix chain 'H' and resid 396 through 407 removed outlier: 3.715A pdb=" N VAL H 401 " --> pdb=" O GLN H 397 " (cutoff:3.500A) Processing helix chain 'I' and resid 14 through 21 Processing helix chain 'I' and resid 24 through 36 removed outlier: 3.569A pdb=" N ARG I 30 " --> pdb=" O PRO I 26 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 78 removed outlier: 3.740A pdb=" N ARG I 64 " --> pdb=" O ALA I 60 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN I 67 " --> pdb=" O ALA I 63 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU I 75 " --> pdb=" O SER I 71 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE I 78 " --> pdb=" O MET I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 107 through 124 removed outlier: 3.522A pdb=" N VAL I 113 " --> pdb=" O GLY I 109 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE I 117 " --> pdb=" O VAL I 113 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N MET I 118 " --> pdb=" O GLU I 114 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU I 122 " --> pdb=" O MET I 118 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER I 123 " --> pdb=" O ASN I 119 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN I 124 " --> pdb=" O TYR I 120 " (cutoff:3.500A) Processing helix chain 'I' and resid 125 through 138 removed outlier: 4.226A pdb=" N THR I 129 " --> pdb=" O SER I 125 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE I 131 " --> pdb=" O ARG I 127 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU I 132 " --> pdb=" O VAL I 128 " (cutoff:3.500A) Processing helix chain 'I' and resid 194 through 199 removed outlier: 3.777A pdb=" N VAL I 198 " --> pdb=" O ILE I 194 " (cutoff:3.500A) Processing helix chain 'I' and resid 272 through 295 removed outlier: 4.396A pdb=" N ALA I 285 " --> pdb=" O ASN I 281 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE I 292 " --> pdb=" O LYS I 288 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS I 295 " --> pdb=" O MET I 291 " (cutoff:3.500A) Processing helix chain 'I' and resid 307 through 313 removed outlier: 3.793A pdb=" N LEU I 311 " --> pdb=" O GLN I 307 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LYS I 313 " --> pdb=" O ARG I 309 " (cutoff:3.500A) Processing helix chain 'I' and resid 335 through 356 removed outlier: 3.503A pdb=" N THR I 339 " --> pdb=" O GLN I 335 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL I 340 " --> pdb=" O ALA I 336 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA I 341 " --> pdb=" O ASP I 337 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE I 354 " --> pdb=" O ALA I 350 " (cutoff:3.500A) Processing helix chain 'I' and resid 372 through 386 removed outlier: 4.070A pdb=" N TYR I 376 " --> pdb=" O GLU I 372 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY I 386 " --> pdb=" O GLU I 382 " (cutoff:3.500A) Processing helix chain 'I' and resid 387 through 392 Processing helix chain 'I' and resid 396 through 407 removed outlier: 3.714A pdb=" N VAL I 401 " --> pdb=" O GLN I 397 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 21 Processing helix chain 'J' and resid 24 through 36 removed outlier: 3.568A pdb=" N ARG J 30 " --> pdb=" O PRO J 26 " (cutoff:3.500A) Processing helix chain 'J' and resid 60 through 78 removed outlier: 3.740A pdb=" N ARG J 64 " --> pdb=" O ALA J 60 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN J 67 " --> pdb=" O ALA J 63 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU J 75 " --> pdb=" O SER J 71 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE J 78 " --> pdb=" O MET J 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 107 through 124 removed outlier: 3.522A pdb=" N VAL J 113 " --> pdb=" O GLY J 109 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE J 117 " --> pdb=" O VAL J 113 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N MET J 118 " --> pdb=" O GLU J 114 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU J 122 " --> pdb=" O MET J 118 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER J 123 " --> pdb=" O ASN J 119 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN J 124 " --> pdb=" O TYR J 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 125 through 138 removed outlier: 4.226A pdb=" N THR J 129 " --> pdb=" O SER J 125 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE J 131 " --> pdb=" O ARG J 127 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLU J 132 " --> pdb=" O VAL J 128 " (cutoff:3.500A) Processing helix chain 'J' and resid 194 through 199 removed outlier: 3.777A pdb=" N VAL J 198 " --> pdb=" O ILE J 194 " (cutoff:3.500A) Processing helix chain 'J' and resid 272 through 295 removed outlier: 4.396A pdb=" N ALA J 285 " --> pdb=" O ASN J 281 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE J 292 " --> pdb=" O LYS J 288 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS J 295 " --> pdb=" O MET J 291 " (cutoff:3.500A) Processing helix chain 'J' and resid 307 through 313 removed outlier: 3.793A pdb=" N LEU J 311 " --> pdb=" O GLN J 307 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LYS J 313 " --> pdb=" O ARG J 309 " (cutoff:3.500A) Processing helix chain 'J' and resid 335 through 356 removed outlier: 3.503A pdb=" N THR J 339 " --> pdb=" O GLN J 335 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL J 340 " --> pdb=" O ALA J 336 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA J 341 " --> pdb=" O ASP J 337 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE J 354 " --> pdb=" O ALA J 350 " (cutoff:3.500A) Processing helix chain 'J' and resid 372 through 386 removed outlier: 4.070A pdb=" N TYR J 376 " --> pdb=" O GLU J 372 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY J 386 " --> pdb=" O GLU J 382 " (cutoff:3.500A) Processing helix chain 'J' and resid 387 through 392 Processing helix chain 'J' and resid 396 through 407 removed outlier: 3.714A pdb=" N VAL J 401 " --> pdb=" O GLN J 397 " (cutoff:3.500A) Processing helix chain 'K' and resid 14 through 21 Processing helix chain 'K' and resid 24 through 36 removed outlier: 3.570A pdb=" N ARG K 30 " --> pdb=" O PRO K 26 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 78 removed outlier: 3.739A pdb=" N ARG K 64 " --> pdb=" O ALA K 60 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN K 67 " --> pdb=" O ALA K 63 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU K 75 " --> pdb=" O SER K 71 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE K 78 " --> pdb=" O MET K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 107 through 124 removed outlier: 3.522A pdb=" N VAL K 113 " --> pdb=" O GLY K 109 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE K 117 " --> pdb=" O VAL K 113 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N MET K 118 " --> pdb=" O GLU K 114 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU K 122 " --> pdb=" O MET K 118 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER K 123 " --> pdb=" O ASN K 119 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN K 124 " --> pdb=" O TYR K 120 " (cutoff:3.500A) Processing helix chain 'K' and resid 125 through 138 removed outlier: 4.226A pdb=" N THR K 129 " --> pdb=" O SER K 125 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE K 131 " --> pdb=" O ARG K 127 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU K 132 " --> pdb=" O VAL K 128 " (cutoff:3.500A) Processing helix chain 'K' and resid 194 through 199 removed outlier: 3.777A pdb=" N VAL K 198 " --> pdb=" O ILE K 194 " (cutoff:3.500A) Processing helix chain 'K' and resid 272 through 295 removed outlier: 4.395A pdb=" N ALA K 285 " --> pdb=" O ASN K 281 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE K 292 " --> pdb=" O LYS K 288 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS K 295 " --> pdb=" O MET K 291 " (cutoff:3.500A) Processing helix chain 'K' and resid 307 through 313 removed outlier: 3.793A pdb=" N LEU K 311 " --> pdb=" O GLN K 307 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LYS K 313 " --> pdb=" O ARG K 309 " (cutoff:3.500A) Processing helix chain 'K' and resid 335 through 356 removed outlier: 3.503A pdb=" N THR K 339 " --> pdb=" O GLN K 335 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL K 340 " --> pdb=" O ALA K 336 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA K 341 " --> pdb=" O ASP K 337 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE K 354 " --> pdb=" O ALA K 350 " (cutoff:3.500A) Processing helix chain 'K' and resid 372 through 386 removed outlier: 4.070A pdb=" N TYR K 376 " --> pdb=" O GLU K 372 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY K 386 " --> pdb=" O GLU K 382 " (cutoff:3.500A) Processing helix chain 'K' and resid 387 through 392 Processing helix chain 'K' and resid 396 through 407 removed outlier: 3.715A pdb=" N VAL K 401 " --> pdb=" O GLN K 397 " (cutoff:3.500A) Processing helix chain 'L' and resid 14 through 21 Processing helix chain 'L' and resid 24 through 36 removed outlier: 3.569A pdb=" N ARG L 30 " --> pdb=" O PRO L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 60 through 78 removed outlier: 3.740A pdb=" N ARG L 64 " --> pdb=" O ALA L 60 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN L 67 " --> pdb=" O ALA L 63 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU L 75 " --> pdb=" O SER L 71 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE L 78 " --> pdb=" O MET L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 107 through 124 removed outlier: 3.523A pdb=" N VAL L 113 " --> pdb=" O GLY L 109 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE L 117 " --> pdb=" O VAL L 113 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N MET L 118 " --> pdb=" O GLU L 114 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU L 122 " --> pdb=" O MET L 118 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER L 123 " --> pdb=" O ASN L 119 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN L 124 " --> pdb=" O TYR L 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 125 through 138 removed outlier: 4.226A pdb=" N THR L 129 " --> pdb=" O SER L 125 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE L 131 " --> pdb=" O ARG L 127 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLU L 132 " --> pdb=" O VAL L 128 " (cutoff:3.500A) Processing helix chain 'L' and resid 194 through 199 removed outlier: 3.777A pdb=" N VAL L 198 " --> pdb=" O ILE L 194 " (cutoff:3.500A) Processing helix chain 'L' and resid 272 through 295 removed outlier: 4.396A pdb=" N ALA L 285 " --> pdb=" O ASN L 281 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE L 292 " --> pdb=" O LYS L 288 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS L 295 " --> pdb=" O MET L 291 " (cutoff:3.500A) Processing helix chain 'L' and resid 307 through 313 removed outlier: 3.793A pdb=" N LEU L 311 " --> pdb=" O GLN L 307 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LYS L 313 " --> pdb=" O ARG L 309 " (cutoff:3.500A) Processing helix chain 'L' and resid 335 through 356 removed outlier: 3.503A pdb=" N THR L 339 " --> pdb=" O GLN L 335 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL L 340 " --> pdb=" O ALA L 336 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA L 341 " --> pdb=" O ASP L 337 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE L 354 " --> pdb=" O ALA L 350 " (cutoff:3.500A) Processing helix chain 'L' and resid 372 through 386 removed outlier: 4.070A pdb=" N TYR L 376 " --> pdb=" O GLU L 372 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY L 386 " --> pdb=" O GLU L 382 " (cutoff:3.500A) Processing helix chain 'L' and resid 387 through 392 Processing helix chain 'L' and resid 396 through 407 removed outlier: 3.715A pdb=" N VAL L 401 " --> pdb=" O GLN L 397 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 161 removed outlier: 3.630A pdb=" N ILE A 252 " --> pdb=" O LEU A 145 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 166 through 170 removed outlier: 3.902A pdb=" N GLN A 178 " --> pdb=" O GLN A 169 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LEU A 177 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE A 211 " --> pdb=" O ILE A 185 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 166 through 170 removed outlier: 3.902A pdb=" N GLN A 178 " --> pdb=" O GLN A 169 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LEU A 177 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE A 211 " --> pdb=" O ILE A 185 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 298 through 300 removed outlier: 5.524A pdb=" N GLY A 298 " --> pdb=" O VAL L 320 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 319 through 321 removed outlier: 3.610A pdb=" N VAL B 300 " --> pdb=" O VAL A 320 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 160 through 161 removed outlier: 3.630A pdb=" N ILE B 252 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 166 through 170 removed outlier: 3.902A pdb=" N GLN B 178 " --> pdb=" O GLN B 169 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LEU B 177 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE B 211 " --> pdb=" O ILE B 185 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 166 through 170 removed outlier: 3.902A pdb=" N GLN B 178 " --> pdb=" O GLN B 169 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LEU B 177 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE B 211 " --> pdb=" O ILE B 185 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 319 through 321 removed outlier: 3.634A pdb=" N VAL C 300 " --> pdb=" O VAL B 320 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 160 through 161 removed outlier: 3.631A pdb=" N ILE C 252 " --> pdb=" O LEU C 145 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 166 through 170 removed outlier: 3.902A pdb=" N GLN C 178 " --> pdb=" O GLN C 169 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LEU C 177 " --> pdb=" O LEU C 219 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE C 211 " --> pdb=" O ILE C 185 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 166 through 170 removed outlier: 3.902A pdb=" N GLN C 178 " --> pdb=" O GLN C 169 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LEU C 177 " --> pdb=" O LEU C 219 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE C 211 " --> pdb=" O ILE C 185 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 319 through 321 removed outlier: 3.670A pdb=" N VAL D 300 " --> pdb=" O VAL C 320 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 160 through 161 removed outlier: 3.630A pdb=" N ILE D 252 " --> pdb=" O LEU D 145 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 166 through 170 removed outlier: 3.902A pdb=" N GLN D 178 " --> pdb=" O GLN D 169 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LEU D 177 " --> pdb=" O LEU D 219 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE D 211 " --> pdb=" O ILE D 185 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 166 through 170 removed outlier: 3.902A pdb=" N GLN D 178 " --> pdb=" O GLN D 169 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LEU D 177 " --> pdb=" O LEU D 219 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE D 211 " --> pdb=" O ILE D 185 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 319 through 321 removed outlier: 3.642A pdb=" N VAL E 300 " --> pdb=" O VAL D 320 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 160 through 161 removed outlier: 3.630A pdb=" N ILE E 252 " --> pdb=" O LEU E 145 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 166 through 170 removed outlier: 3.902A pdb=" N GLN E 178 " --> pdb=" O GLN E 169 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LEU E 177 " --> pdb=" O LEU E 219 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE E 211 " --> pdb=" O ILE E 185 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 166 through 170 removed outlier: 3.902A pdb=" N GLN E 178 " --> pdb=" O GLN E 169 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LEU E 177 " --> pdb=" O LEU E 219 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE E 211 " --> pdb=" O ILE E 185 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 319 through 321 removed outlier: 3.584A pdb=" N VAL F 300 " --> pdb=" O VAL E 320 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 160 through 161 removed outlier: 3.630A pdb=" N ILE F 252 " --> pdb=" O LEU F 145 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 166 through 170 removed outlier: 3.902A pdb=" N GLN F 178 " --> pdb=" O GLN F 169 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N LEU F 177 " --> pdb=" O LEU F 219 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE F 211 " --> pdb=" O ILE F 185 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 166 through 170 removed outlier: 3.902A pdb=" N GLN F 178 " --> pdb=" O GLN F 169 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N LEU F 177 " --> pdb=" O LEU F 219 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE F 211 " --> pdb=" O ILE F 185 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 319 through 321 removed outlier: 3.723A pdb=" N VAL G 300 " --> pdb=" O VAL F 320 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 160 through 161 removed outlier: 3.629A pdb=" N ILE G 252 " --> pdb=" O LEU G 145 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 166 through 170 removed outlier: 3.902A pdb=" N GLN G 178 " --> pdb=" O GLN G 169 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LEU G 177 " --> pdb=" O LEU G 219 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE G 211 " --> pdb=" O ILE G 185 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 166 through 170 removed outlier: 3.902A pdb=" N GLN G 178 " --> pdb=" O GLN G 169 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LEU G 177 " --> pdb=" O LEU G 219 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE G 211 " --> pdb=" O ILE G 185 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 319 through 321 removed outlier: 3.611A pdb=" N VAL H 300 " --> pdb=" O VAL G 320 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 160 through 161 removed outlier: 3.631A pdb=" N ILE H 252 " --> pdb=" O LEU H 145 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 166 through 170 removed outlier: 3.902A pdb=" N GLN H 178 " --> pdb=" O GLN H 169 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LEU H 177 " --> pdb=" O LEU H 219 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE H 211 " --> pdb=" O ILE H 185 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 166 through 170 removed outlier: 3.902A pdb=" N GLN H 178 " --> pdb=" O GLN H 169 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LEU H 177 " --> pdb=" O LEU H 219 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE H 211 " --> pdb=" O ILE H 185 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 319 through 321 removed outlier: 3.600A pdb=" N VAL I 300 " --> pdb=" O VAL H 320 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 160 through 161 removed outlier: 3.630A pdb=" N ILE I 252 " --> pdb=" O LEU I 145 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 166 through 170 removed outlier: 3.903A pdb=" N GLN I 178 " --> pdb=" O GLN I 169 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N LEU I 177 " --> pdb=" O LEU I 219 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE I 211 " --> pdb=" O ILE I 185 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 166 through 170 removed outlier: 3.903A pdb=" N GLN I 178 " --> pdb=" O GLN I 169 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N LEU I 177 " --> pdb=" O LEU I 219 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE I 211 " --> pdb=" O ILE I 185 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 319 through 321 removed outlier: 3.725A pdb=" N VAL J 300 " --> pdb=" O VAL I 320 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 160 through 161 removed outlier: 3.629A pdb=" N ILE J 252 " --> pdb=" O LEU J 145 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 166 through 170 removed outlier: 3.902A pdb=" N GLN J 178 " --> pdb=" O GLN J 169 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N LEU J 177 " --> pdb=" O LEU J 219 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE J 211 " --> pdb=" O ILE J 185 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 166 through 170 removed outlier: 3.902A pdb=" N GLN J 178 " --> pdb=" O GLN J 169 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N LEU J 177 " --> pdb=" O LEU J 219 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE J 211 " --> pdb=" O ILE J 185 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 319 through 321 removed outlier: 3.613A pdb=" N VAL K 300 " --> pdb=" O VAL J 320 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 160 through 161 removed outlier: 3.630A pdb=" N ILE K 252 " --> pdb=" O LEU K 145 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 166 through 170 removed outlier: 3.901A pdb=" N GLN K 178 " --> pdb=" O GLN K 169 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LEU K 177 " --> pdb=" O LEU K 219 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE K 211 " --> pdb=" O ILE K 185 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 166 through 170 removed outlier: 3.901A pdb=" N GLN K 178 " --> pdb=" O GLN K 169 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LEU K 177 " --> pdb=" O LEU K 219 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE K 211 " --> pdb=" O ILE K 185 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 319 through 321 removed outlier: 3.583A pdb=" N VAL L 300 " --> pdb=" O VAL K 320 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 160 through 161 removed outlier: 3.629A pdb=" N ILE L 252 " --> pdb=" O LEU L 145 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 166 through 170 removed outlier: 3.901A pdb=" N GLN L 178 " --> pdb=" O GLN L 169 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N LEU L 177 " --> pdb=" O LEU L 219 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE L 211 " --> pdb=" O ILE L 185 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 166 through 170 removed outlier: 3.901A pdb=" N GLN L 178 " --> pdb=" O GLN L 169 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N LEU L 177 " --> pdb=" O LEU L 219 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE L 211 " --> pdb=" O ILE L 185 " (cutoff:3.500A) 1595 hydrogen bonds defined for protein. 4641 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: 7.69 Time building geometry restraints manager: 3.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12229 1.34 - 1.46: 6591 1.46 - 1.58: 18632 1.58 - 1.69: 24 1.69 - 1.81: 312 Bond restraints: 37788 Sorted by residual: bond pdb=" C LEU E 417 " pdb=" N PRO E 418 " ideal model delta sigma weight residual 1.328 1.377 -0.049 1.25e-02 6.40e+03 1.52e+01 bond pdb=" C LEU I 417 " pdb=" N PRO I 418 " ideal model delta sigma weight residual 1.328 1.376 -0.048 1.25e-02 6.40e+03 1.50e+01 bond pdb=" C LEU F 417 " pdb=" N PRO F 418 " ideal model delta sigma weight residual 1.328 1.376 -0.048 1.25e-02 6.40e+03 1.49e+01 bond pdb=" C LEU C 417 " pdb=" N PRO C 418 " ideal model delta sigma weight residual 1.328 1.376 -0.048 1.25e-02 6.40e+03 1.47e+01 bond pdb=" C LEU J 417 " pdb=" N PRO J 418 " ideal model delta sigma weight residual 1.328 1.376 -0.048 1.25e-02 6.40e+03 1.47e+01 ... (remaining 37783 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 48860 2.65 - 5.30: 1936 5.30 - 7.95: 239 7.95 - 10.61: 85 10.61 - 13.26: 12 Bond angle restraints: 51132 Sorted by residual: angle pdb=" N ILE I 305 " pdb=" CA ILE I 305 " pdb=" C ILE I 305 " ideal model delta sigma weight residual 112.96 106.84 6.12 1.00e+00 1.00e+00 3.75e+01 angle pdb=" N ILE D 305 " pdb=" CA ILE D 305 " pdb=" C ILE D 305 " ideal model delta sigma weight residual 112.96 106.85 6.11 1.00e+00 1.00e+00 3.73e+01 angle pdb=" N ILE H 305 " pdb=" CA ILE H 305 " pdb=" C ILE H 305 " ideal model delta sigma weight residual 112.96 106.86 6.10 1.00e+00 1.00e+00 3.72e+01 angle pdb=" N ILE B 305 " pdb=" CA ILE B 305 " pdb=" C ILE B 305 " ideal model delta sigma weight residual 112.96 106.86 6.10 1.00e+00 1.00e+00 3.72e+01 angle pdb=" N ILE E 305 " pdb=" CA ILE E 305 " pdb=" C ILE E 305 " ideal model delta sigma weight residual 112.96 106.87 6.09 1.00e+00 1.00e+00 3.71e+01 ... (remaining 51127 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.23: 19316 17.23 - 34.46: 2657 34.46 - 51.69: 935 51.69 - 68.92: 240 68.92 - 86.15: 96 Dihedral angle restraints: 23244 sinusoidal: 9516 harmonic: 13728 Sorted by residual: dihedral pdb=" CA GLN H 59 " pdb=" C GLN H 59 " pdb=" N ALA H 60 " pdb=" CA ALA H 60 " ideal model delta harmonic sigma weight residual 180.00 -153.75 -26.25 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" CA GLN A 59 " pdb=" C GLN A 59 " pdb=" N ALA A 60 " pdb=" CA ALA A 60 " ideal model delta harmonic sigma weight residual -180.00 -153.77 -26.23 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" CA GLN F 59 " pdb=" C GLN F 59 " pdb=" N ALA F 60 " pdb=" CA ALA F 60 " ideal model delta harmonic sigma weight residual -180.00 -153.77 -26.23 0 5.00e+00 4.00e-02 2.75e+01 ... (remaining 23241 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 4242 0.059 - 0.117: 1159 0.117 - 0.176: 325 0.176 - 0.234: 22 0.234 - 0.293: 12 Chirality restraints: 5760 Sorted by residual: chirality pdb=" CB VAL F 237 " pdb=" CA VAL F 237 " pdb=" CG1 VAL F 237 " pdb=" CG2 VAL F 237 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" CB VAL B 237 " pdb=" CA VAL B 237 " pdb=" CG1 VAL B 237 " pdb=" CG2 VAL B 237 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" CB VAL C 237 " pdb=" CA VAL C 237 " pdb=" CG1 VAL C 237 " pdb=" CG2 VAL C 237 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.13e+00 ... (remaining 5757 not shown) Planarity restraints: 6660 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS I 419 " -0.014 2.00e-02 2.50e+03 2.76e-02 7.64e+00 pdb=" C LYS I 419 " 0.048 2.00e-02 2.50e+03 pdb=" O LYS I 419 " -0.018 2.00e-02 2.50e+03 pdb=" N GLU I 420 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 419 " 0.014 2.00e-02 2.50e+03 2.76e-02 7.61e+00 pdb=" C LYS C 419 " -0.048 2.00e-02 2.50e+03 pdb=" O LYS C 419 " 0.018 2.00e-02 2.50e+03 pdb=" N GLU C 420 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS D 419 " 0.014 2.00e-02 2.50e+03 2.76e-02 7.59e+00 pdb=" C LYS D 419 " -0.048 2.00e-02 2.50e+03 pdb=" O LYS D 419 " 0.018 2.00e-02 2.50e+03 pdb=" N GLU D 420 " 0.016 2.00e-02 2.50e+03 ... (remaining 6657 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 12389 2.85 - 3.36: 33862 3.36 - 3.87: 59613 3.87 - 4.39: 63121 4.39 - 4.90: 108188 Nonbonded interactions: 277173 Sorted by model distance: nonbonded pdb=" O GLU B 380 " pdb=" OG1 THR B 384 " model vdw 2.333 3.040 nonbonded pdb=" O GLU G 380 " pdb=" OG1 THR G 384 " model vdw 2.333 3.040 nonbonded pdb=" O GLU F 380 " pdb=" OG1 THR F 384 " model vdw 2.333 3.040 nonbonded pdb=" O GLU H 380 " pdb=" OG1 THR H 384 " model vdw 2.333 3.040 nonbonded pdb=" O GLU I 380 " pdb=" OG1 THR I 384 " model vdw 2.333 3.040 ... (remaining 277168 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: 0.11 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=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.820 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: 0.060 Extract box with map and model: 0.670 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 28.580 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.070 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:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6593 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 : 0.008 0.062 37788 Z= 0.374 Angle : 1.251 13.257 51132 Z= 0.719 Chirality : 0.058 0.293 5760 Planarity : 0.008 0.068 6660 Dihedral : 18.913 86.145 14436 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.28 % Favored : 90.72 % Rotamer: Outliers : 8.63 % Allowed : 13.96 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.78 (0.09), residues: 4632 helix: -3.25 (0.07), residues: 1728 sheet: -1.94 (0.17), residues: 576 loop : -3.47 (0.11), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 255 TYR 0.015 0.002 TYR C 268 PHE 0.027 0.002 PHE K 78 TRP 0.021 0.004 TRP L 58 HIS 0.005 0.003 HIS K 216 Details of bonding type rmsd covalent geometry : bond 0.00779 (37788) covalent geometry : angle 1.25095 (51132) hydrogen bonds : bond 0.18753 ( 1391) hydrogen bonds : angle 6.98340 ( 4641) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1365 residues out of total 4032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 348 poor density : 1017 time to evaluate : 1.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 TYR cc_start: 0.5900 (t80) cc_final: 0.5537 (t80) REVERT: A 58 TRP cc_start: 0.8133 (t-100) cc_final: 0.6761 (m100) REVERT: A 64 ARG cc_start: 0.7621 (ttp-110) cc_final: 0.7398 (ttp-110) REVERT: A 72 LYS cc_start: 0.7363 (mmtt) cc_final: 0.6925 (mmtm) REVERT: A 116 ILE cc_start: 0.6965 (mm) cc_final: 0.6739 (mm) REVERT: A 124 ASN cc_start: 0.7393 (t0) cc_final: 0.7150 (t0) REVERT: A 132 GLU cc_start: 0.6642 (OUTLIER) cc_final: 0.6343 (mt-10) REVERT: A 179 MET cc_start: 0.6112 (mtm) cc_final: 0.5789 (mtt) REVERT: A 214 TYR cc_start: 0.7699 (m-80) cc_final: 0.7340 (m-10) REVERT: A 291 MET cc_start: 0.6999 (ttp) cc_final: 0.6767 (ttm) REVERT: A 323 ARG cc_start: 0.7271 (tpp80) cc_final: 0.6891 (mtt-85) REVERT: B 58 TRP cc_start: 0.8102 (t-100) cc_final: 0.6739 (m100) REVERT: B 72 LYS cc_start: 0.7707 (mmtt) cc_final: 0.7276 (mmtp) REVERT: B 80 MET cc_start: 0.7788 (mmt) cc_final: 0.7259 (mmm) REVERT: B 108 GLU cc_start: 0.7445 (mp0) cc_final: 0.6056 (tm-30) REVERT: B 116 ILE cc_start: 0.6460 (mm) cc_final: 0.6249 (mm) REVERT: B 124 ASN cc_start: 0.7448 (t0) cc_final: 0.7146 (t0) REVERT: B 258 ARG cc_start: 0.6847 (tpp80) cc_final: 0.6613 (tpp80) REVERT: B 290 SER cc_start: 0.8802 (t) cc_final: 0.8414 (p) REVERT: B 323 ARG cc_start: 0.7285 (tpp80) cc_final: 0.6934 (mtt-85) REVERT: B 389 TYR cc_start: 0.7767 (t80) cc_final: 0.6999 (t80) REVERT: B 406 LYS cc_start: 0.6274 (OUTLIER) cc_final: 0.6020 (mmtp) REVERT: C 54 TYR cc_start: 0.5748 (t80) cc_final: 0.5468 (t80) REVERT: C 58 TRP cc_start: 0.8178 (t-100) cc_final: 0.6705 (m100) REVERT: C 66 LEU cc_start: 0.7789 (tt) cc_final: 0.7529 (tp) REVERT: C 72 LYS cc_start: 0.7498 (mmtt) cc_final: 0.7026 (mmtm) REVERT: C 80 MET cc_start: 0.7772 (mmt) cc_final: 0.7415 (mmt) REVERT: C 108 GLU cc_start: 0.6628 (mp0) cc_final: 0.4974 (tm-30) REVERT: C 124 ASN cc_start: 0.7528 (t0) cc_final: 0.7238 (t0) REVERT: C 233 GLU cc_start: 0.6327 (OUTLIER) cc_final: 0.5988 (tp30) REVERT: C 258 ARG cc_start: 0.6980 (tpp80) cc_final: 0.6060 (tpp80) REVERT: C 295 LYS cc_start: 0.8748 (ptmt) cc_final: 0.8364 (mtmm) REVERT: C 307 GLN cc_start: 0.8036 (mp10) cc_final: 0.7431 (mp10) REVERT: C 323 ARG cc_start: 0.7224 (tpp80) cc_final: 0.6925 (mtt-85) REVERT: C 325 GLU cc_start: 0.7940 (tm-30) cc_final: 0.7628 (tm-30) REVERT: C 395 GLU cc_start: 0.6717 (mm-30) cc_final: 0.5965 (mm-30) REVERT: D 39 ILE cc_start: 0.7414 (tp) cc_final: 0.6850 (tt) REVERT: D 54 TYR cc_start: 0.6050 (t80) cc_final: 0.5636 (t80) REVERT: D 58 TRP cc_start: 0.8078 (t-100) cc_final: 0.6810 (m100) REVERT: D 64 ARG cc_start: 0.7560 (ttp-110) cc_final: 0.7139 (ttp-110) REVERT: D 80 MET cc_start: 0.7709 (mmt) cc_final: 0.7495 (mmt) REVERT: D 116 ILE cc_start: 0.6741 (mm) cc_final: 0.6505 (mm) REVERT: D 124 ASN cc_start: 0.7451 (t0) cc_final: 0.6996 (t0) REVERT: D 213 VAL cc_start: 0.7395 (m) cc_final: 0.7135 (m) REVERT: D 214 TYR cc_start: 0.7580 (m-80) cc_final: 0.7231 (m-10) REVERT: D 258 ARG cc_start: 0.6840 (tpp80) cc_final: 0.6589 (tpp80) REVERT: D 262 GLU cc_start: 0.7301 (pt0) cc_final: 0.7047 (pt0) REVERT: D 290 SER cc_start: 0.9011 (t) cc_final: 0.8810 (t) REVERT: D 291 MET cc_start: 0.7091 (ttp) cc_final: 0.6828 (ttm) REVERT: D 323 ARG cc_start: 0.7241 (tpp80) cc_final: 0.6814 (mtt-85) REVERT: E 58 TRP cc_start: 0.8112 (t-100) cc_final: 0.6754 (m100) REVERT: E 72 LYS cc_start: 0.7709 (mmtt) cc_final: 0.7256 (mmtp) REVERT: E 80 MET cc_start: 0.7791 (mmt) cc_final: 0.7251 (mmm) REVERT: E 108 GLU cc_start: 0.7471 (mp0) cc_final: 0.6444 (tm-30) REVERT: E 116 ILE cc_start: 0.6628 (mm) cc_final: 0.6380 (mm) REVERT: E 124 ASN cc_start: 0.7375 (t0) cc_final: 0.7055 (t0) REVERT: E 179 MET cc_start: 0.5779 (mtm) cc_final: 0.5564 (mtt) REVERT: E 230 GLU cc_start: 0.6612 (mp0) cc_final: 0.6207 (mp0) REVERT: E 290 SER cc_start: 0.8813 (t) cc_final: 0.8384 (p) REVERT: E 323 ARG cc_start: 0.7401 (tpp80) cc_final: 0.7105 (mtt-85) REVERT: E 325 GLU cc_start: 0.8108 (tm-30) cc_final: 0.7870 (tm-30) REVERT: F 54 TYR cc_start: 0.5488 (t80) cc_final: 0.5182 (t80) REVERT: F 58 TRP cc_start: 0.8187 (t-100) cc_final: 0.6680 (m100) REVERT: F 66 LEU cc_start: 0.7740 (tt) cc_final: 0.7475 (tp) REVERT: F 72 LYS cc_start: 0.7526 (mmtt) cc_final: 0.7042 (mmtm) REVERT: F 80 MET cc_start: 0.7701 (mmt) cc_final: 0.7311 (mmt) REVERT: F 124 ASN cc_start: 0.7531 (t0) cc_final: 0.7037 (t0) REVERT: F 134 LEU cc_start: 0.7408 (tt) cc_final: 0.7160 (mt) REVERT: F 295 LYS cc_start: 0.8760 (ptmt) cc_final: 0.8372 (mtmm) REVERT: F 307 GLN cc_start: 0.7991 (mp10) cc_final: 0.7327 (mp10) REVERT: F 323 ARG cc_start: 0.7234 (tpp80) cc_final: 0.6908 (mtt-85) REVERT: F 325 GLU cc_start: 0.7934 (tm-30) cc_final: 0.7628 (tm-30) REVERT: F 395 GLU cc_start: 0.6672 (mm-30) cc_final: 0.6047 (mm-30) REVERT: G 39 ILE cc_start: 0.7283 (tp) cc_final: 0.7014 (mm) REVERT: G 54 TYR cc_start: 0.6006 (t80) cc_final: 0.5593 (t80) REVERT: G 58 TRP cc_start: 0.8114 (t-100) cc_final: 0.6744 (m100) REVERT: G 64 ARG cc_start: 0.7568 (ttp-110) cc_final: 0.7367 (ttp-110) REVERT: G 116 ILE cc_start: 0.6832 (mm) cc_final: 0.6611 (mm) REVERT: G 124 ASN cc_start: 0.7400 (t0) cc_final: 0.7156 (t0) REVERT: G 132 GLU cc_start: 0.6786 (OUTLIER) cc_final: 0.6571 (mt-10) REVERT: G 213 VAL cc_start: 0.7473 (m) cc_final: 0.7238 (m) REVERT: G 214 TYR cc_start: 0.7664 (m-80) cc_final: 0.7292 (m-10) REVERT: G 258 ARG cc_start: 0.6782 (tpp80) cc_final: 0.6485 (tpp80) REVERT: G 262 GLU cc_start: 0.7303 (pt0) cc_final: 0.7055 (pt0) REVERT: G 291 MET cc_start: 0.7010 (ttp) cc_final: 0.6783 (ttm) REVERT: G 323 ARG cc_start: 0.7250 (tpp80) cc_final: 0.6807 (mtt-85) REVERT: H 58 TRP cc_start: 0.8100 (t-100) cc_final: 0.6719 (m100) REVERT: H 72 LYS cc_start: 0.7693 (mmtt) cc_final: 0.7263 (mmtp) REVERT: H 80 MET cc_start: 0.7819 (mmt) cc_final: 0.7311 (mmm) REVERT: H 108 GLU cc_start: 0.7590 (mp0) cc_final: 0.6342 (tm-30) REVERT: H 116 ILE cc_start: 0.6429 (mm) cc_final: 0.6227 (mm) REVERT: H 124 ASN cc_start: 0.7479 (t0) cc_final: 0.7158 (t0) REVERT: H 290 SER cc_start: 0.8821 (t) cc_final: 0.8439 (p) REVERT: H 323 ARG cc_start: 0.7247 (tpp80) cc_final: 0.6904 (mtt-85) REVERT: H 389 TYR cc_start: 0.7757 (t80) cc_final: 0.6968 (t80) REVERT: I 54 TYR cc_start: 0.5977 (t80) cc_final: 0.5630 (t80) REVERT: I 58 TRP cc_start: 0.8188 (t-100) cc_final: 0.6682 (m100) REVERT: I 66 LEU cc_start: 0.7679 (tt) cc_final: 0.7462 (tp) REVERT: I 72 LYS cc_start: 0.7557 (mmtt) cc_final: 0.7101 (mmtm) REVERT: I 80 MET cc_start: 0.7733 (mmt) cc_final: 0.7388 (mmt) REVERT: I 108 GLU cc_start: 0.6797 (mp0) cc_final: 0.5158 (tm-30) REVERT: I 124 ASN cc_start: 0.7587 (t0) cc_final: 0.7141 (t0) REVERT: I 307 GLN cc_start: 0.8021 (mp10) cc_final: 0.7423 (mp10) REVERT: I 323 ARG cc_start: 0.7254 (tpp80) cc_final: 0.6942 (mtt-85) REVERT: I 325 GLU cc_start: 0.7944 (tm-30) cc_final: 0.7613 (tm-30) REVERT: I 395 GLU cc_start: 0.6674 (mm-30) cc_final: 0.5964 (mm-30) REVERT: J 54 TYR cc_start: 0.5991 (t80) cc_final: 0.5649 (t80) REVERT: J 58 TRP cc_start: 0.8114 (t-100) cc_final: 0.6753 (m100) REVERT: J 64 ARG cc_start: 0.7606 (ttp-110) cc_final: 0.7384 (ttp-110) REVERT: J 116 ILE cc_start: 0.6958 (mm) cc_final: 0.6723 (mm) REVERT: J 124 ASN cc_start: 0.7411 (t0) cc_final: 0.7176 (t0) REVERT: J 132 GLU cc_start: 0.6568 (OUTLIER) cc_final: 0.6279 (mt-10) REVERT: J 179 MET cc_start: 0.6133 (mtm) cc_final: 0.5814 (mtt) REVERT: J 213 VAL cc_start: 0.7462 (m) cc_final: 0.7253 (m) REVERT: J 214 TYR cc_start: 0.7719 (m-80) cc_final: 0.7363 (m-10) REVERT: J 258 ARG cc_start: 0.6789 (tpp80) cc_final: 0.6476 (tpp80) REVERT: J 262 GLU cc_start: 0.7301 (pt0) cc_final: 0.7025 (pt0) REVERT: J 323 ARG cc_start: 0.7268 (tpp80) cc_final: 0.6830 (mtt-85) REVERT: K 58 TRP cc_start: 0.8087 (t-100) cc_final: 0.7447 (m100) REVERT: K 72 LYS cc_start: 0.7725 (mmtt) cc_final: 0.7281 (mmtp) REVERT: K 80 MET cc_start: 0.7852 (mmt) cc_final: 0.7329 (mmm) REVERT: K 108 GLU cc_start: 0.7598 (mp0) cc_final: 0.6169 (tm-30) REVERT: K 124 ASN cc_start: 0.7543 (t0) cc_final: 0.7222 (t0) REVERT: K 290 SER cc_start: 0.8808 (t) cc_final: 0.8438 (p) REVERT: K 323 ARG cc_start: 0.7256 (tpp80) cc_final: 0.6919 (mtt-85) REVERT: K 389 TYR cc_start: 0.7805 (t80) cc_final: 0.6962 (t80) REVERT: K 406 LYS cc_start: 0.6360 (OUTLIER) cc_final: 0.6159 (mmtp) REVERT: L 54 TYR cc_start: 0.6020 (t80) cc_final: 0.5736 (t80) REVERT: L 66 LEU cc_start: 0.7712 (tt) cc_final: 0.7465 (tp) REVERT: L 72 LYS cc_start: 0.7561 (mmtt) cc_final: 0.7128 (mmtm) REVERT: L 80 MET cc_start: 0.7724 (mmt) cc_final: 0.7372 (mmt) REVERT: L 108 GLU cc_start: 0.6700 (mp0) cc_final: 0.5062 (tm-30) REVERT: L 124 ASN cc_start: 0.7576 (t0) cc_final: 0.7323 (t0) REVERT: L 233 GLU cc_start: 0.6262 (OUTLIER) cc_final: 0.5958 (tp30) REVERT: L 295 LYS cc_start: 0.8789 (ptmt) cc_final: 0.8414 (mtmm) REVERT: L 307 GLN cc_start: 0.8069 (mp10) cc_final: 0.7506 (mp10) REVERT: L 323 ARG cc_start: 0.7253 (tpp80) cc_final: 0.6994 (mtt-85) REVERT: L 325 GLU cc_start: 0.7966 (tm-30) cc_final: 0.7642 (tm-30) REVERT: L 395 GLU cc_start: 0.6674 (mm-30) cc_final: 0.5992 (mm-30) outliers start: 348 outliers final: 138 residues processed: 1269 average time/residue: 0.2296 time to fit residues: 468.8939 Evaluate side-chains 1005 residues out of total 4032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 860 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 432 optimal weight: 3.9990 chunk 197 optimal weight: 7.9990 chunk 388 optimal weight: 0.2980 chunk 455 optimal weight: 10.0000 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.3980 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 0.6980 chunk 401 optimal weight: 8.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN B 175 ASN ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 GLN C 175 ASN C 184 GLN ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 GLN D 175 ASN ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 409 GLN E 175 ASN E 409 GLN F 175 ASN ** F 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 409 GLN G 175 ASN G 409 GLN H 175 ASN ** H 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 409 GLN I 175 ASN ** I 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 409 GLN J 409 GLN K 175 ASN ** K 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 409 GLN L 175 ASN L 184 GLN ** L 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 409 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.178604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.145456 restraints weight = 51668.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.149747 restraints weight = 32291.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.152715 restraints weight = 22628.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.154694 restraints weight = 17422.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.155968 restraints weight = 14518.646| |-----------------------------------------------------------------------------| r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3881 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3881 r_free = 0.3881 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3869 r_free = 0.3869 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 51 | |-----------------------------------------------------------------------------| r_final: 0.3869 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6356 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 37788 Z= 0.136 Angle : 0.698 8.500 51132 Z= 0.354 Chirality : 0.043 0.156 5760 Planarity : 0.005 0.053 6660 Dihedral : 5.699 25.842 5208 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 0.05 % Allowed : 3.20 % Favored : 96.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.30 (0.11), residues: 4632 helix: -1.43 (0.11), residues: 1836 sheet: -1.55 (0.18), residues: 576 loop : -3.07 (0.11), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 258 TYR 0.017 0.001 TYR E 268 PHE 0.016 0.002 PHE D 356 TRP 0.020 0.003 TRP K 83 HIS 0.003 0.001 HIS D 216 Details of bonding type rmsd covalent geometry : bond 0.00309 (37788) covalent geometry : angle 0.69801 (51132) hydrogen bonds : bond 0.04354 ( 1391) hydrogen bonds : angle 4.55338 ( 4641) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 939 residues out of total 4032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 937 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 TYR cc_start: 0.5841 (t80) cc_final: 0.5557 (t80) REVERT: A 64 ARG cc_start: 0.7480 (ttp-110) cc_final: 0.7041 (ttp-110) REVERT: A 112 MET cc_start: 0.6458 (mtm) cc_final: 0.6106 (mtm) REVERT: A 124 ASN cc_start: 0.7476 (t0) cc_final: 0.7236 (t0) REVERT: A 214 TYR cc_start: 0.7673 (m-80) cc_final: 0.7359 (m-10) REVERT: A 323 ARG cc_start: 0.7435 (tpp80) cc_final: 0.6904 (mtt-85) REVERT: A 394 GLN cc_start: 0.7366 (mm-40) cc_final: 0.6673 (mm110) REVERT: B 72 LYS cc_start: 0.7609 (mmtt) cc_final: 0.7329 (mmtp) REVERT: B 80 MET cc_start: 0.7919 (mmt) cc_final: 0.7516 (mmm) REVERT: B 108 GLU cc_start: 0.7217 (mp0) cc_final: 0.5907 (tm-30) REVERT: B 112 MET cc_start: 0.6213 (mtt) cc_final: 0.5629 (mtt) REVERT: B 124 ASN cc_start: 0.7521 (t0) cc_final: 0.7105 (t0) REVERT: B 134 LEU cc_start: 0.6541 (tp) cc_final: 0.6222 (tp) REVERT: B 323 ARG cc_start: 0.7490 (tpp80) cc_final: 0.7031 (mtt-85) REVERT: C 27 TYR cc_start: 0.7495 (m-80) cc_final: 0.6798 (m-80) REVERT: C 54 TYR cc_start: 0.5727 (t80) cc_final: 0.5339 (t80) REVERT: C 72 LYS cc_start: 0.7171 (mmtt) cc_final: 0.6833 (mmtm) REVERT: C 80 MET cc_start: 0.7780 (mmt) cc_final: 0.7551 (mmt) REVERT: C 129 THR cc_start: 0.7895 (m) cc_final: 0.7693 (m) REVERT: C 295 LYS cc_start: 0.8698 (ptmt) cc_final: 0.8220 (mtmm) REVERT: C 307 GLN cc_start: 0.8029 (mp10) cc_final: 0.7799 (mp10) REVERT: C 323 ARG cc_start: 0.7408 (tpp80) cc_final: 0.7048 (mtt-85) REVERT: C 349 GLU cc_start: 0.7177 (tt0) cc_final: 0.6847 (tt0) REVERT: D 14 LYS cc_start: 0.6649 (tmtt) cc_final: 0.6407 (tptp) REVERT: D 54 TYR cc_start: 0.6021 (t80) cc_final: 0.5584 (t80) REVERT: D 64 ARG cc_start: 0.7417 (ttp-110) cc_final: 0.7191 (ttp-110) REVERT: D 213 VAL cc_start: 0.7320 (m) cc_final: 0.7043 (m) REVERT: D 214 TYR cc_start: 0.7640 (m-80) cc_final: 0.7290 (m-10) REVERT: D 323 ARG cc_start: 0.7375 (tpp80) cc_final: 0.6922 (mtt-85) REVERT: D 330 LEU cc_start: 0.5390 (mt) cc_final: 0.4662 (mp) REVERT: D 394 GLN cc_start: 0.7316 (mm-40) cc_final: 0.6447 (mm-40) REVERT: E 72 LYS cc_start: 0.7617 (mmtt) cc_final: 0.7299 (mmtp) REVERT: E 80 MET cc_start: 0.7793 (mmt) cc_final: 0.7379 (mmm) REVERT: E 108 GLU cc_start: 0.7206 (mp0) cc_final: 0.5917 (tm-30) REVERT: E 124 ASN cc_start: 0.7410 (t0) cc_final: 0.7068 (t0) REVERT: E 138 VAL cc_start: 0.6983 (t) cc_final: 0.6776 (m) REVERT: E 323 ARG cc_start: 0.7613 (tpp80) cc_final: 0.7181 (mtt-85) REVERT: E 330 LEU cc_start: 0.5112 (mt) cc_final: 0.3852 (mp) REVERT: E 389 TYR cc_start: 0.7498 (t80) cc_final: 0.7037 (t80) REVERT: F 27 TYR cc_start: 0.7526 (m-80) cc_final: 0.6690 (m-80) REVERT: F 54 TYR cc_start: 0.5260 (t80) cc_final: 0.4950 (t80) REVERT: F 72 LYS cc_start: 0.7385 (mmtt) cc_final: 0.6833 (mttt) REVERT: F 80 MET cc_start: 0.7819 (mmt) cc_final: 0.7503 (mmp) REVERT: F 134 LEU cc_start: 0.6693 (tt) cc_final: 0.6416 (mp) REVERT: F 154 ASN cc_start: 0.6940 (m110) cc_final: 0.6677 (m110) REVERT: F 295 LYS cc_start: 0.8684 (ptmt) cc_final: 0.8248 (mtmm) REVERT: F 307 GLN cc_start: 0.8039 (mp10) cc_final: 0.7811 (mp10) REVERT: F 323 ARG cc_start: 0.7403 (tpp80) cc_final: 0.7010 (mtt-85) REVERT: F 349 GLU cc_start: 0.7044 (tt0) cc_final: 0.6772 (tt0) REVERT: F 357 MET cc_start: 0.7487 (tpt) cc_final: 0.7186 (tpp) REVERT: G 27 TYR cc_start: 0.7550 (m-80) cc_final: 0.7213 (m-80) REVERT: G 54 TYR cc_start: 0.5920 (t80) cc_final: 0.5611 (t80) REVERT: G 64 ARG cc_start: 0.7404 (ttp-110) cc_final: 0.6985 (ttp-110) REVERT: G 112 MET cc_start: 0.6374 (mtm) cc_final: 0.6042 (mtm) REVERT: G 124 ASN cc_start: 0.7531 (t0) cc_final: 0.7331 (t0) REVERT: G 213 VAL cc_start: 0.7339 (m) cc_final: 0.7095 (m) REVERT: G 214 TYR cc_start: 0.7660 (m-80) cc_final: 0.7345 (m-10) REVERT: G 262 GLU cc_start: 0.7504 (pt0) cc_final: 0.7268 (pt0) REVERT: G 323 ARG cc_start: 0.7434 (tpp80) cc_final: 0.6900 (mtt-85) REVERT: G 394 GLN cc_start: 0.7354 (mm-40) cc_final: 0.6626 (mm-40) REVERT: H 72 LYS cc_start: 0.7590 (mmtt) cc_final: 0.7324 (mmtp) REVERT: H 80 MET cc_start: 0.7888 (mmt) cc_final: 0.7476 (mmm) REVERT: H 81 GLN cc_start: 0.7396 (mt0) cc_final: 0.7172 (mt0) REVERT: H 108 GLU cc_start: 0.7326 (mp0) cc_final: 0.6176 (tm-30) REVERT: H 124 ASN cc_start: 0.7550 (t0) cc_final: 0.7137 (t0) REVERT: H 134 LEU cc_start: 0.6524 (tp) cc_final: 0.6245 (tp) REVERT: H 258 ARG cc_start: 0.7050 (tpp80) cc_final: 0.6768 (tpp80) REVERT: H 323 ARG cc_start: 0.7475 (tpp80) cc_final: 0.7021 (mtt-85) REVERT: I 27 TYR cc_start: 0.7497 (m-80) cc_final: 0.6812 (m-80) REVERT: I 54 TYR cc_start: 0.5678 (t80) cc_final: 0.5356 (t80) REVERT: I 72 LYS cc_start: 0.7156 (mmtt) cc_final: 0.6828 (mmtm) REVERT: I 116 ILE cc_start: 0.6176 (mm) cc_final: 0.5972 (mm) REVERT: I 323 ARG cc_start: 0.7426 (tpp80) cc_final: 0.7058 (mtt-85) REVERT: I 349 GLU cc_start: 0.7072 (tt0) cc_final: 0.6799 (tt0) REVERT: J 54 TYR cc_start: 0.5895 (t80) cc_final: 0.5591 (t80) REVERT: J 64 ARG cc_start: 0.7439 (ttp-110) cc_final: 0.6985 (ttp-110) REVERT: J 112 MET cc_start: 0.6385 (mtm) cc_final: 0.6055 (mtm) REVERT: J 124 ASN cc_start: 0.7470 (t0) cc_final: 0.7212 (t0) REVERT: J 213 VAL cc_start: 0.7333 (m) cc_final: 0.7108 (m) REVERT: J 214 TYR cc_start: 0.7631 (m-80) cc_final: 0.7322 (m-10) REVERT: J 323 ARG cc_start: 0.7431 (tpp80) cc_final: 0.6901 (mtt-85) REVERT: J 394 GLN cc_start: 0.7357 (mm-40) cc_final: 0.6626 (mm-40) REVERT: K 72 LYS cc_start: 0.7604 (mmtt) cc_final: 0.7292 (mmtp) REVERT: K 80 MET cc_start: 0.7936 (mmt) cc_final: 0.7505 (mmm) REVERT: K 108 GLU cc_start: 0.7206 (mp0) cc_final: 0.5911 (tm-30) REVERT: K 112 MET cc_start: 0.6201 (mtt) cc_final: 0.5836 (mtt) REVERT: K 124 ASN cc_start: 0.7588 (t0) cc_final: 0.7163 (t0) REVERT: K 323 ARG cc_start: 0.7478 (tpp80) cc_final: 0.7045 (mtt-85) REVERT: K 394 GLN cc_start: 0.7531 (mm-40) cc_final: 0.7044 (mm-40) REVERT: L 27 TYR cc_start: 0.7520 (m-80) cc_final: 0.6805 (m-80) REVERT: L 54 TYR cc_start: 0.5796 (t80) cc_final: 0.5402 (t80) REVERT: L 72 LYS cc_start: 0.7183 (mmtt) cc_final: 0.6818 (mmtm) REVERT: L 116 ILE cc_start: 0.6170 (mm) cc_final: 0.5961 (mm) REVERT: L 129 THR cc_start: 0.7866 (m) cc_final: 0.7639 (m) REVERT: L 295 LYS cc_start: 0.8680 (ptmt) cc_final: 0.8192 (mtmm) REVERT: L 307 GLN cc_start: 0.7988 (mp10) cc_final: 0.7738 (mp10) REVERT: L 323 ARG cc_start: 0.7394 (tpp80) cc_final: 0.7033 (mtt-85) REVERT: L 349 GLU cc_start: 0.7163 (tt0) cc_final: 0.6842 (tt0) outliers start: 2 outliers final: 0 residues processed: 938 average time/residue: 0.2155 time to fit residues: 331.5997 Evaluate side-chains 842 residues out of total 4032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 842 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 379 optimal weight: 0.7980 chunk 415 optimal weight: 2.9990 chunk 449 optimal weight: 0.0570 chunk 339 optimal weight: 5.9990 chunk 50 optimal weight: 0.1980 chunk 145 optimal weight: 2.9990 chunk 380 optimal weight: 0.9990 chunk 450 optimal weight: 7.9990 chunk 98 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 342 optimal weight: 0.8980 overall best weight: 0.5900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 81 GLN A 412 GLN B 59 GLN B 412 GLN C 59 GLN ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 281 ASN C 412 GLN D 59 GLN D 124 ASN D 412 GLN E 59 GLN ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 59 GLN ** F 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 281 ASN F 412 GLN G 59 GLN G 412 GLN H 59 GLN H 412 GLN I 59 GLN ** I 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 281 ASN I 412 GLN J 59 GLN J 412 GLN K 59 GLN K 412 GLN ** L 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 281 ASN L 412 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.178731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.146318 restraints weight = 51492.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.150612 restraints weight = 32018.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.153461 restraints weight = 22344.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.155410 restraints weight = 17236.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.156892 restraints weight = 14300.092| |-----------------------------------------------------------------------------| r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3878 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3878 r_free = 0.3878 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 51 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3877 r_free = 0.3877 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 67 | |-----------------------------------------------------------------------------| r_final: 0.3877 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6328 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 37788 Z= 0.112 Angle : 0.604 8.009 51132 Z= 0.305 Chirality : 0.041 0.153 5760 Planarity : 0.004 0.040 6660 Dihedral : 5.071 22.106 5208 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 0.10 % Allowed : 4.66 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.38 (0.12), residues: 4632 helix: -0.43 (0.13), residues: 1788 sheet: -1.22 (0.19), residues: 564 loop : -2.70 (0.12), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 266 TYR 0.020 0.001 TYR D 268 PHE 0.020 0.001 PHE E 356 TRP 0.017 0.002 TRP J 83 HIS 0.003 0.001 HIS I 216 Details of bonding type rmsd covalent geometry : bond 0.00262 (37788) covalent geometry : angle 0.60411 (51132) hydrogen bonds : bond 0.03537 ( 1391) hydrogen bonds : angle 4.06074 ( 4641) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 922 residues out of total 4032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 918 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 TYR cc_start: 0.5842 (t80) cc_final: 0.5474 (t80) REVERT: A 64 ARG cc_start: 0.7427 (ttp-110) cc_final: 0.6933 (ttp-110) REVERT: A 112 MET cc_start: 0.6451 (mtm) cc_final: 0.6033 (mtm) REVERT: A 124 ASN cc_start: 0.7472 (t0) cc_final: 0.7230 (t0) REVERT: A 214 TYR cc_start: 0.7601 (m-80) cc_final: 0.7347 (m-10) REVERT: A 262 GLU cc_start: 0.7484 (pt0) cc_final: 0.7234 (pt0) REVERT: A 323 ARG cc_start: 0.7441 (tpp80) cc_final: 0.6944 (mtt-85) REVERT: A 330 LEU cc_start: 0.5353 (mt) cc_final: 0.4828 (mp) REVERT: A 349 GLU cc_start: 0.7162 (tt0) cc_final: 0.6820 (tt0) REVERT: A 394 GLN cc_start: 0.7395 (mm-40) cc_final: 0.7089 (mm-40) REVERT: B 27 TYR cc_start: 0.6779 (m-80) cc_final: 0.6323 (m-10) REVERT: B 59 GLN cc_start: 0.8102 (mt0) cc_final: 0.7867 (mt0) REVERT: B 80 MET cc_start: 0.7922 (mmt) cc_final: 0.7530 (mmm) REVERT: B 108 GLU cc_start: 0.7167 (mp0) cc_final: 0.5536 (tm-30) REVERT: B 112 MET cc_start: 0.6053 (mtt) cc_final: 0.5619 (mtt) REVERT: B 116 ILE cc_start: 0.6484 (mm) cc_final: 0.6231 (mm) REVERT: B 124 ASN cc_start: 0.7464 (t0) cc_final: 0.7073 (t0) REVERT: B 323 ARG cc_start: 0.7449 (tpp80) cc_final: 0.7013 (mtt-85) REVERT: B 330 LEU cc_start: 0.5313 (mt) cc_final: 0.4748 (mp) REVERT: B 389 TYR cc_start: 0.7529 (t80) cc_final: 0.7077 (t80) REVERT: B 394 GLN cc_start: 0.7547 (mm-40) cc_final: 0.7167 (mm-40) REVERT: C 27 TYR cc_start: 0.7414 (m-80) cc_final: 0.6713 (m-80) REVERT: C 54 TYR cc_start: 0.5621 (t80) cc_final: 0.5282 (t80) REVERT: C 116 ILE cc_start: 0.6119 (mm) cc_final: 0.5906 (mm) REVERT: C 124 ASN cc_start: 0.7382 (t0) cc_final: 0.7026 (t0) REVERT: C 295 LYS cc_start: 0.8666 (ptmt) cc_final: 0.8231 (mtmm) REVERT: C 323 ARG cc_start: 0.7425 (tpp80) cc_final: 0.6992 (mtt-85) REVERT: C 389 TYR cc_start: 0.7779 (t80) cc_final: 0.7145 (t80) REVERT: D 54 TYR cc_start: 0.5890 (t80) cc_final: 0.5572 (t80) REVERT: D 64 ARG cc_start: 0.7403 (ttp-110) cc_final: 0.7008 (ttp-110) REVERT: D 214 TYR cc_start: 0.7597 (m-80) cc_final: 0.7290 (m-10) REVERT: D 294 SER cc_start: 0.8306 (t) cc_final: 0.8014 (m) REVERT: D 323 ARG cc_start: 0.7438 (tpp80) cc_final: 0.6943 (mtt-85) REVERT: D 330 LEU cc_start: 0.5341 (mt) cc_final: 0.4824 (mp) REVERT: D 394 GLN cc_start: 0.7294 (mm-40) cc_final: 0.6471 (mm-40) REVERT: E 27 TYR cc_start: 0.6515 (m-80) cc_final: 0.6195 (m-10) REVERT: E 75 LEU cc_start: 0.8171 (mt) cc_final: 0.7961 (mt) REVERT: E 80 MET cc_start: 0.7961 (mmt) cc_final: 0.7550 (mmm) REVERT: E 108 GLU cc_start: 0.7084 (mp0) cc_final: 0.5661 (tm-30) REVERT: E 112 MET cc_start: 0.6088 (mtt) cc_final: 0.5684 (mtt) REVERT: E 124 ASN cc_start: 0.7316 (t0) cc_final: 0.6990 (t0) REVERT: E 323 ARG cc_start: 0.7489 (tpp80) cc_final: 0.7060 (mtt-85) REVERT: E 330 LEU cc_start: 0.5051 (mt) cc_final: 0.4513 (mp) REVERT: E 389 TYR cc_start: 0.7466 (t80) cc_final: 0.7087 (t80) REVERT: E 394 GLN cc_start: 0.7614 (mm-40) cc_final: 0.7242 (mm-40) REVERT: F 27 TYR cc_start: 0.7453 (m-80) cc_final: 0.6611 (m-80) REVERT: F 54 TYR cc_start: 0.5197 (t80) cc_final: 0.4933 (t80) REVERT: F 72 LYS cc_start: 0.7325 (mmtt) cc_final: 0.6795 (mttt) REVERT: F 80 MET cc_start: 0.7839 (mmt) cc_final: 0.7591 (mmt) REVERT: F 124 ASN cc_start: 0.7434 (t0) cc_final: 0.7158 (t0) REVERT: F 129 THR cc_start: 0.7924 (m) cc_final: 0.7719 (m) REVERT: F 256 MET cc_start: 0.5469 (ppp) cc_final: 0.4680 (ttp) REVERT: F 323 ARG cc_start: 0.7432 (tpp80) cc_final: 0.7025 (mtt-85) REVERT: F 349 GLU cc_start: 0.7075 (tt0) cc_final: 0.6805 (tt0) REVERT: F 357 MET cc_start: 0.7485 (tpt) cc_final: 0.7263 (tpp) REVERT: F 389 TYR cc_start: 0.7446 (t80) cc_final: 0.7175 (t80) REVERT: F 394 GLN cc_start: 0.7574 (mm-40) cc_final: 0.7124 (mm-40) REVERT: G 27 TYR cc_start: 0.7400 (m-80) cc_final: 0.7160 (m-80) REVERT: G 54 TYR cc_start: 0.5839 (t80) cc_final: 0.5507 (t80) REVERT: G 64 ARG cc_start: 0.7383 (ttp-110) cc_final: 0.6920 (ttp-110) REVERT: G 72 LYS cc_start: 0.7105 (mmtt) cc_final: 0.6882 (mmtm) REVERT: G 112 MET cc_start: 0.6391 (mtm) cc_final: 0.5961 (mtm) REVERT: G 124 ASN cc_start: 0.7481 (t0) cc_final: 0.7259 (t0) REVERT: G 214 TYR cc_start: 0.7594 (m-80) cc_final: 0.7287 (m-10) REVERT: G 258 ARG cc_start: 0.6470 (tpp80) cc_final: 0.5974 (ttm-80) REVERT: G 323 ARG cc_start: 0.7437 (tpp80) cc_final: 0.6919 (mtt-85) REVERT: G 330 LEU cc_start: 0.5355 (mt) cc_final: 0.4868 (mp) REVERT: G 394 GLN cc_start: 0.7358 (mm-40) cc_final: 0.6428 (mm-40) REVERT: H 27 TYR cc_start: 0.6788 (m-80) cc_final: 0.6375 (m-10) REVERT: H 59 GLN cc_start: 0.8067 (mt0) cc_final: 0.7835 (mt0) REVERT: H 80 MET cc_start: 0.7781 (mmt) cc_final: 0.7467 (mmm) REVERT: H 108 GLU cc_start: 0.7119 (mp0) cc_final: 0.5551 (tm-30) REVERT: H 116 ILE cc_start: 0.6376 (mm) cc_final: 0.6132 (mm) REVERT: H 124 ASN cc_start: 0.7471 (t0) cc_final: 0.7043 (t0) REVERT: H 262 GLU cc_start: 0.7485 (pt0) cc_final: 0.7168 (pt0) REVERT: H 323 ARG cc_start: 0.7434 (tpp80) cc_final: 0.7055 (mtt-85) REVERT: H 389 TYR cc_start: 0.7555 (t80) cc_final: 0.7114 (t80) REVERT: H 394 GLN cc_start: 0.7520 (mm-40) cc_final: 0.7130 (mm-40) REVERT: I 27 TYR cc_start: 0.7371 (m-80) cc_final: 0.6681 (m-80) REVERT: I 54 TYR cc_start: 0.5611 (t80) cc_final: 0.5248 (t80) REVERT: I 116 ILE cc_start: 0.6083 (mm) cc_final: 0.5845 (mm) REVERT: I 323 ARG cc_start: 0.7397 (tpp80) cc_final: 0.7002 (mtt-85) REVERT: I 357 MET cc_start: 0.7843 (tpp) cc_final: 0.7593 (tpp) REVERT: I 394 GLN cc_start: 0.7570 (mm-40) cc_final: 0.6882 (mm-40) REVERT: I 395 GLU cc_start: 0.6814 (mm-30) cc_final: 0.6228 (mm-30) REVERT: J 54 TYR cc_start: 0.5849 (t80) cc_final: 0.5472 (t80) REVERT: J 64 ARG cc_start: 0.7449 (ttp-110) cc_final: 0.6966 (ttp-110) REVERT: J 72 LYS cc_start: 0.7117 (mmtt) cc_final: 0.6866 (mmtm) REVERT: J 112 MET cc_start: 0.6437 (mtm) cc_final: 0.6011 (mtm) REVERT: J 124 ASN cc_start: 0.7473 (t0) cc_final: 0.7216 (t0) REVERT: J 214 TYR cc_start: 0.7604 (m-80) cc_final: 0.7323 (m-10) REVERT: J 323 ARG cc_start: 0.7440 (tpp80) cc_final: 0.6944 (mtt-85) REVERT: J 330 LEU cc_start: 0.5325 (mt) cc_final: 0.4828 (mp) REVERT: J 394 GLN cc_start: 0.7392 (mm-40) cc_final: 0.6347 (mm-40) REVERT: K 27 TYR cc_start: 0.6881 (m-80) cc_final: 0.6507 (m-10) REVERT: K 72 LYS cc_start: 0.7589 (mmtt) cc_final: 0.7304 (mmtp) REVERT: K 80 MET cc_start: 0.7797 (mmt) cc_final: 0.7482 (mmm) REVERT: K 108 GLU cc_start: 0.7082 (mp0) cc_final: 0.5519 (tm-30) REVERT: K 112 MET cc_start: 0.6094 (mtt) cc_final: 0.5712 (mtt) REVERT: K 116 ILE cc_start: 0.6412 (mm) cc_final: 0.6159 (mm) REVERT: K 124 ASN cc_start: 0.7415 (t0) cc_final: 0.6951 (t0) REVERT: K 323 ARG cc_start: 0.7445 (tpp80) cc_final: 0.7026 (mtt-85) REVERT: K 330 LEU cc_start: 0.5302 (mt) cc_final: 0.4715 (mp) REVERT: K 389 TYR cc_start: 0.7455 (t80) cc_final: 0.7004 (t80) REVERT: K 394 GLN cc_start: 0.7503 (mm-40) cc_final: 0.7123 (mm-40) REVERT: L 27 TYR cc_start: 0.7575 (m-80) cc_final: 0.6943 (m-80) REVERT: L 54 TYR cc_start: 0.5632 (t80) cc_final: 0.5282 (t80) REVERT: L 116 ILE cc_start: 0.6152 (mm) cc_final: 0.5886 (mm) REVERT: L 257 VAL cc_start: 0.6541 (m) cc_final: 0.5690 (t) REVERT: L 258 ARG cc_start: 0.7465 (ttm170) cc_final: 0.7208 (ttm-80) REVERT: L 323 ARG cc_start: 0.7428 (tpp80) cc_final: 0.7006 (mtt-85) REVERT: L 349 GLU cc_start: 0.7099 (tt0) cc_final: 0.6897 (tt0) REVERT: L 389 TYR cc_start: 0.7788 (t80) cc_final: 0.7131 (t80) outliers start: 4 outliers final: 4 residues processed: 922 average time/residue: 0.2073 time to fit residues: 317.6907 Evaluate side-chains 836 residues out of total 4032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 832 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 27 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 112 optimal weight: 7.9990 chunk 430 optimal weight: 4.9990 chunk 197 optimal weight: 0.5980 chunk 195 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 chunk 437 optimal weight: 3.9990 chunk 319 optimal weight: 3.9990 chunk 105 optimal weight: 0.0870 chunk 253 optimal weight: 3.9990 overall best weight: 1.9162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 GLN ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 GLN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 59 GLN L 59 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.176577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.144463 restraints weight = 51301.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.148662 restraints weight = 32185.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.151546 restraints weight = 22587.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.153652 restraints weight = 17355.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.154916 restraints weight = 14242.546| |-----------------------------------------------------------------------------| r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3854 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3854 r_free = 0.3854 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 67 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3853 r_free = 0.3853 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 71 | |-----------------------------------------------------------------------------| r_final: 0.3853 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6373 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 37788 Z= 0.164 Angle : 0.648 10.087 51132 Z= 0.326 Chirality : 0.043 0.159 5760 Planarity : 0.004 0.037 6660 Dihedral : 5.049 25.178 5208 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.12), residues: 4632 helix: -0.29 (0.13), residues: 1836 sheet: -0.99 (0.19), residues: 564 loop : -2.69 (0.12), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG K 195 TYR 0.024 0.002 TYR H 268 PHE 0.020 0.002 PHE H 78 TRP 0.015 0.002 TRP E 58 HIS 0.003 0.001 HIS L 216 Details of bonding type rmsd covalent geometry : bond 0.00388 (37788) covalent geometry : angle 0.64823 (51132) hydrogen bonds : bond 0.03749 ( 1391) hydrogen bonds : angle 4.00132 ( 4641) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 901 residues out of total 4032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 901 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 TYR cc_start: 0.5769 (t80) cc_final: 0.5523 (t80) REVERT: A 64 ARG cc_start: 0.7467 (ttp-110) cc_final: 0.7159 (ttp-110) REVERT: A 72 LYS cc_start: 0.7244 (mmtt) cc_final: 0.6937 (mmtm) REVERT: A 112 MET cc_start: 0.6434 (mtm) cc_final: 0.6032 (mtm) REVERT: A 124 ASN cc_start: 0.7584 (t0) cc_final: 0.7281 (t0) REVERT: A 214 TYR cc_start: 0.7609 (m-80) cc_final: 0.7334 (m-10) REVERT: A 262 GLU cc_start: 0.7378 (pt0) cc_final: 0.7059 (pt0) REVERT: A 291 MET cc_start: 0.7084 (ttp) cc_final: 0.6821 (ttm) REVERT: A 294 SER cc_start: 0.8249 (t) cc_final: 0.7974 (m) REVERT: A 323 ARG cc_start: 0.7461 (tpp80) cc_final: 0.6957 (mtt-85) REVERT: A 330 LEU cc_start: 0.5486 (mt) cc_final: 0.4779 (mp) REVERT: A 394 GLN cc_start: 0.7432 (mm-40) cc_final: 0.6735 (mm110) REVERT: B 27 TYR cc_start: 0.6945 (m-80) cc_final: 0.6656 (m-10) REVERT: B 72 LYS cc_start: 0.7446 (mmtt) cc_final: 0.6905 (mttt) REVERT: B 80 MET cc_start: 0.7900 (mmt) cc_final: 0.7500 (mmm) REVERT: B 108 GLU cc_start: 0.7086 (mp0) cc_final: 0.5498 (tm-30) REVERT: B 112 MET cc_start: 0.6182 (mtt) cc_final: 0.5680 (mtt) REVERT: B 124 ASN cc_start: 0.7506 (t0) cc_final: 0.7035 (t0) REVERT: B 323 ARG cc_start: 0.7457 (tpp80) cc_final: 0.7027 (mtt-85) REVERT: B 330 LEU cc_start: 0.5413 (mt) cc_final: 0.4768 (mp) REVERT: B 349 GLU cc_start: 0.6982 (tp30) cc_final: 0.6475 (tp30) REVERT: B 389 TYR cc_start: 0.7482 (t80) cc_final: 0.7099 (t80) REVERT: C 27 TYR cc_start: 0.7443 (m-80) cc_final: 0.6666 (m-80) REVERT: C 54 TYR cc_start: 0.5515 (t80) cc_final: 0.5211 (t80) REVERT: C 116 ILE cc_start: 0.6466 (mm) cc_final: 0.6236 (mm) REVERT: C 124 ASN cc_start: 0.7572 (t0) cc_final: 0.7202 (t0) REVERT: C 144 LEU cc_start: 0.7380 (tp) cc_final: 0.7173 (tp) REVERT: C 256 MET cc_start: 0.5609 (ppp) cc_final: 0.5136 (ppp) REVERT: C 295 LYS cc_start: 0.8621 (ptmt) cc_final: 0.8360 (mtmm) REVERT: C 323 ARG cc_start: 0.7443 (tpp80) cc_final: 0.6976 (mtt-85) REVERT: C 349 GLU cc_start: 0.7153 (tt0) cc_final: 0.6941 (tt0) REVERT: C 389 TYR cc_start: 0.7792 (t80) cc_final: 0.7568 (t80) REVERT: C 394 GLN cc_start: 0.7707 (mm-40) cc_final: 0.7198 (mm-40) REVERT: D 54 TYR cc_start: 0.5924 (t80) cc_final: 0.5545 (t80) REVERT: D 64 ARG cc_start: 0.7488 (ttp-110) cc_final: 0.7179 (ttp-110) REVERT: D 112 MET cc_start: 0.6185 (mtt) cc_final: 0.5943 (mtt) REVERT: D 235 MET cc_start: 0.5344 (tpt) cc_final: 0.4889 (mmm) REVERT: D 294 SER cc_start: 0.8234 (t) cc_final: 0.8005 (m) REVERT: D 323 ARG cc_start: 0.7402 (tpp80) cc_final: 0.6947 (mtt-85) REVERT: D 330 LEU cc_start: 0.5453 (mt) cc_final: 0.4923 (mp) REVERT: D 370 THR cc_start: 0.7897 (p) cc_final: 0.7640 (p) REVERT: D 394 GLN cc_start: 0.7298 (mm-40) cc_final: 0.6512 (mm-40) REVERT: E 27 TYR cc_start: 0.6770 (m-80) cc_final: 0.6550 (m-10) REVERT: E 80 MET cc_start: 0.7907 (mmt) cc_final: 0.7576 (mmm) REVERT: E 108 GLU cc_start: 0.7033 (mp0) cc_final: 0.5701 (tm-30) REVERT: E 112 MET cc_start: 0.6119 (mtt) cc_final: 0.5673 (mtt) REVERT: E 124 ASN cc_start: 0.7419 (t0) cc_final: 0.6988 (t0) REVERT: E 182 ARG cc_start: 0.5181 (ptm160) cc_final: 0.4958 (ptm160) REVERT: E 323 ARG cc_start: 0.7593 (tpp80) cc_final: 0.7132 (mtt-85) REVERT: E 330 LEU cc_start: 0.5264 (mt) cc_final: 0.4687 (mp) REVERT: E 349 GLU cc_start: 0.6808 (tp30) cc_final: 0.6316 (tp30) REVERT: E 389 TYR cc_start: 0.7546 (t80) cc_final: 0.7170 (t80) REVERT: F 27 TYR cc_start: 0.7371 (m-80) cc_final: 0.6684 (m-80) REVERT: F 54 TYR cc_start: 0.5306 (t80) cc_final: 0.4985 (t80) REVERT: F 72 LYS cc_start: 0.7417 (mmtt) cc_final: 0.6935 (mttt) REVERT: F 80 MET cc_start: 0.7849 (mmt) cc_final: 0.7637 (mmt) REVERT: F 124 ASN cc_start: 0.7597 (t0) cc_final: 0.7357 (t0) REVERT: F 262 GLU cc_start: 0.7376 (pt0) cc_final: 0.7158 (pt0) REVERT: F 305 ILE cc_start: 0.7112 (mp) cc_final: 0.6862 (mp) REVERT: F 307 GLN cc_start: 0.7914 (mp10) cc_final: 0.7666 (mp10) REVERT: F 323 ARG cc_start: 0.7375 (tpp80) cc_final: 0.6941 (mtt-85) REVERT: F 349 GLU cc_start: 0.7110 (tt0) cc_final: 0.6856 (tt0) REVERT: F 357 MET cc_start: 0.7792 (tpt) cc_final: 0.7128 (tpp) REVERT: G 27 TYR cc_start: 0.7540 (m-80) cc_final: 0.7150 (m-80) REVERT: G 54 TYR cc_start: 0.5922 (t80) cc_final: 0.5666 (t80) REVERT: G 64 ARG cc_start: 0.7495 (ttp-110) cc_final: 0.7172 (ttp-110) REVERT: G 72 LYS cc_start: 0.7211 (mmtt) cc_final: 0.6878 (mmtm) REVERT: G 112 MET cc_start: 0.6428 (mtm) cc_final: 0.5985 (mtm) REVERT: G 124 ASN cc_start: 0.7581 (t0) cc_final: 0.7328 (t0) REVERT: G 262 GLU cc_start: 0.7322 (pt0) cc_final: 0.6920 (pt0) REVERT: G 323 ARG cc_start: 0.7445 (tpp80) cc_final: 0.6948 (mtt-85) REVERT: G 330 LEU cc_start: 0.5554 (mt) cc_final: 0.4908 (mp) REVERT: H 27 TYR cc_start: 0.7013 (m-80) cc_final: 0.6722 (m-10) REVERT: H 80 MET cc_start: 0.7918 (mmt) cc_final: 0.7595 (mmm) REVERT: H 108 GLU cc_start: 0.7046 (mp0) cc_final: 0.5502 (tm-30) REVERT: H 124 ASN cc_start: 0.7514 (t0) cc_final: 0.7046 (t0) REVERT: H 323 ARG cc_start: 0.7481 (tpp80) cc_final: 0.7007 (mtt-85) REVERT: H 330 LEU cc_start: 0.5463 (mt) cc_final: 0.4784 (mp) REVERT: H 349 GLU cc_start: 0.6942 (tp30) cc_final: 0.6460 (tp30) REVERT: H 389 TYR cc_start: 0.7492 (t80) cc_final: 0.7122 (t80) REVERT: I 27 TYR cc_start: 0.7398 (m-80) cc_final: 0.6630 (m-80) REVERT: I 54 TYR cc_start: 0.5504 (t80) cc_final: 0.5130 (t80) REVERT: I 72 LYS cc_start: 0.7279 (mmpt) cc_final: 0.6796 (mttt) REVERT: I 116 ILE cc_start: 0.6294 (mm) cc_final: 0.6045 (mm) REVERT: I 124 ASN cc_start: 0.7574 (t0) cc_final: 0.7226 (t0) REVERT: I 256 MET cc_start: 0.5514 (ppp) cc_final: 0.5062 (ppp) REVERT: I 323 ARG cc_start: 0.7378 (tpp80) cc_final: 0.6932 (mtt-85) REVERT: I 349 GLU cc_start: 0.7180 (tt0) cc_final: 0.6918 (tt0) REVERT: I 389 TYR cc_start: 0.7793 (t80) cc_final: 0.7565 (t80) REVERT: I 394 GLN cc_start: 0.7657 (mm-40) cc_final: 0.6879 (mm-40) REVERT: I 395 GLU cc_start: 0.6812 (mm-30) cc_final: 0.6252 (mm-30) REVERT: J 54 TYR cc_start: 0.5794 (t80) cc_final: 0.5555 (t80) REVERT: J 64 ARG cc_start: 0.7493 (ttp-110) cc_final: 0.7167 (ttp-110) REVERT: J 72 LYS cc_start: 0.7203 (mmtt) cc_final: 0.6871 (mmtm) REVERT: J 112 MET cc_start: 0.6431 (mtm) cc_final: 0.6025 (mtm) REVERT: J 124 ASN cc_start: 0.7561 (t0) cc_final: 0.7320 (t0) REVERT: J 294 SER cc_start: 0.8198 (t) cc_final: 0.7960 (m) REVERT: J 323 ARG cc_start: 0.7465 (tpp80) cc_final: 0.6949 (mtt-85) REVERT: J 330 LEU cc_start: 0.5511 (mt) cc_final: 0.4924 (mp) REVERT: K 27 TYR cc_start: 0.7075 (m-80) cc_final: 0.6830 (m-10) REVERT: K 45 LYS cc_start: 0.5075 (mtmm) cc_final: 0.4562 (ttmm) REVERT: K 72 LYS cc_start: 0.7490 (mmtt) cc_final: 0.6956 (mttt) REVERT: K 80 MET cc_start: 0.7920 (mmt) cc_final: 0.7636 (mmm) REVERT: K 108 GLU cc_start: 0.7111 (mp0) cc_final: 0.5564 (tm-30) REVERT: K 112 MET cc_start: 0.6214 (mtt) cc_final: 0.5780 (mtt) REVERT: K 116 ILE cc_start: 0.6410 (mm) cc_final: 0.6200 (mm) REVERT: K 124 ASN cc_start: 0.7417 (t0) cc_final: 0.6959 (t0) REVERT: K 129 THR cc_start: 0.7316 (p) cc_final: 0.7037 (p) REVERT: K 294 SER cc_start: 0.7840 (t) cc_final: 0.7597 (m) REVERT: K 323 ARG cc_start: 0.7462 (tpp80) cc_final: 0.7007 (mtt-85) REVERT: K 330 LEU cc_start: 0.5415 (mt) cc_final: 0.3958 (mp) REVERT: K 349 GLU cc_start: 0.6990 (tp30) cc_final: 0.6452 (tp30) REVERT: K 389 TYR cc_start: 0.7473 (t80) cc_final: 0.7085 (t80) REVERT: L 27 TYR cc_start: 0.7509 (m-80) cc_final: 0.6755 (m-80) REVERT: L 54 TYR cc_start: 0.5560 (t80) cc_final: 0.5233 (t80) REVERT: L 124 ASN cc_start: 0.7571 (t0) cc_final: 0.7131 (t0) REVERT: L 258 ARG cc_start: 0.7453 (ttm170) cc_final: 0.7241 (ttm-80) REVERT: L 323 ARG cc_start: 0.7447 (tpp80) cc_final: 0.7012 (mtt-85) REVERT: L 349 GLU cc_start: 0.7124 (tt0) cc_final: 0.6919 (tt0) REVERT: L 389 TYR cc_start: 0.7820 (t80) cc_final: 0.7157 (t80) REVERT: L 394 GLN cc_start: 0.7706 (mm-40) cc_final: 0.7060 (mm-40) REVERT: L 395 GLU cc_start: 0.6850 (mm-30) cc_final: 0.6491 (mm-30) outliers start: 0 outliers final: 0 residues processed: 901 average time/residue: 0.2081 time to fit residues: 311.1528 Evaluate side-chains 820 residues out of total 4032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 820 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 70 optimal weight: 0.7980 chunk 435 optimal weight: 0.8980 chunk 120 optimal weight: 0.9980 chunk 234 optimal weight: 10.0000 chunk 438 optimal weight: 6.9990 chunk 455 optimal weight: 2.9990 chunk 359 optimal weight: 0.4980 chunk 20 optimal weight: 0.0670 chunk 122 optimal weight: 7.9990 chunk 443 optimal weight: 6.9990 chunk 404 optimal weight: 0.8980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 307 GLN B 136 GLN C 59 GLN D 81 GLN D 307 GLN E 59 GLN E 136 GLN ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 59 GLN ** F 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 281 ASN G 59 GLN G 307 GLN H 136 GLN ** H 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 281 ASN J 59 GLN J 307 GLN K 136 GLN ** K 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.179837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.147949 restraints weight = 51247.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.152335 restraints weight = 31587.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.155365 restraints weight = 21809.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.157511 restraints weight = 16585.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.158876 restraints weight = 13494.227| |-----------------------------------------------------------------------------| r_work (final): 0.3904 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3906 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3906 r_free = 0.3906 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 71 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3906 r_free = 0.3906 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 75 | |-----------------------------------------------------------------------------| r_final: 0.3906 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6312 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 37788 Z= 0.110 Angle : 0.600 10.537 51132 Z= 0.300 Chirality : 0.041 0.168 5760 Planarity : 0.004 0.054 6660 Dihedral : 4.813 24.347 5208 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 0.05 % Allowed : 2.41 % Favored : 97.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.12), residues: 4632 helix: 0.35 (0.13), residues: 1764 sheet: -0.67 (0.20), residues: 564 loop : -2.36 (0.12), residues: 2304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG J 266 TYR 0.023 0.001 TYR D 27 PHE 0.018 0.001 PHE K 78 TRP 0.016 0.002 TRP K 83 HIS 0.004 0.001 HIS L 216 Details of bonding type rmsd covalent geometry : bond 0.00264 (37788) covalent geometry : angle 0.59958 (51132) hydrogen bonds : bond 0.03166 ( 1391) hydrogen bonds : angle 3.75819 ( 4641) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 881 residues out of total 4032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 879 time to evaluate : 1.278 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: A 64 ARG cc_start: 0.7375 (ttp-110) cc_final: 0.7172 (ttp-110) REVERT: A 72 LYS cc_start: 0.7173 (mmtt) cc_final: 0.6887 (mmtm) REVERT: A 108 GLU cc_start: 0.5784 (mp0) cc_final: 0.4561 (mp0) REVERT: A 112 MET cc_start: 0.6397 (mtm) cc_final: 0.5867 (mtm) REVERT: A 124 ASN cc_start: 0.7483 (t0) cc_final: 0.7262 (t0) REVERT: A 262 GLU cc_start: 0.7321 (pt0) cc_final: 0.7066 (pt0) REVERT: A 291 MET cc_start: 0.7117 (ttp) cc_final: 0.6884 (ttm) REVERT: A 323 ARG cc_start: 0.7411 (tpp80) cc_final: 0.6898 (mtt-85) REVERT: A 330 LEU cc_start: 0.5373 (mt) cc_final: 0.4684 (mp) REVERT: A 394 GLN cc_start: 0.7407 (mm-40) cc_final: 0.6837 (mm-40) REVERT: B 27 TYR cc_start: 0.6747 (m-80) cc_final: 0.6230 (m-10) REVERT: B 80 MET cc_start: 0.7842 (mmt) cc_final: 0.7482 (mmm) REVERT: B 108 GLU cc_start: 0.7026 (mp0) cc_final: 0.5495 (tm-30) REVERT: B 112 MET cc_start: 0.6157 (mtt) cc_final: 0.5626 (mtt) REVERT: B 124 ASN cc_start: 0.7412 (t0) cc_final: 0.6981 (t0) REVERT: B 323 ARG cc_start: 0.7431 (tpp80) cc_final: 0.7023 (mtt-85) REVERT: B 349 GLU cc_start: 0.6967 (tp30) cc_final: 0.6447 (tp30) REVERT: C 27 TYR cc_start: 0.7206 (m-80) cc_final: 0.6520 (m-80) REVERT: C 54 TYR cc_start: 0.5329 (t80) cc_final: 0.5070 (t80) REVERT: C 124 ASN cc_start: 0.7524 (t0) cc_final: 0.7171 (t0) REVERT: C 134 LEU cc_start: 0.6840 (tp) cc_final: 0.6490 (mp) REVERT: C 256 MET cc_start: 0.5532 (ppp) cc_final: 0.5093 (ppp) REVERT: C 323 ARG cc_start: 0.7404 (tpp80) cc_final: 0.6929 (mtt-85) REVERT: C 349 GLU cc_start: 0.7013 (tt0) cc_final: 0.6786 (tt0) REVERT: C 394 GLN cc_start: 0.7729 (mm-40) cc_final: 0.7251 (mm-40) REVERT: D 27 TYR cc_start: 0.7361 (m-80) cc_final: 0.6992 (m-10) REVERT: D 54 TYR cc_start: 0.5845 (t80) cc_final: 0.5599 (t80) REVERT: D 64 ARG cc_start: 0.7402 (ttp-110) cc_final: 0.7178 (ttp-110) REVERT: D 72 LYS cc_start: 0.6977 (mmtt) cc_final: 0.6706 (mmtt) REVERT: D 235 MET cc_start: 0.5273 (tpt) cc_final: 0.4864 (mmm) REVERT: D 262 GLU cc_start: 0.7074 (pt0) cc_final: 0.6799 (pt0) REVERT: D 289 MET cc_start: 0.7130 (ppp) cc_final: 0.6898 (ttp) REVERT: D 294 SER cc_start: 0.8400 (t) cc_final: 0.8029 (m) REVERT: D 323 ARG cc_start: 0.7346 (tpp80) cc_final: 0.6925 (mtt-85) REVERT: D 330 LEU cc_start: 0.5345 (mt) cc_final: 0.4740 (mp) REVERT: D 370 THR cc_start: 0.7887 (p) cc_final: 0.7649 (p) REVERT: D 394 GLN cc_start: 0.7338 (mm-40) cc_final: 0.6416 (mm-40) REVERT: E 27 TYR cc_start: 0.6616 (m-80) cc_final: 0.6147 (m-10) REVERT: E 72 LYS cc_start: 0.7634 (mmtt) cc_final: 0.7164 (mttt) REVERT: E 80 MET cc_start: 0.7862 (mmt) cc_final: 0.7554 (mmm) REVERT: E 108 GLU cc_start: 0.6938 (mp0) cc_final: 0.5651 (tm-30) REVERT: E 112 MET cc_start: 0.5975 (mtt) cc_final: 0.5536 (mtt) REVERT: E 124 ASN cc_start: 0.7252 (t0) cc_final: 0.6891 (t0) REVERT: E 323 ARG cc_start: 0.7526 (tpp80) cc_final: 0.7123 (mtt-85) REVERT: E 330 LEU cc_start: 0.5403 (mt) cc_final: 0.4836 (mp) REVERT: E 349 GLU cc_start: 0.6796 (tp30) cc_final: 0.6183 (tp30) REVERT: F 27 TYR cc_start: 0.7246 (m-80) cc_final: 0.6330 (m-80) REVERT: F 54 TYR cc_start: 0.5067 (t80) cc_final: 0.4792 (t80) REVERT: F 72 LYS cc_start: 0.7229 (mmtt) cc_final: 0.6813 (mttt) REVERT: F 80 MET cc_start: 0.7762 (mmt) cc_final: 0.7521 (mmt) REVERT: F 124 ASN cc_start: 0.7103 (t0) cc_final: 0.6641 (t0) REVERT: F 256 MET cc_start: 0.5541 (ppp) cc_final: 0.5037 (ppp) REVERT: F 262 GLU cc_start: 0.7391 (pt0) cc_final: 0.6980 (pt0) REVERT: F 307 GLN cc_start: 0.7843 (mp10) cc_final: 0.7549 (mp10) REVERT: F 323 ARG cc_start: 0.7375 (tpp80) cc_final: 0.6996 (mtt-85) REVERT: F 349 GLU cc_start: 0.7000 (tt0) cc_final: 0.6750 (tt0) REVERT: F 357 MET cc_start: 0.7710 (tpt) cc_final: 0.7022 (tpp) REVERT: F 394 GLN cc_start: 0.7788 (mm-40) cc_final: 0.7099 (mm-40) REVERT: F 395 GLU cc_start: 0.6785 (mm-30) cc_final: 0.6513 (mm-30) REVERT: G 27 TYR cc_start: 0.7393 (m-80) cc_final: 0.7006 (m-80) REVERT: G 54 TYR cc_start: 0.5858 (t80) cc_final: 0.5610 (t80) REVERT: G 64 ARG cc_start: 0.7374 (ttp-110) cc_final: 0.7172 (ttp-110) REVERT: G 72 LYS cc_start: 0.7115 (mmtt) cc_final: 0.6823 (mmtm) REVERT: G 108 GLU cc_start: 0.5958 (mp0) cc_final: 0.4722 (mp0) REVERT: G 112 MET cc_start: 0.6378 (mtm) cc_final: 0.5866 (mtm) REVERT: G 124 ASN cc_start: 0.7488 (t0) cc_final: 0.7269 (t0) REVERT: G 262 GLU cc_start: 0.7066 (pt0) cc_final: 0.6682 (pt0) REVERT: G 323 ARG cc_start: 0.7401 (tpp80) cc_final: 0.6891 (mtt-85) REVERT: G 330 LEU cc_start: 0.5375 (mt) cc_final: 0.4800 (mp) REVERT: G 394 GLN cc_start: 0.7372 (mm-40) cc_final: 0.6532 (mm-40) REVERT: H 27 TYR cc_start: 0.6804 (m-80) cc_final: 0.6245 (m-10) REVERT: H 80 MET cc_start: 0.7922 (mmt) cc_final: 0.7543 (mmm) REVERT: H 108 GLU cc_start: 0.7006 (mp0) cc_final: 0.5488 (tm-30) REVERT: H 116 ILE cc_start: 0.6466 (mm) cc_final: 0.6259 (mm) REVERT: H 124 ASN cc_start: 0.7347 (t0) cc_final: 0.6892 (t0) REVERT: H 323 ARG cc_start: 0.7456 (tpp80) cc_final: 0.7077 (mtt-85) REVERT: H 349 GLU cc_start: 0.6962 (tp30) cc_final: 0.6438 (tp30) REVERT: H 389 TYR cc_start: 0.7586 (t80) cc_final: 0.7270 (t80) REVERT: I 27 TYR cc_start: 0.7139 (m-80) cc_final: 0.6482 (m-80) REVERT: I 54 TYR cc_start: 0.5529 (t80) cc_final: 0.5194 (t80) REVERT: I 116 ILE cc_start: 0.6175 (mm) cc_final: 0.5955 (mm) REVERT: I 124 ASN cc_start: 0.7589 (t0) cc_final: 0.7108 (t0) REVERT: I 323 ARG cc_start: 0.7378 (tpp80) cc_final: 0.6953 (mtt-85) REVERT: I 395 GLU cc_start: 0.6838 (mm-30) cc_final: 0.6380 (mm-30) REVERT: J 64 ARG cc_start: 0.7390 (ttp-110) cc_final: 0.7189 (ttp-110) REVERT: J 72 LYS cc_start: 0.7133 (mmtt) cc_final: 0.6844 (mmtm) REVERT: J 108 GLU cc_start: 0.5862 (mp0) cc_final: 0.4616 (mp0) REVERT: J 112 MET cc_start: 0.6363 (mtm) cc_final: 0.5866 (mtm) REVERT: J 124 ASN cc_start: 0.7438 (t0) cc_final: 0.7223 (t0) REVERT: J 323 ARG cc_start: 0.7437 (tpp80) cc_final: 0.6912 (mtt-85) REVERT: J 325 GLU cc_start: 0.8140 (tm-30) cc_final: 0.7921 (tm-30) REVERT: J 330 LEU cc_start: 0.5376 (mt) cc_final: 0.4814 (mp) REVERT: J 394 GLN cc_start: 0.7457 (mm-40) cc_final: 0.6604 (mm110) REVERT: K 27 TYR cc_start: 0.6809 (m-80) cc_final: 0.6337 (m-10) REVERT: K 72 LYS cc_start: 0.7409 (mmtt) cc_final: 0.6876 (mttt) REVERT: K 80 MET cc_start: 0.7891 (mmt) cc_final: 0.7516 (mmm) REVERT: K 108 GLU cc_start: 0.6986 (mp0) cc_final: 0.5516 (tm-30) REVERT: K 112 MET cc_start: 0.6171 (mtt) cc_final: 0.5479 (mtt) REVERT: K 116 ILE cc_start: 0.6571 (mm) cc_final: 0.6350 (mm) REVERT: K 124 ASN cc_start: 0.7391 (t0) cc_final: 0.6926 (t0) REVERT: K 323 ARG cc_start: 0.7493 (tpp80) cc_final: 0.7022 (mtt-85) REVERT: K 330 LEU cc_start: 0.5104 (mt) cc_final: 0.4498 (mp) REVERT: K 349 GLU cc_start: 0.6989 (tp30) cc_final: 0.6573 (tp30) REVERT: K 389 TYR cc_start: 0.7581 (t80) cc_final: 0.7253 (t80) REVERT: L 27 TYR cc_start: 0.7365 (m-80) cc_final: 0.6693 (m-80) REVERT: L 54 TYR cc_start: 0.5418 (t80) cc_final: 0.5157 (t80) REVERT: L 323 ARG cc_start: 0.7336 (tpp80) cc_final: 0.6898 (mtt-85) REVERT: L 349 GLU cc_start: 0.7040 (tt0) cc_final: 0.6832 (tt0) REVERT: L 394 GLN cc_start: 0.7745 (mm-40) cc_final: 0.7227 (mm-40) outliers start: 2 outliers final: 1 residues processed: 881 average time/residue: 0.2153 time to fit residues: 309.5731 Evaluate side-chains 797 residues out of total 4032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 796 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 252 optimal weight: 20.0000 chunk 306 optimal weight: 4.9990 chunk 104 optimal weight: 8.9990 chunk 345 optimal weight: 4.9990 chunk 286 optimal weight: 4.9990 chunk 180 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 156 optimal weight: 10.0000 chunk 284 optimal weight: 0.0070 chunk 214 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 overall best weight: 1.3202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 ASN B 178 GLN C 59 GLN D 124 ASN D 307 GLN E 59 GLN ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 175 ASN K 178 GLN L 59 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.177823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.145414 restraints weight = 51149.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.149900 restraints weight = 31443.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.152984 restraints weight = 21639.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.155021 restraints weight = 16350.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.156611 restraints weight = 13368.741| |-----------------------------------------------------------------------------| r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3882 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3882 r_free = 0.3882 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 75 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3881 r_free = 0.3881 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 74 | |-----------------------------------------------------------------------------| r_final: 0.3881 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6356 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 37788 Z= 0.128 Angle : 0.617 8.407 51132 Z= 0.308 Chirality : 0.042 0.179 5760 Planarity : 0.004 0.090 6660 Dihedral : 4.860 24.971 5208 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.12), residues: 4632 helix: 0.29 (0.13), residues: 1836 sheet: -0.33 (0.21), residues: 504 loop : -2.44 (0.12), residues: 2292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG K 195 TYR 0.013 0.001 TYR F 126 PHE 0.019 0.001 PHE H 78 TRP 0.029 0.002 TRP E 83 HIS 0.003 0.001 HIS L 216 Details of bonding type rmsd covalent geometry : bond 0.00305 (37788) covalent geometry : angle 0.61724 (51132) hydrogen bonds : bond 0.03268 ( 1391) hydrogen bonds : angle 3.71463 ( 4641) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 884 residues out of total 4032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 884 time to evaluate : 1.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ARG cc_start: 0.7448 (ttp-110) cc_final: 0.7172 (ttp-110) REVERT: A 72 LYS cc_start: 0.7237 (mmtt) cc_final: 0.6950 (mmtt) REVERT: A 112 MET cc_start: 0.6362 (mtm) cc_final: 0.5784 (mtm) REVERT: A 124 ASN cc_start: 0.7561 (t0) cc_final: 0.7285 (t0) REVERT: A 161 TYR cc_start: 0.7632 (m-80) cc_final: 0.7366 (m-10) REVERT: A 262 GLU cc_start: 0.7263 (pt0) cc_final: 0.7034 (pt0) REVERT: A 291 MET cc_start: 0.7039 (ttp) cc_final: 0.6808 (ttm) REVERT: A 323 ARG cc_start: 0.7376 (tpp80) cc_final: 0.6939 (mtt-85) REVERT: A 330 LEU cc_start: 0.5629 (mt) cc_final: 0.4983 (mp) REVERT: B 27 TYR cc_start: 0.6829 (m-80) cc_final: 0.6435 (m-10) REVERT: B 45 LYS cc_start: 0.4853 (mtmm) cc_final: 0.4389 (ttmm) REVERT: B 72 LYS cc_start: 0.7467 (mmtt) cc_final: 0.6876 (mttt) REVERT: B 80 MET cc_start: 0.7917 (mmt) cc_final: 0.7515 (mmm) REVERT: B 108 GLU cc_start: 0.6971 (mp0) cc_final: 0.5475 (tm-30) REVERT: B 112 MET cc_start: 0.6094 (mtt) cc_final: 0.5562 (mtt) REVERT: B 124 ASN cc_start: 0.7387 (t0) cc_final: 0.6917 (t0) REVERT: B 323 ARG cc_start: 0.7457 (tpp80) cc_final: 0.7014 (mtt-85) REVERT: B 330 LEU cc_start: 0.5478 (mt) cc_final: 0.4790 (mp) REVERT: B 349 GLU cc_start: 0.6935 (tp30) cc_final: 0.6466 (tp30) REVERT: B 394 GLN cc_start: 0.7531 (mm-40) cc_final: 0.7080 (mm-40) REVERT: C 27 TYR cc_start: 0.7270 (m-80) cc_final: 0.6532 (m-80) REVERT: C 54 TYR cc_start: 0.5369 (t80) cc_final: 0.5099 (t80) REVERT: C 124 ASN cc_start: 0.7533 (t0) cc_final: 0.7181 (t0) REVERT: C 256 MET cc_start: 0.5697 (ppp) cc_final: 0.5162 (ppp) REVERT: C 295 LYS cc_start: 0.8738 (ptmt) cc_final: 0.8414 (pttt) REVERT: C 323 ARG cc_start: 0.7334 (tpp80) cc_final: 0.6861 (mtt-85) REVERT: C 349 GLU cc_start: 0.6981 (tt0) cc_final: 0.6767 (tt0) REVERT: C 394 GLN cc_start: 0.7734 (mm-40) cc_final: 0.6981 (mm-40) REVERT: C 395 GLU cc_start: 0.6802 (mm-30) cc_final: 0.6493 (mm-30) REVERT: D 27 TYR cc_start: 0.7404 (m-80) cc_final: 0.6956 (m-10) REVERT: D 54 TYR cc_start: 0.5828 (t80) cc_final: 0.5500 (t80) REVERT: D 72 LYS cc_start: 0.6997 (mmtt) cc_final: 0.6718 (mmtt) REVERT: D 108 GLU cc_start: 0.5944 (mp0) cc_final: 0.4996 (mp0) REVERT: D 112 MET cc_start: 0.6181 (mtt) cc_final: 0.5796 (mtt) REVERT: D 235 MET cc_start: 0.5263 (tpt) cc_final: 0.4821 (mmm) REVERT: D 255 ARG cc_start: 0.6652 (mpp80) cc_final: 0.5999 (mtm110) REVERT: D 262 GLU cc_start: 0.7175 (pt0) cc_final: 0.6773 (pt0) REVERT: D 289 MET cc_start: 0.7275 (ppp) cc_final: 0.6924 (ttp) REVERT: D 291 MET cc_start: 0.7089 (ttp) cc_final: 0.6829 (ttm) REVERT: D 294 SER cc_start: 0.8433 (t) cc_final: 0.8073 (m) REVERT: D 323 ARG cc_start: 0.7348 (tpp80) cc_final: 0.6939 (mtt-85) REVERT: D 330 LEU cc_start: 0.5415 (mt) cc_final: 0.4794 (mp) REVERT: D 370 THR cc_start: 0.7878 (p) cc_final: 0.7622 (p) REVERT: D 394 GLN cc_start: 0.7163 (mm-40) cc_final: 0.6543 (mm-40) REVERT: E 27 TYR cc_start: 0.6648 (m-80) cc_final: 0.6327 (m-10) REVERT: E 45 LYS cc_start: 0.4948 (mtmm) cc_final: 0.4354 (ttmm) REVERT: E 72 LYS cc_start: 0.7674 (mmtt) cc_final: 0.7212 (mttt) REVERT: E 80 MET cc_start: 0.7926 (mmt) cc_final: 0.7519 (mmm) REVERT: E 108 GLU cc_start: 0.6904 (mp0) cc_final: 0.5621 (tm-30) REVERT: E 112 MET cc_start: 0.5935 (mtt) cc_final: 0.5509 (mtt) REVERT: E 124 ASN cc_start: 0.7245 (t0) cc_final: 0.6840 (t0) REVERT: E 323 ARG cc_start: 0.7536 (tpp80) cc_final: 0.7112 (mtt-85) REVERT: E 330 LEU cc_start: 0.5490 (mt) cc_final: 0.4849 (mp) REVERT: E 349 GLU cc_start: 0.6766 (tp30) cc_final: 0.6280 (tp30) REVERT: F 27 TYR cc_start: 0.7292 (m-80) cc_final: 0.6317 (m-80) REVERT: F 72 LYS cc_start: 0.7150 (mmtt) cc_final: 0.6731 (mttt) REVERT: F 80 MET cc_start: 0.7761 (mmt) cc_final: 0.7509 (mmt) REVERT: F 124 ASN cc_start: 0.7319 (t0) cc_final: 0.6821 (t0) REVERT: F 256 MET cc_start: 0.5689 (ppp) cc_final: 0.5098 (ppp) REVERT: F 262 GLU cc_start: 0.7399 (pt0) cc_final: 0.7022 (pt0) REVERT: F 307 GLN cc_start: 0.7851 (mp10) cc_final: 0.7486 (mp10) REVERT: F 323 ARG cc_start: 0.7375 (tpp80) cc_final: 0.6918 (mtt-85) REVERT: F 349 GLU cc_start: 0.6961 (tt0) cc_final: 0.6759 (tt0) REVERT: F 394 GLN cc_start: 0.7799 (mm-40) cc_final: 0.7198 (mm-40) REVERT: F 395 GLU cc_start: 0.6690 (mm-30) cc_final: 0.6397 (mm-30) REVERT: G 27 TYR cc_start: 0.7463 (m-80) cc_final: 0.7213 (m-80) REVERT: G 64 ARG cc_start: 0.7452 (ttp-110) cc_final: 0.7173 (ttp-110) REVERT: G 72 LYS cc_start: 0.7154 (mmtt) cc_final: 0.6851 (mmtt) REVERT: G 112 MET cc_start: 0.6279 (mtm) cc_final: 0.5822 (mtm) REVERT: G 124 ASN cc_start: 0.7557 (t0) cc_final: 0.7269 (t0) REVERT: G 323 ARG cc_start: 0.7383 (tpp80) cc_final: 0.6928 (mtt-85) REVERT: G 330 LEU cc_start: 0.5513 (mt) cc_final: 0.4928 (mp) REVERT: H 27 TYR cc_start: 0.6899 (m-80) cc_final: 0.6495 (m-10) REVERT: H 45 LYS cc_start: 0.4969 (mtmm) cc_final: 0.4489 (ttmm) REVERT: H 72 LYS cc_start: 0.7491 (mmtp) cc_final: 0.6873 (mttt) REVERT: H 80 MET cc_start: 0.7912 (mmt) cc_final: 0.7531 (mmm) REVERT: H 108 GLU cc_start: 0.6959 (mp0) cc_final: 0.5452 (tm-30) REVERT: H 116 ILE cc_start: 0.6571 (mm) cc_final: 0.6366 (mm) REVERT: H 124 ASN cc_start: 0.7299 (t0) cc_final: 0.6839 (t0) REVERT: H 323 ARG cc_start: 0.7452 (tpp80) cc_final: 0.7014 (mtt-85) REVERT: H 330 LEU cc_start: 0.5624 (mt) cc_final: 0.4932 (mp) REVERT: H 334 LYS cc_start: 0.8569 (ptmt) cc_final: 0.8333 (ptpt) REVERT: H 349 GLU cc_start: 0.6915 (tp30) cc_final: 0.6463 (tp30) REVERT: H 389 TYR cc_start: 0.7497 (t80) cc_final: 0.7187 (t80) REVERT: H 394 GLN cc_start: 0.7490 (mm-40) cc_final: 0.7081 (mm-40) REVERT: I 27 TYR cc_start: 0.7221 (m-80) cc_final: 0.6469 (m-80) REVERT: I 54 TYR cc_start: 0.5516 (t80) cc_final: 0.5227 (t80) REVERT: I 124 ASN cc_start: 0.7564 (t0) cc_final: 0.7213 (t0) REVERT: I 262 GLU cc_start: 0.7418 (pt0) cc_final: 0.7125 (pt0) REVERT: I 305 ILE cc_start: 0.7103 (mp) cc_final: 0.6697 (mp) REVERT: I 323 ARG cc_start: 0.7396 (tpp80) cc_final: 0.7010 (mtt-85) REVERT: I 349 GLU cc_start: 0.6590 (tp30) cc_final: 0.5859 (tp30) REVERT: I 394 GLN cc_start: 0.7799 (mm-40) cc_final: 0.7208 (mm-40) REVERT: I 395 GLU cc_start: 0.6771 (mm-30) cc_final: 0.6170 (mm-30) REVERT: J 64 ARG cc_start: 0.7469 (ttp-110) cc_final: 0.7195 (ttp-110) REVERT: J 72 LYS cc_start: 0.7209 (mmtt) cc_final: 0.6897 (mmtt) REVERT: J 112 MET cc_start: 0.6348 (mtm) cc_final: 0.5822 (mtm) REVERT: J 124 ASN cc_start: 0.7539 (t0) cc_final: 0.7278 (t0) REVERT: J 294 SER cc_start: 0.8311 (t) cc_final: 0.8015 (m) REVERT: J 323 ARG cc_start: 0.7417 (tpp80) cc_final: 0.6901 (mtt-85) REVERT: J 330 LEU cc_start: 0.5379 (mt) cc_final: 0.4773 (mp) REVERT: K 27 TYR cc_start: 0.6909 (m-80) cc_final: 0.6500 (m-10) REVERT: K 72 LYS cc_start: 0.7466 (mmtt) cc_final: 0.6967 (mttt) REVERT: K 80 MET cc_start: 0.7905 (mmt) cc_final: 0.7564 (mmm) REVERT: K 108 GLU cc_start: 0.6930 (mp0) cc_final: 0.5481 (tm-30) REVERT: K 112 MET cc_start: 0.6082 (mtt) cc_final: 0.5389 (mtt) REVERT: K 116 ILE cc_start: 0.6700 (mm) cc_final: 0.6452 (mm) REVERT: K 124 ASN cc_start: 0.7323 (t0) cc_final: 0.6894 (t0) REVERT: K 129 THR cc_start: 0.7161 (p) cc_final: 0.6915 (p) REVERT: K 323 ARG cc_start: 0.7436 (tpp80) cc_final: 0.6987 (mtt-85) REVERT: K 330 LEU cc_start: 0.5160 (mt) cc_final: 0.4502 (mp) REVERT: K 349 GLU cc_start: 0.6953 (tp30) cc_final: 0.6580 (tp30) REVERT: K 389 TYR cc_start: 0.7620 (t80) cc_final: 0.7316 (t80) REVERT: K 394 GLN cc_start: 0.7561 (mm-40) cc_final: 0.7152 (mm-40) REVERT: L 27 TYR cc_start: 0.7309 (m-80) cc_final: 0.6646 (m-80) REVERT: L 54 TYR cc_start: 0.5479 (t80) cc_final: 0.5221 (t80) REVERT: L 124 ASN cc_start: 0.7605 (t0) cc_final: 0.7293 (t0) REVERT: L 305 ILE cc_start: 0.6975 (mp) cc_final: 0.6600 (mp) REVERT: L 323 ARG cc_start: 0.7405 (tpp80) cc_final: 0.6950 (mtt-85) REVERT: L 349 GLU cc_start: 0.7014 (tt0) cc_final: 0.6743 (tt0) REVERT: L 394 GLN cc_start: 0.7737 (mm-40) cc_final: 0.6845 (mm-40) REVERT: L 395 GLU cc_start: 0.6837 (mm-30) cc_final: 0.6537 (mm-30) outliers start: 0 outliers final: 0 residues processed: 884 average time/residue: 0.2120 time to fit residues: 310.6419 Evaluate side-chains 812 residues out of total 4032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 812 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 81 optimal weight: 0.1980 chunk 372 optimal weight: 0.0040 chunk 240 optimal weight: 7.9990 chunk 255 optimal weight: 2.9990 chunk 401 optimal weight: 0.0570 chunk 116 optimal weight: 6.9990 chunk 234 optimal weight: 9.9990 chunk 206 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 chunk 436 optimal weight: 4.9990 overall best weight: 0.8312 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN B 136 GLN B 178 GLN D 124 ASN D 178 GLN E 59 GLN E 394 GLN ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 59 GLN G 59 GLN G 136 GLN H 136 GLN H 178 GLN ** I 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 59 GLN J 307 GLN K 178 GLN L 59 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.179386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.148230 restraints weight = 51185.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.152506 restraints weight = 31801.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.155424 restraints weight = 22033.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.157466 restraints weight = 16799.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.158721 restraints weight = 13756.159| |-----------------------------------------------------------------------------| r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3909 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3909 r_free = 0.3909 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 74 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3909 r_free = 0.3909 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 76 | |-----------------------------------------------------------------------------| r_final: 0.3909 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6296 moved from start: 0.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 37788 Z= 0.114 Angle : 0.598 9.559 51132 Z= 0.298 Chirality : 0.042 0.183 5760 Planarity : 0.004 0.054 6660 Dihedral : 4.736 25.812 5208 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.12), residues: 4632 helix: 0.46 (0.13), residues: 1848 sheet: -0.20 (0.21), residues: 504 loop : -2.35 (0.12), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG J 351 TYR 0.023 0.001 TYR C 389 PHE 0.020 0.001 PHE K 78 TRP 0.010 0.001 TRP G 58 HIS 0.003 0.001 HIS L 216 Details of bonding type rmsd covalent geometry : bond 0.00275 (37788) covalent geometry : angle 0.59803 (51132) hydrogen bonds : bond 0.03145 ( 1391) hydrogen bonds : angle 3.64134 ( 4641) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 877 residues out of total 4032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 877 time to evaluate : 1.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ARG cc_start: 0.7381 (ttp-110) cc_final: 0.6929 (ttp-110) REVERT: A 72 LYS cc_start: 0.7263 (mmtt) cc_final: 0.6952 (mmtt) REVERT: A 112 MET cc_start: 0.6378 (mtm) cc_final: 0.5865 (mtm) REVERT: A 161 TYR cc_start: 0.7524 (m-80) cc_final: 0.7304 (m-10) REVERT: A 291 MET cc_start: 0.7015 (ttp) cc_final: 0.6782 (ttm) REVERT: A 323 ARG cc_start: 0.7431 (tpp80) cc_final: 0.6973 (mtt-85) REVERT: A 330 LEU cc_start: 0.5268 (mt) cc_final: 0.4764 (mp) REVERT: B 27 TYR cc_start: 0.6748 (m-80) cc_final: 0.6251 (m-10) REVERT: B 72 LYS cc_start: 0.7534 (mmtt) cc_final: 0.6997 (mttt) REVERT: B 80 MET cc_start: 0.7931 (mmt) cc_final: 0.7576 (mmm) REVERT: B 108 GLU cc_start: 0.7048 (mp0) cc_final: 0.5517 (tm-30) REVERT: B 124 ASN cc_start: 0.7367 (t0) cc_final: 0.6872 (t0) REVERT: B 323 ARG cc_start: 0.7458 (tpp80) cc_final: 0.6986 (mtt-85) REVERT: B 349 GLU cc_start: 0.7000 (tp30) cc_final: 0.6435 (tp30) REVERT: B 394 GLN cc_start: 0.7492 (mm-40) cc_final: 0.7090 (mm-40) REVERT: C 27 TYR cc_start: 0.7167 (m-80) cc_final: 0.6413 (m-80) REVERT: C 54 TYR cc_start: 0.5313 (t80) cc_final: 0.5017 (t80) REVERT: C 85 ARG cc_start: 0.6458 (ttp-170) cc_final: 0.6225 (ttm170) REVERT: C 256 MET cc_start: 0.5667 (ppp) cc_final: 0.5138 (ppp) REVERT: C 295 LYS cc_start: 0.8764 (ptmt) cc_final: 0.8416 (pttt) REVERT: C 323 ARG cc_start: 0.7408 (tpp80) cc_final: 0.6968 (mtt-85) REVERT: C 349 GLU cc_start: 0.7053 (tt0) cc_final: 0.6837 (tt0) REVERT: C 389 TYR cc_start: 0.7332 (t80) cc_final: 0.6869 (t80) REVERT: C 394 GLN cc_start: 0.7749 (mm-40) cc_final: 0.7330 (mm-40) REVERT: D 27 TYR cc_start: 0.7296 (m-80) cc_final: 0.6902 (m-10) REVERT: D 54 TYR cc_start: 0.5792 (t80) cc_final: 0.5487 (t80) REVERT: D 72 LYS cc_start: 0.7018 (mmtt) cc_final: 0.6739 (mmtt) REVERT: D 108 GLU cc_start: 0.6058 (mp0) cc_final: 0.5821 (mp0) REVERT: D 235 MET cc_start: 0.5342 (tpt) cc_final: 0.4874 (mmm) REVERT: D 262 GLU cc_start: 0.7217 (pt0) cc_final: 0.6895 (pt0) REVERT: D 289 MET cc_start: 0.7200 (ppp) cc_final: 0.6868 (ttp) REVERT: D 323 ARG cc_start: 0.7383 (tpp80) cc_final: 0.6997 (mtt-85) REVERT: D 330 LEU cc_start: 0.5323 (mt) cc_final: 0.4738 (mp) REVERT: D 394 GLN cc_start: 0.7377 (mm-40) cc_final: 0.6555 (mm-40) REVERT: E 27 TYR cc_start: 0.6657 (m-80) cc_final: 0.6248 (m-10) REVERT: E 72 LYS cc_start: 0.7632 (mmtt) cc_final: 0.7132 (mttt) REVERT: E 80 MET cc_start: 0.8051 (mmt) cc_final: 0.7605 (mmm) REVERT: E 108 GLU cc_start: 0.6978 (mp0) cc_final: 0.5711 (tm-30) REVERT: E 112 MET cc_start: 0.6055 (mtt) cc_final: 0.5588 (mtt) REVERT: E 323 ARG cc_start: 0.7605 (tpp80) cc_final: 0.7179 (mtt-85) REVERT: E 330 LEU cc_start: 0.5626 (mt) cc_final: 0.4968 (mp) REVERT: E 349 GLU cc_start: 0.6914 (tp30) cc_final: 0.6369 (tp30) REVERT: E 394 GLN cc_start: 0.7649 (mm-40) cc_final: 0.7176 (mm-40) REVERT: F 27 TYR cc_start: 0.7219 (m-80) cc_final: 0.6287 (m-80) REVERT: F 80 MET cc_start: 0.7788 (mmt) cc_final: 0.7503 (mmt) REVERT: F 124 ASN cc_start: 0.7476 (t0) cc_final: 0.6910 (t0) REVERT: F 256 MET cc_start: 0.5604 (ppp) cc_final: 0.4991 (ppp) REVERT: F 262 GLU cc_start: 0.7401 (pt0) cc_final: 0.7008 (pt0) REVERT: F 323 ARG cc_start: 0.7474 (tpp80) cc_final: 0.6988 (mtt-85) REVERT: F 349 GLU cc_start: 0.6999 (tt0) cc_final: 0.6763 (tt0) REVERT: F 394 GLN cc_start: 0.7777 (mm-40) cc_final: 0.7104 (mm-40) REVERT: F 395 GLU cc_start: 0.6796 (mm-30) cc_final: 0.6502 (mm-30) REVERT: G 64 ARG cc_start: 0.7315 (ttp-110) cc_final: 0.7009 (ttp-110) REVERT: G 72 LYS cc_start: 0.7068 (mmtt) cc_final: 0.6758 (mmtt) REVERT: G 112 MET cc_start: 0.6334 (mtm) cc_final: 0.5865 (mtm) REVERT: G 323 ARG cc_start: 0.7345 (tpp80) cc_final: 0.6938 (mtt-85) REVERT: G 330 LEU cc_start: 0.5414 (mt) cc_final: 0.4840 (mp) REVERT: G 394 GLN cc_start: 0.7351 (mm-40) cc_final: 0.6721 (mm-40) REVERT: H 27 TYR cc_start: 0.6821 (m-80) cc_final: 0.6215 (m-10) REVERT: H 72 LYS cc_start: 0.7583 (mmtp) cc_final: 0.6977 (mttt) REVERT: H 80 MET cc_start: 0.7923 (mmt) cc_final: 0.7621 (mmm) REVERT: H 108 GLU cc_start: 0.6967 (mp0) cc_final: 0.5450 (tm-30) REVERT: H 116 ILE cc_start: 0.6599 (mm) cc_final: 0.6364 (mm) REVERT: H 124 ASN cc_start: 0.7312 (t0) cc_final: 0.6804 (t0) REVERT: H 323 ARG cc_start: 0.7424 (tpp80) cc_final: 0.7053 (mtt-85) REVERT: H 349 GLU cc_start: 0.6989 (tp30) cc_final: 0.6476 (tp30) REVERT: H 370 THR cc_start: 0.7892 (p) cc_final: 0.7672 (p) REVERT: H 389 TYR cc_start: 0.7193 (t80) cc_final: 0.6720 (t80) REVERT: H 394 GLN cc_start: 0.7466 (mm-40) cc_final: 0.7083 (mm-40) REVERT: I 27 TYR cc_start: 0.7087 (m-80) cc_final: 0.6400 (m-80) REVERT: I 54 TYR cc_start: 0.5455 (t80) cc_final: 0.5155 (t80) REVERT: I 124 ASN cc_start: 0.7301 (t0) cc_final: 0.6915 (t0) REVERT: I 262 GLU cc_start: 0.7466 (pt0) cc_final: 0.7256 (pt0) REVERT: I 323 ARG cc_start: 0.7484 (tpp80) cc_final: 0.7013 (mtt-85) REVERT: I 349 GLU cc_start: 0.6579 (tp30) cc_final: 0.5902 (tp30) REVERT: I 359 ASN cc_start: 0.6587 (t0) cc_final: 0.6361 (t0) REVERT: I 389 TYR cc_start: 0.7333 (t80) cc_final: 0.6850 (t80) REVERT: I 394 GLN cc_start: 0.7816 (mm-40) cc_final: 0.7233 (mm-40) REVERT: I 395 GLU cc_start: 0.6793 (mm-30) cc_final: 0.6239 (mm-30) REVERT: J 64 ARG cc_start: 0.7392 (ttp-110) cc_final: 0.7074 (ttp-110) REVERT: J 72 LYS cc_start: 0.7195 (mmtt) cc_final: 0.6851 (mmtt) REVERT: J 112 MET cc_start: 0.6400 (mtm) cc_final: 0.5916 (mtm) REVERT: J 294 SER cc_start: 0.8186 (t) cc_final: 0.7872 (m) REVERT: J 323 ARG cc_start: 0.7445 (tpp80) cc_final: 0.6967 (mtt-85) REVERT: J 330 LEU cc_start: 0.5229 (mt) cc_final: 0.4661 (mp) REVERT: K 27 TYR cc_start: 0.6814 (m-80) cc_final: 0.6362 (m-10) REVERT: K 80 MET cc_start: 0.7908 (mmt) cc_final: 0.7526 (mmm) REVERT: K 108 GLU cc_start: 0.6927 (mp0) cc_final: 0.5454 (tm-30) REVERT: K 112 MET cc_start: 0.6215 (mtt) cc_final: 0.5456 (mtt) REVERT: K 116 ILE cc_start: 0.6681 (mm) cc_final: 0.6448 (mm) REVERT: K 124 ASN cc_start: 0.7372 (t0) cc_final: 0.6875 (t0) REVERT: K 323 ARG cc_start: 0.7480 (tpp80) cc_final: 0.6990 (mtt-85) REVERT: K 330 LEU cc_start: 0.5127 (mt) cc_final: 0.4517 (mp) REVERT: K 349 GLU cc_start: 0.6973 (tp30) cc_final: 0.6595 (tp30) REVERT: K 389 TYR cc_start: 0.7551 (t80) cc_final: 0.7229 (t80) REVERT: K 394 GLN cc_start: 0.7525 (mm-40) cc_final: 0.7144 (mm-40) REVERT: L 27 TYR cc_start: 0.7223 (m-80) cc_final: 0.6664 (m-80) REVERT: L 54 TYR cc_start: 0.5361 (t80) cc_final: 0.5092 (t80) REVERT: L 81 GLN cc_start: 0.7838 (mt0) cc_final: 0.7545 (tt0) REVERT: L 124 ASN cc_start: 0.7598 (t0) cc_final: 0.7264 (t0) REVERT: L 256 MET cc_start: 0.5612 (ppp) cc_final: 0.5070 (ttp) REVERT: L 262 GLU cc_start: 0.7406 (pt0) cc_final: 0.7124 (pt0) REVERT: L 323 ARG cc_start: 0.7479 (tpp80) cc_final: 0.7009 (mtt-85) REVERT: L 349 GLU cc_start: 0.7029 (tt0) cc_final: 0.6760 (tt0) REVERT: L 394 GLN cc_start: 0.7753 (mm-40) cc_final: 0.7254 (mm-40) outliers start: 0 outliers final: 0 residues processed: 877 average time/residue: 0.2140 time to fit residues: 310.2427 Evaluate side-chains 798 residues out of total 4032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 798 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 291 optimal weight: 8.9990 chunk 372 optimal weight: 6.9990 chunk 433 optimal weight: 4.9990 chunk 99 optimal weight: 0.7980 chunk 57 optimal weight: 8.9990 chunk 41 optimal weight: 0.9990 chunk 393 optimal weight: 0.6980 chunk 226 optimal weight: 0.8980 chunk 255 optimal weight: 0.9990 chunk 423 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 ASN B 59 GLN B 178 GLN C 124 ASN D 136 GLN D 178 GLN E 59 GLN E 124 ASN E 136 GLN E 178 GLN E 216 HIS ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 124 ASN H 59 GLN H 178 GLN J 124 ASN J 307 GLN K 178 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.179439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.148264 restraints weight = 50813.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.152486 restraints weight = 31717.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.155364 restraints weight = 21997.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.157133 restraints weight = 16839.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.158694 restraints weight = 13994.836| |-----------------------------------------------------------------------------| r_work (final): 0.3904 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3902 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3902 r_free = 0.3902 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 76 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3902 r_free = 0.3902 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 76 | |-----------------------------------------------------------------------------| r_final: 0.3902 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6305 moved from start: 0.4032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 37788 Z= 0.116 Angle : 0.601 11.474 51132 Z= 0.299 Chirality : 0.042 0.192 5760 Planarity : 0.004 0.050 6660 Dihedral : 4.707 22.924 5208 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 0.05 % Allowed : 1.19 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.12), residues: 4632 helix: 0.59 (0.13), residues: 1848 sheet: -0.12 (0.21), residues: 504 loop : -2.31 (0.12), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 195 TYR 0.023 0.001 TYR L 389 PHE 0.020 0.001 PHE G 78 TRP 0.019 0.001 TRP F 83 HIS 0.003 0.001 HIS L 216 Details of bonding type rmsd covalent geometry : bond 0.00278 (37788) covalent geometry : angle 0.60116 (51132) hydrogen bonds : bond 0.03124 ( 1391) hydrogen bonds : angle 3.60328 ( 4641) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 840 residues out of total 4032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 838 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ARG cc_start: 0.7386 (ttp-110) cc_final: 0.6924 (ttp-110) REVERT: A 72 LYS cc_start: 0.7226 (mmtt) cc_final: 0.6891 (mmtt) REVERT: A 112 MET cc_start: 0.6341 (mtm) cc_final: 0.5868 (mtm) REVERT: A 161 TYR cc_start: 0.7523 (m-80) cc_final: 0.7308 (m-10) REVERT: A 291 MET cc_start: 0.7014 (ttp) cc_final: 0.6764 (ttm) REVERT: A 323 ARG cc_start: 0.7366 (tpp80) cc_final: 0.6972 (mtt-85) REVERT: A 330 LEU cc_start: 0.5251 (mt) cc_final: 0.4672 (mp) REVERT: B 27 TYR cc_start: 0.6811 (m-80) cc_final: 0.6276 (m-10) REVERT: B 72 LYS cc_start: 0.7568 (mmtt) cc_final: 0.6979 (mttt) REVERT: B 74 MET cc_start: 0.7773 (ttm) cc_final: 0.7564 (mtt) REVERT: B 80 MET cc_start: 0.7908 (mmt) cc_final: 0.7572 (mmm) REVERT: B 108 GLU cc_start: 0.6952 (mp0) cc_final: 0.5497 (tm-30) REVERT: B 112 MET cc_start: 0.6231 (mtt) cc_final: 0.5479 (mtt) REVERT: B 116 ILE cc_start: 0.6666 (mm) cc_final: 0.6433 (mm) REVERT: B 323 ARG cc_start: 0.7444 (tpp80) cc_final: 0.6972 (mtt-85) REVERT: B 330 LEU cc_start: 0.5027 (mt) cc_final: 0.4463 (mp) REVERT: B 349 GLU cc_start: 0.6974 (tp30) cc_final: 0.6389 (tp30) REVERT: B 389 TYR cc_start: 0.7575 (t80) cc_final: 0.7152 (t80) REVERT: B 394 GLN cc_start: 0.7528 (mm-40) cc_final: 0.7144 (mm-40) REVERT: C 27 TYR cc_start: 0.7071 (m-80) cc_final: 0.6401 (m-80) REVERT: C 54 TYR cc_start: 0.5299 (t80) cc_final: 0.5002 (t80) REVERT: C 295 LYS cc_start: 0.8724 (ptmt) cc_final: 0.8374 (pttt) REVERT: C 307 GLN cc_start: 0.8058 (mp10) cc_final: 0.7763 (mp10) REVERT: C 323 ARG cc_start: 0.7422 (tpp80) cc_final: 0.6964 (mtt-85) REVERT: C 349 GLU cc_start: 0.7047 (tt0) cc_final: 0.6797 (tt0) REVERT: C 389 TYR cc_start: 0.7297 (t80) cc_final: 0.6956 (t80) REVERT: C 394 GLN cc_start: 0.7780 (mm-40) cc_final: 0.7369 (mm-40) REVERT: D 54 TYR cc_start: 0.5741 (t80) cc_final: 0.5451 (t80) REVERT: D 72 LYS cc_start: 0.6984 (mmtt) cc_final: 0.6709 (mmtt) REVERT: D 235 MET cc_start: 0.5388 (tpt) cc_final: 0.4905 (mmm) REVERT: D 289 MET cc_start: 0.7249 (ppp) cc_final: 0.6837 (ttp) REVERT: D 323 ARG cc_start: 0.7396 (tpp80) cc_final: 0.7003 (mtt-85) REVERT: D 330 LEU cc_start: 0.5247 (mt) cc_final: 0.4659 (mp) REVERT: D 356 PHE cc_start: 0.5958 (m-80) cc_final: 0.5750 (m-80) REVERT: D 394 GLN cc_start: 0.7387 (mm-40) cc_final: 0.6523 (mm-40) REVERT: E 27 TYR cc_start: 0.6584 (m-80) cc_final: 0.6206 (m-10) REVERT: E 45 LYS cc_start: 0.6289 (ttmt) cc_final: 0.5954 (ttmm) REVERT: E 72 LYS cc_start: 0.7582 (mmtt) cc_final: 0.7192 (mttp) REVERT: E 80 MET cc_start: 0.8022 (mmt) cc_final: 0.7626 (mmm) REVERT: E 108 GLU cc_start: 0.6938 (mp0) cc_final: 0.5755 (tm-30) REVERT: E 112 MET cc_start: 0.5993 (mtt) cc_final: 0.5616 (mtt) REVERT: E 323 ARG cc_start: 0.7605 (tpp80) cc_final: 0.7170 (mtt-85) REVERT: E 330 LEU cc_start: 0.4939 (mt) cc_final: 0.4339 (mp) REVERT: E 349 GLU cc_start: 0.6902 (tp30) cc_final: 0.6292 (tp30) REVERT: E 394 GLN cc_start: 0.7627 (mm-40) cc_final: 0.7219 (mm-40) REVERT: F 27 TYR cc_start: 0.7174 (m-80) cc_final: 0.6256 (m-80) REVERT: F 80 MET cc_start: 0.7778 (mmt) cc_final: 0.7526 (mmt) REVERT: F 124 ASN cc_start: 0.7505 (t0) cc_final: 0.6919 (t0) REVERT: F 154 ASN cc_start: 0.7015 (m-40) cc_final: 0.6797 (m110) REVERT: F 262 GLU cc_start: 0.7406 (pt0) cc_final: 0.7037 (pt0) REVERT: F 323 ARG cc_start: 0.7477 (tpp80) cc_final: 0.6961 (mtt-85) REVERT: F 349 GLU cc_start: 0.7039 (tt0) cc_final: 0.6791 (tt0) REVERT: F 394 GLN cc_start: 0.7743 (mm-40) cc_final: 0.7125 (mm-40) REVERT: F 395 GLU cc_start: 0.6754 (mm-30) cc_final: 0.6423 (mm-30) REVERT: G 64 ARG cc_start: 0.7323 (ttp-110) cc_final: 0.7004 (ttp-110) REVERT: G 72 LYS cc_start: 0.7057 (mmtt) cc_final: 0.6735 (mmtt) REVERT: G 112 MET cc_start: 0.6318 (mtm) cc_final: 0.5847 (mtm) REVERT: G 323 ARG cc_start: 0.7365 (tpp80) cc_final: 0.6948 (mtt-85) REVERT: G 330 LEU cc_start: 0.5197 (mt) cc_final: 0.4722 (mp) REVERT: G 394 GLN cc_start: 0.7350 (mm-40) cc_final: 0.6735 (mm-40) REVERT: H 27 TYR cc_start: 0.6798 (m-80) cc_final: 0.6253 (m-10) REVERT: H 80 MET cc_start: 0.7869 (mmt) cc_final: 0.7598 (mmm) REVERT: H 108 GLU cc_start: 0.6938 (mp0) cc_final: 0.5459 (tm-30) REVERT: H 116 ILE cc_start: 0.6609 (mm) cc_final: 0.6391 (mm) REVERT: H 323 ARG cc_start: 0.7417 (tpp80) cc_final: 0.7037 (mtt-85) REVERT: H 330 LEU cc_start: 0.4965 (mt) cc_final: 0.4440 (mp) REVERT: H 349 GLU cc_start: 0.7007 (tp30) cc_final: 0.6435 (tp30) REVERT: H 370 THR cc_start: 0.7928 (p) cc_final: 0.7702 (p) REVERT: H 389 TYR cc_start: 0.7207 (t80) cc_final: 0.6737 (t80) REVERT: H 394 GLN cc_start: 0.7529 (mm-40) cc_final: 0.7179 (mm-40) REVERT: I 27 TYR cc_start: 0.7056 (m-80) cc_final: 0.6392 (m-80) REVERT: I 54 TYR cc_start: 0.5467 (t80) cc_final: 0.5245 (t80) REVERT: I 124 ASN cc_start: 0.7349 (t0) cc_final: 0.6872 (t0) REVERT: I 262 GLU cc_start: 0.7466 (pt0) cc_final: 0.7252 (pt0) REVERT: I 323 ARG cc_start: 0.7499 (tpp80) cc_final: 0.7037 (mtt-85) REVERT: I 349 GLU cc_start: 0.6536 (tp30) cc_final: 0.6189 (tp30) REVERT: I 389 TYR cc_start: 0.7335 (t80) cc_final: 0.6959 (t80) REVERT: I 394 GLN cc_start: 0.7826 (mm-40) cc_final: 0.7180 (mm-40) REVERT: I 395 GLU cc_start: 0.6848 (mm-30) cc_final: 0.6406 (mm-30) REVERT: J 64 ARG cc_start: 0.7400 (ttp-110) cc_final: 0.6927 (ttp-110) REVERT: J 72 LYS cc_start: 0.7192 (mmtt) cc_final: 0.6829 (mmtt) REVERT: J 112 MET cc_start: 0.6342 (mtm) cc_final: 0.5884 (mtm) REVERT: J 161 TYR cc_start: 0.7556 (m-80) cc_final: 0.7314 (m-10) REVERT: J 294 SER cc_start: 0.8190 (t) cc_final: 0.7851 (m) REVERT: J 323 ARG cc_start: 0.7356 (tpp80) cc_final: 0.6957 (mtt-85) REVERT: J 330 LEU cc_start: 0.5048 (mt) cc_final: 0.4576 (mp) REVERT: K 27 TYR cc_start: 0.6809 (m-80) cc_final: 0.6359 (m-10) REVERT: K 80 MET cc_start: 0.7827 (mmt) cc_final: 0.7577 (mmm) REVERT: K 108 GLU cc_start: 0.6984 (mp0) cc_final: 0.5824 (tm-30) REVERT: K 112 MET cc_start: 0.6257 (mtt) cc_final: 0.5736 (mtt) REVERT: K 116 ILE cc_start: 0.6757 (mm) cc_final: 0.6506 (mm) REVERT: K 124 ASN cc_start: 0.7329 (t0) cc_final: 0.6808 (t0) REVERT: K 323 ARG cc_start: 0.7466 (tpp80) cc_final: 0.6994 (mtt-85) REVERT: K 330 LEU cc_start: 0.5164 (mt) cc_final: 0.4546 (mp) REVERT: K 349 GLU cc_start: 0.6938 (tp30) cc_final: 0.6501 (tp30) REVERT: K 389 TYR cc_start: 0.7480 (t80) cc_final: 0.7178 (t80) REVERT: K 394 GLN cc_start: 0.7508 (mm-40) cc_final: 0.7155 (mm-40) REVERT: L 27 TYR cc_start: 0.7241 (m-80) cc_final: 0.6601 (m-80) REVERT: L 54 TYR cc_start: 0.5386 (t80) cc_final: 0.5079 (t80) REVERT: L 81 GLN cc_start: 0.7824 (mt0) cc_final: 0.7572 (tt0) REVERT: L 124 ASN cc_start: 0.7594 (t0) cc_final: 0.7233 (t0) REVERT: L 256 MET cc_start: 0.5575 (ppp) cc_final: 0.5052 (ttp) REVERT: L 262 GLU cc_start: 0.7375 (pt0) cc_final: 0.7142 (pt0) REVERT: L 323 ARG cc_start: 0.7484 (tpp80) cc_final: 0.6999 (mtt-85) REVERT: L 349 GLU cc_start: 0.7063 (tt0) cc_final: 0.6775 (tt0) REVERT: L 389 TYR cc_start: 0.7314 (t80) cc_final: 0.6837 (t80) REVERT: L 394 GLN cc_start: 0.7746 (mm-40) cc_final: 0.7327 (mm-40) outliers start: 2 outliers final: 0 residues processed: 838 average time/residue: 0.2079 time to fit residues: 289.8213 Evaluate side-chains 800 residues out of total 4032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 800 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 191 optimal weight: 3.9990 chunk 93 optimal weight: 20.0000 chunk 2 optimal weight: 5.9990 chunk 110 optimal weight: 20.0000 chunk 459 optimal weight: 2.9990 chunk 332 optimal weight: 0.0870 chunk 460 optimal weight: 0.6980 chunk 78 optimal weight: 10.0000 chunk 398 optimal weight: 2.9990 chunk 124 optimal weight: 9.9990 chunk 426 optimal weight: 0.9980 overall best weight: 1.5562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 ASN B 124 ASN B 136 GLN B 178 GLN C 124 ASN D 124 ASN D 178 GLN E 59 GLN E 124 ASN E 136 GLN E 178 GLN F 307 GLN F 412 GLN G 124 ASN G 178 GLN H 124 ASN H 136 GLN H 178 GLN I 136 GLN I 281 ASN J 32 GLN J 124 ASN K 136 GLN K 178 GLN L 178 GLN L 407 GLN L 412 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.177623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.145445 restraints weight = 51210.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.149822 restraints weight = 31557.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.152861 restraints weight = 21823.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.155002 restraints weight = 16559.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.156351 restraints weight = 13488.838| |-----------------------------------------------------------------------------| r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3876 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3876 r_free = 0.3876 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 76 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3877 r_free = 0.3877 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 77 | |-----------------------------------------------------------------------------| r_final: 0.3877 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6344 moved from start: 0.4085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 37788 Z= 0.140 Angle : 0.631 11.677 51132 Z= 0.314 Chirality : 0.043 0.202 5760 Planarity : 0.004 0.091 6660 Dihedral : 4.761 30.452 5208 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 0.12 % Allowed : 1.07 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.12), residues: 4632 helix: 0.56 (0.13), residues: 1848 sheet: -0.02 (0.21), residues: 504 loop : -2.27 (0.12), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG D 351 TYR 0.031 0.001 TYR D 27 PHE 0.022 0.001 PHE G 78 TRP 0.038 0.002 TRP E 83 HIS 0.003 0.001 HIS L 216 Details of bonding type rmsd covalent geometry : bond 0.00336 (37788) covalent geometry : angle 0.63109 (51132) hydrogen bonds : bond 0.03329 ( 1391) hydrogen bonds : angle 3.67140 ( 4641) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 875 residues out of total 4032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 870 time to evaluate : 1.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ARG cc_start: 0.7423 (ttp-110) cc_final: 0.6928 (ttp-110) REVERT: A 72 LYS cc_start: 0.7261 (mmtt) cc_final: 0.6939 (mmtt) REVERT: A 112 MET cc_start: 0.6334 (mtm) cc_final: 0.5851 (mtm) REVERT: A 161 TYR cc_start: 0.7547 (m-80) cc_final: 0.7235 (m-10) REVERT: A 291 MET cc_start: 0.7019 (ttp) cc_final: 0.6790 (ttm) REVERT: A 323 ARG cc_start: 0.7352 (tpp80) cc_final: 0.6967 (mtt-85) REVERT: B 27 TYR cc_start: 0.6906 (m-80) cc_final: 0.6462 (m-10) REVERT: B 72 LYS cc_start: 0.7582 (mmtt) cc_final: 0.6999 (mttm) REVERT: B 80 MET cc_start: 0.8018 (mmt) cc_final: 0.7657 (mmm) REVERT: B 108 GLU cc_start: 0.7008 (mp0) cc_final: 0.5521 (tm-30) REVERT: B 112 MET cc_start: 0.6262 (mtt) cc_final: 0.5485 (mtt) REVERT: B 294 SER cc_start: 0.7751 (t) cc_final: 0.7541 (m) REVERT: B 323 ARG cc_start: 0.7546 (tpp80) cc_final: 0.7077 (mtt-85) REVERT: B 330 LEU cc_start: 0.4875 (mt) cc_final: 0.4389 (mp) REVERT: B 349 GLU cc_start: 0.7013 (tp30) cc_final: 0.6427 (tp30) REVERT: B 394 GLN cc_start: 0.7491 (mm-40) cc_final: 0.7151 (mm-40) REVERT: C 27 TYR cc_start: 0.7456 (m-80) cc_final: 0.6737 (m-80) REVERT: C 54 TYR cc_start: 0.4996 (t80) cc_final: 0.4749 (t80) REVERT: C 256 MET cc_start: 0.5804 (ppp) cc_final: 0.5525 (ttp) REVERT: C 295 LYS cc_start: 0.8794 (ptmt) cc_final: 0.8519 (pttt) REVERT: C 307 GLN cc_start: 0.8106 (mp10) cc_final: 0.7877 (mp10) REVERT: C 323 ARG cc_start: 0.7431 (tpp80) cc_final: 0.6977 (mtt-85) REVERT: C 349 GLU cc_start: 0.7007 (tt0) cc_final: 0.6767 (tt0) REVERT: C 389 TYR cc_start: 0.7382 (t80) cc_final: 0.6973 (t80) REVERT: C 394 GLN cc_start: 0.7777 (mm-40) cc_final: 0.7313 (mm-40) REVERT: C 395 GLU cc_start: 0.6857 (mm-30) cc_final: 0.6493 (mm-30) REVERT: D 54 TYR cc_start: 0.5765 (t80) cc_final: 0.5457 (t80) REVERT: D 72 LYS cc_start: 0.7018 (mmtt) cc_final: 0.6754 (mmtt) REVERT: D 235 MET cc_start: 0.5197 (tpt) cc_final: 0.4693 (mmm) REVERT: D 323 ARG cc_start: 0.7380 (tpp80) cc_final: 0.6975 (mtt-85) REVERT: D 325 GLU cc_start: 0.8206 (pp20) cc_final: 0.7876 (pp20) REVERT: D 356 PHE cc_start: 0.6057 (m-80) cc_final: 0.5819 (m-80) REVERT: D 394 GLN cc_start: 0.7349 (mm-40) cc_final: 0.6591 (mm-40) REVERT: E 27 TYR cc_start: 0.6720 (m-80) cc_final: 0.6436 (m-10) REVERT: E 45 LYS cc_start: 0.6207 (ttmt) cc_final: 0.5973 (ttmm) REVERT: E 72 LYS cc_start: 0.7709 (mmtt) cc_final: 0.7151 (mttp) REVERT: E 80 MET cc_start: 0.8050 (mmt) cc_final: 0.7645 (mmm) REVERT: E 108 GLU cc_start: 0.6978 (mp0) cc_final: 0.5444 (tm-30) REVERT: E 323 ARG cc_start: 0.7602 (tpp80) cc_final: 0.7144 (mtt-85) REVERT: E 330 LEU cc_start: 0.4935 (mt) cc_final: 0.4396 (mp) REVERT: E 349 GLU cc_start: 0.6942 (tp30) cc_final: 0.6369 (tp30) REVERT: E 394 GLN cc_start: 0.7654 (mm-40) cc_final: 0.7174 (mm-40) REVERT: F 27 TYR cc_start: 0.7513 (m-80) cc_final: 0.6725 (m-80) REVERT: F 80 MET cc_start: 0.7777 (mmt) cc_final: 0.7522 (mmt) REVERT: F 124 ASN cc_start: 0.7517 (t0) cc_final: 0.6958 (t0) REVERT: F 262 GLU cc_start: 0.7330 (pt0) cc_final: 0.7055 (pt0) REVERT: F 294 SER cc_start: 0.8040 (t) cc_final: 0.7716 (m) REVERT: F 323 ARG cc_start: 0.7463 (tpp80) cc_final: 0.7024 (mtt-85) REVERT: F 349 GLU cc_start: 0.7062 (tt0) cc_final: 0.6831 (tt0) REVERT: F 394 GLN cc_start: 0.7709 (mm-40) cc_final: 0.7002 (mm-40) REVERT: F 395 GLU cc_start: 0.6696 (mm-30) cc_final: 0.6450 (mm-30) REVERT: G 64 ARG cc_start: 0.7384 (ttp-110) cc_final: 0.6894 (ttp-110) REVERT: G 72 LYS cc_start: 0.7087 (mmtt) cc_final: 0.6742 (mmtt) REVERT: G 112 MET cc_start: 0.6261 (mtm) cc_final: 0.5805 (mtm) REVERT: G 161 TYR cc_start: 0.7519 (m-80) cc_final: 0.7195 (m-10) REVERT: G 235 MET cc_start: 0.5374 (tpt) cc_final: 0.4984 (mmm) REVERT: G 256 MET cc_start: 0.6115 (ppp) cc_final: 0.5449 (ppp) REVERT: G 323 ARG cc_start: 0.7359 (tpp80) cc_final: 0.6949 (mtt-85) REVERT: G 325 GLU cc_start: 0.8175 (pp20) cc_final: 0.7975 (pp20) REVERT: G 394 GLN cc_start: 0.7364 (mm-40) cc_final: 0.6661 (mm-40) REVERT: H 27 TYR cc_start: 0.6908 (m-80) cc_final: 0.6483 (m-10) REVERT: H 67 ASN cc_start: 0.6921 (m-40) cc_final: 0.6704 (m-40) REVERT: H 80 MET cc_start: 0.7898 (mmt) cc_final: 0.7574 (mmm) REVERT: H 108 GLU cc_start: 0.6988 (mp0) cc_final: 0.5454 (tm-30) REVERT: H 116 ILE cc_start: 0.6683 (mm) cc_final: 0.6443 (mm) REVERT: H 323 ARG cc_start: 0.7488 (tpp80) cc_final: 0.7037 (mtt-85) REVERT: H 330 LEU cc_start: 0.4904 (mt) cc_final: 0.4396 (mp) REVERT: H 349 GLU cc_start: 0.7014 (tp30) cc_final: 0.6421 (tp30) REVERT: H 370 THR cc_start: 0.7990 (p) cc_final: 0.7760 (p) REVERT: H 389 TYR cc_start: 0.7245 (t80) cc_final: 0.6783 (t80) REVERT: H 394 GLN cc_start: 0.7512 (mm-40) cc_final: 0.7216 (mm-40) REVERT: H 395 GLU cc_start: 0.6743 (mm-30) cc_final: 0.6038 (mm-30) REVERT: I 27 TYR cc_start: 0.7205 (m-80) cc_final: 0.6450 (m-80) REVERT: I 112 MET cc_start: 0.5951 (mtt) cc_final: 0.5627 (mtt) REVERT: I 124 ASN cc_start: 0.7490 (t0) cc_final: 0.7026 (t0) REVERT: I 256 MET cc_start: 0.5632 (ppp) cc_final: 0.5062 (ppp) REVERT: I 262 GLU cc_start: 0.7463 (pt0) cc_final: 0.7234 (pt0) REVERT: I 323 ARG cc_start: 0.7522 (tpp80) cc_final: 0.7036 (mtt-85) REVERT: I 349 GLU cc_start: 0.6572 (tp30) cc_final: 0.6258 (tp30) REVERT: I 394 GLN cc_start: 0.7808 (mm-40) cc_final: 0.7139 (mm-40) REVERT: I 395 GLU cc_start: 0.6844 (mm-30) cc_final: 0.6311 (mm-30) REVERT: J 64 ARG cc_start: 0.7438 (ttp-110) cc_final: 0.7145 (ttp-110) REVERT: J 72 LYS cc_start: 0.7214 (mmtt) cc_final: 0.6910 (mmtt) REVERT: J 112 MET cc_start: 0.6402 (mtm) cc_final: 0.5899 (mtm) REVERT: J 161 TYR cc_start: 0.7602 (m-80) cc_final: 0.7270 (m-10) REVERT: J 294 SER cc_start: 0.8095 (t) cc_final: 0.7849 (m) REVERT: J 323 ARG cc_start: 0.7376 (tpp80) cc_final: 0.6971 (mtt-85) REVERT: J 330 LEU cc_start: 0.5139 (mt) cc_final: 0.4583 (mp) REVERT: K 27 TYR cc_start: 0.7080 (m-80) cc_final: 0.6731 (m-10) REVERT: K 80 MET cc_start: 0.7875 (mmt) cc_final: 0.7576 (mmm) REVERT: K 108 GLU cc_start: 0.7068 (mp0) cc_final: 0.5618 (tm-30) REVERT: K 112 MET cc_start: 0.6295 (mtt) cc_final: 0.5634 (mtt) REVERT: K 116 ILE cc_start: 0.6767 (mm) cc_final: 0.6511 (mm) REVERT: K 262 GLU cc_start: 0.7545 (pt0) cc_final: 0.7286 (pt0) REVERT: K 294 SER cc_start: 0.7706 (t) cc_final: 0.7391 (m) REVERT: K 323 ARG cc_start: 0.7506 (tpp80) cc_final: 0.7028 (mtt-85) REVERT: K 330 LEU cc_start: 0.5190 (mt) cc_final: 0.4622 (mp) REVERT: K 349 GLU cc_start: 0.6958 (tp30) cc_final: 0.6499 (tp30) REVERT: K 389 TYR cc_start: 0.7352 (t80) cc_final: 0.7062 (t80) REVERT: K 394 GLN cc_start: 0.7517 (mm-40) cc_final: 0.7176 (mm-40) REVERT: L 27 TYR cc_start: 0.7294 (m-80) cc_final: 0.6692 (m-80) REVERT: L 54 TYR cc_start: 0.5381 (t80) cc_final: 0.4983 (t80) REVERT: L 81 GLN cc_start: 0.7832 (mt0) cc_final: 0.7528 (tt0) REVERT: L 124 ASN cc_start: 0.7645 (t0) cc_final: 0.7269 (t0) REVERT: L 256 MET cc_start: 0.5684 (ppp) cc_final: 0.5279 (ttp) REVERT: L 323 ARG cc_start: 0.7500 (tpp80) cc_final: 0.7004 (mtt-85) REVERT: L 349 GLU cc_start: 0.7112 (tt0) cc_final: 0.6797 (tt0) REVERT: L 389 TYR cc_start: 0.7322 (t80) cc_final: 0.6928 (t80) outliers start: 5 outliers final: 1 residues processed: 871 average time/residue: 0.2038 time to fit residues: 296.1629 Evaluate side-chains 813 residues out of total 4032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 812 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 456 optimal weight: 0.9990 chunk 183 optimal weight: 4.9990 chunk 386 optimal weight: 0.9980 chunk 400 optimal weight: 0.8980 chunk 268 optimal weight: 9.9990 chunk 352 optimal weight: 5.9990 chunk 377 optimal weight: 5.9990 chunk 254 optimal weight: 0.8980 chunk 292 optimal weight: 0.5980 chunk 154 optimal weight: 0.6980 chunk 139 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN B 124 ASN B 178 GLN C 59 GLN C 124 ASN D 32 GLN D 178 GLN E 59 GLN E 124 ASN E 178 GLN G 178 GLN H 124 ASN H 178 GLN K 124 ASN K 136 GLN K 178 GLN L 178 GLN L 394 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.180195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.148061 restraints weight = 50792.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.152561 restraints weight = 31108.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.155612 restraints weight = 21381.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.157788 restraints weight = 16174.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.159320 restraints weight = 13126.543| |-----------------------------------------------------------------------------| r_work (final): 0.3913 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3913 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3913 r_free = 0.3913 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 77 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3913 r_free = 0.3913 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 75 | |-----------------------------------------------------------------------------| r_final: 0.3913 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6298 moved from start: 0.4263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 37788 Z= 0.114 Angle : 0.607 8.919 51132 Z= 0.301 Chirality : 0.042 0.207 5760 Planarity : 0.004 0.076 6660 Dihedral : 4.728 32.208 5208 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 0.10 % Allowed : 0.62 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.12), residues: 4632 helix: 0.75 (0.13), residues: 1836 sheet: -0.05 (0.21), residues: 504 loop : -2.19 (0.12), residues: 2292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 351 TYR 0.021 0.001 TYR D 27 PHE 0.022 0.001 PHE A 78 TRP 0.017 0.001 TRP D 83 HIS 0.003 0.001 HIS F 216 Details of bonding type rmsd covalent geometry : bond 0.00274 (37788) covalent geometry : angle 0.60694 (51132) hydrogen bonds : bond 0.03111 ( 1391) hydrogen bonds : angle 3.59162 ( 4641) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 849 residues out of total 4032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 845 time to evaluate : 1.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ARG cc_start: 0.7388 (ttp-110) cc_final: 0.6928 (ttp-110) REVERT: A 72 LYS cc_start: 0.7254 (mmtt) cc_final: 0.6906 (mmtt) REVERT: A 112 MET cc_start: 0.6308 (mtm) cc_final: 0.5851 (mtm) REVERT: A 291 MET cc_start: 0.7014 (ttp) cc_final: 0.6795 (ttm) REVERT: A 323 ARG cc_start: 0.7361 (tpp80) cc_final: 0.6957 (mtt-85) REVERT: A 330 LEU cc_start: 0.5358 (mt) cc_final: 0.4725 (mp) REVERT: B 27 TYR cc_start: 0.6816 (m-80) cc_final: 0.6290 (m-10) REVERT: B 80 MET cc_start: 0.8028 (mmt) cc_final: 0.7678 (mmm) REVERT: B 108 GLU cc_start: 0.6988 (mp0) cc_final: 0.5506 (tm-30) REVERT: B 323 ARG cc_start: 0.7530 (tpp80) cc_final: 0.7085 (mtt-85) REVERT: B 330 LEU cc_start: 0.4774 (mt) cc_final: 0.4318 (mp) REVERT: B 349 GLU cc_start: 0.6969 (tp30) cc_final: 0.6370 (tp30) REVERT: B 370 THR cc_start: 0.7810 (p) cc_final: 0.7434 (p) REVERT: B 389 TYR cc_start: 0.7588 (t80) cc_final: 0.7113 (t80) REVERT: B 394 GLN cc_start: 0.7462 (mm-40) cc_final: 0.7147 (mm-40) REVERT: C 27 TYR cc_start: 0.7357 (m-80) cc_final: 0.6539 (m-80) REVERT: C 295 LYS cc_start: 0.8771 (ptmt) cc_final: 0.8431 (pttt) REVERT: C 307 GLN cc_start: 0.8092 (mp10) cc_final: 0.7888 (mp10) REVERT: C 323 ARG cc_start: 0.7420 (tpp80) cc_final: 0.6970 (mtt-85) REVERT: C 349 GLU cc_start: 0.7039 (tt0) cc_final: 0.6761 (tt0) REVERT: C 389 TYR cc_start: 0.7264 (t80) cc_final: 0.6874 (t80) REVERT: D 54 TYR cc_start: 0.5750 (t80) cc_final: 0.5431 (t80) REVERT: D 72 LYS cc_start: 0.7022 (mmtt) cc_final: 0.6765 (mmtt) REVERT: D 235 MET cc_start: 0.5176 (tpt) cc_final: 0.4670 (mmm) REVERT: D 256 MET cc_start: 0.5932 (ppp) cc_final: 0.5202 (ppp) REVERT: D 289 MET cc_start: 0.7316 (ppp) cc_final: 0.6941 (ttp) REVERT: D 291 MET cc_start: 0.7059 (ttp) cc_final: 0.6842 (ttm) REVERT: D 323 ARG cc_start: 0.7334 (tpp80) cc_final: 0.6942 (mtt-85) REVERT: D 325 GLU cc_start: 0.8106 (pp20) cc_final: 0.7787 (pp20) REVERT: D 394 GLN cc_start: 0.7334 (mm-40) cc_final: 0.6600 (mm-40) REVERT: E 27 TYR cc_start: 0.6489 (m-80) cc_final: 0.6097 (m-10) REVERT: E 45 LYS cc_start: 0.6058 (ttmt) cc_final: 0.5792 (ttmm) REVERT: E 72 LYS cc_start: 0.7602 (mmtt) cc_final: 0.7100 (mttt) REVERT: E 80 MET cc_start: 0.7980 (mmt) cc_final: 0.7602 (mmm) REVERT: E 323 ARG cc_start: 0.7636 (tpp80) cc_final: 0.7166 (mtt-85) REVERT: E 330 LEU cc_start: 0.4829 (mt) cc_final: 0.4300 (mp) REVERT: E 349 GLU cc_start: 0.6884 (tp30) cc_final: 0.6243 (tp30) REVERT: E 394 GLN cc_start: 0.7712 (mm-40) cc_final: 0.7268 (mm-40) REVERT: F 27 TYR cc_start: 0.7319 (m-80) cc_final: 0.6474 (m-80) REVERT: F 80 MET cc_start: 0.7770 (mmt) cc_final: 0.7519 (mmt) REVERT: F 124 ASN cc_start: 0.7513 (t0) cc_final: 0.6976 (t0) REVERT: F 154 ASN cc_start: 0.7140 (m110) cc_final: 0.6927 (m110) REVERT: F 262 GLU cc_start: 0.7280 (pt0) cc_final: 0.6992 (pt0) REVERT: F 323 ARG cc_start: 0.7405 (tpp80) cc_final: 0.6892 (mtt-85) REVERT: F 349 GLU cc_start: 0.7026 (tt0) cc_final: 0.6769 (tt0) REVERT: F 389 TYR cc_start: 0.6675 (t80) cc_final: 0.6283 (t80) REVERT: F 394 GLN cc_start: 0.7680 (mm-40) cc_final: 0.7015 (mm-40) REVERT: F 395 GLU cc_start: 0.6723 (mm-30) cc_final: 0.6470 (mm-30) REVERT: G 27 TYR cc_start: 0.7312 (m-80) cc_final: 0.6820 (m-80) REVERT: G 64 ARG cc_start: 0.7329 (ttp-110) cc_final: 0.6855 (ttp-110) REVERT: G 72 LYS cc_start: 0.7082 (mmtt) cc_final: 0.6772 (mmtt) REVERT: G 112 MET cc_start: 0.6116 (mtm) cc_final: 0.5707 (mtm) REVERT: G 235 MET cc_start: 0.5334 (tpt) cc_final: 0.4962 (mmm) REVERT: G 256 MET cc_start: 0.5917 (ppp) cc_final: 0.5452 (ppp) REVERT: G 262 GLU cc_start: 0.7158 (pt0) cc_final: 0.6689 (pt0) REVERT: G 323 ARG cc_start: 0.7363 (tpp80) cc_final: 0.6931 (mtt-85) REVERT: G 394 GLN cc_start: 0.7322 (mm-40) cc_final: 0.6631 (mm-40) REVERT: H 27 TYR cc_start: 0.6844 (m-80) cc_final: 0.6272 (m-10) REVERT: H 80 MET cc_start: 0.7865 (mmt) cc_final: 0.7568 (mmm) REVERT: H 108 GLU cc_start: 0.6960 (mp0) cc_final: 0.5485 (tm-30) REVERT: H 116 ILE cc_start: 0.6701 (mm) cc_final: 0.6446 (mm) REVERT: H 323 ARG cc_start: 0.7440 (tpp80) cc_final: 0.7054 (mtt-85) REVERT: H 330 LEU cc_start: 0.4775 (mt) cc_final: 0.4362 (mp) REVERT: H 349 GLU cc_start: 0.6924 (tp30) cc_final: 0.6359 (tp30) REVERT: H 370 THR cc_start: 0.8003 (p) cc_final: 0.7763 (p) REVERT: H 389 TYR cc_start: 0.7206 (t80) cc_final: 0.6743 (t80) REVERT: I 27 TYR cc_start: 0.7416 (m-80) cc_final: 0.6776 (m-80) REVERT: I 81 GLN cc_start: 0.7855 (mt0) cc_final: 0.7574 (tt0) REVERT: I 112 MET cc_start: 0.5828 (mtt) cc_final: 0.5527 (mtt) REVERT: I 124 ASN cc_start: 0.7480 (t0) cc_final: 0.6967 (t0) REVERT: I 323 ARG cc_start: 0.7513 (tpp80) cc_final: 0.7003 (mtt-85) REVERT: I 349 GLU cc_start: 0.6582 (tp30) cc_final: 0.6212 (tp30) REVERT: I 394 GLN cc_start: 0.7812 (mm-40) cc_final: 0.7140 (mm-40) REVERT: I 395 GLU cc_start: 0.6856 (mm-30) cc_final: 0.6315 (mm-30) REVERT: J 64 ARG cc_start: 0.7393 (ttp-110) cc_final: 0.6929 (ttp-110) REVERT: J 72 LYS cc_start: 0.7222 (mmtt) cc_final: 0.6926 (mmtt) REVERT: J 112 MET cc_start: 0.6352 (mtm) cc_final: 0.5896 (mtm) REVERT: J 235 MET cc_start: 0.5327 (tpt) cc_final: 0.5040 (mmm) REVERT: J 294 SER cc_start: 0.8109 (t) cc_final: 0.7856 (m) REVERT: J 323 ARG cc_start: 0.7330 (tpp80) cc_final: 0.6959 (mtt-85) REVERT: K 27 TYR cc_start: 0.7048 (m-80) cc_final: 0.6692 (m-10) REVERT: K 80 MET cc_start: 0.7866 (mmt) cc_final: 0.7547 (mmm) REVERT: K 108 GLU cc_start: 0.6980 (mp0) cc_final: 0.5520 (tm-30) REVERT: K 112 MET cc_start: 0.6249 (mtt) cc_final: 0.5626 (mtt) REVERT: K 116 ILE cc_start: 0.6765 (mm) cc_final: 0.6507 (mm) REVERT: K 262 GLU cc_start: 0.7502 (pt0) cc_final: 0.7252 (pt0) REVERT: K 323 ARG cc_start: 0.7554 (tpp80) cc_final: 0.7214 (mtt-85) REVERT: K 330 LEU cc_start: 0.5205 (mt) cc_final: 0.4555 (mp) REVERT: K 349 GLU cc_start: 0.6944 (tp30) cc_final: 0.6470 (tp30) REVERT: K 389 TYR cc_start: 0.7494 (t80) cc_final: 0.7206 (t80) REVERT: K 394 GLN cc_start: 0.7451 (mm-40) cc_final: 0.7115 (mm-40) REVERT: L 27 TYR cc_start: 0.7468 (m-80) cc_final: 0.6908 (m-80) REVERT: L 54 TYR cc_start: 0.5306 (t80) cc_final: 0.5023 (t80) REVERT: L 81 GLN cc_start: 0.7759 (mt0) cc_final: 0.7546 (tt0) REVERT: L 124 ASN cc_start: 0.7603 (t0) cc_final: 0.7270 (t0) REVERT: L 256 MET cc_start: 0.5584 (ppp) cc_final: 0.5104 (ttp) REVERT: L 323 ARG cc_start: 0.7471 (tpp80) cc_final: 0.6986 (mtt-85) REVERT: L 349 GLU cc_start: 0.7033 (tt0) cc_final: 0.6737 (tt0) REVERT: L 389 TYR cc_start: 0.7233 (t80) cc_final: 0.6857 (t80) REVERT: L 394 GLN cc_start: 0.7679 (mm110) cc_final: 0.7477 (mm110) outliers start: 4 outliers final: 0 residues processed: 845 average time/residue: 0.2021 time to fit residues: 286.1991 Evaluate side-chains 796 residues out of total 4032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 796 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 153 optimal weight: 0.8980 chunk 368 optimal weight: 0.6980 chunk 356 optimal weight: 4.9990 chunk 407 optimal weight: 0.2980 chunk 415 optimal weight: 3.9990 chunk 448 optimal weight: 9.9990 chunk 398 optimal weight: 0.8980 chunk 116 optimal weight: 0.0570 chunk 420 optimal weight: 0.0980 chunk 296 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 ASN B 124 ASN B 178 GLN C 59 GLN C 124 ASN C 178 GLN C 394 GLN D 124 ASN D 178 GLN E 124 ASN E 178 GLN F 81 GLN G 124 ASN G 178 GLN H 124 ASN H 178 GLN I 178 GLN I 412 GLN J 32 GLN J 124 ASN K 124 ASN K 178 GLN L 178 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.181934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.150942 restraints weight = 51084.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.155108 restraints weight = 31732.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.158022 restraints weight = 22098.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.159816 restraints weight = 16842.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.161318 restraints weight = 14041.407| |-----------------------------------------------------------------------------| r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3935 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3935 r_free = 0.3935 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 75 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3935 r_free = 0.3935 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 76 | |-----------------------------------------------------------------------------| r_final: 0.3935 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6263 moved from start: 0.4465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 37788 Z= 0.105 Angle : 0.589 10.329 51132 Z= 0.292 Chirality : 0.041 0.206 5760 Planarity : 0.004 0.062 6660 Dihedral : 4.627 29.222 5208 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 0.12 % Allowed : 0.64 % Favored : 99.23 % 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: -0.88 (0.12), residues: 4632 helix: 0.88 (0.13), residues: 1836 sheet: -0.13 (0.20), residues: 564 loop : -2.05 (0.12), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 266 TYR 0.022 0.001 TYR I 54 PHE 0.022 0.001 PHE A 78 TRP 0.012 0.001 TRP E 83 HIS 0.003 0.001 HIS L 216 Details of bonding type rmsd covalent geometry : bond 0.00252 (37788) covalent geometry : angle 0.58933 (51132) hydrogen bonds : bond 0.02986 ( 1391) hydrogen bonds : angle 3.53680 ( 4641) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7224.79 seconds wall clock time: 124 minutes 37.70 seconds (7477.70 seconds total)