Starting phenix.real_space_refine on Fri Aug 7 19:35:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9skk_54967/08_2026/9skk_54967.cif Found real_map, /net/cci-nas-00/data/ceres_data/9skk_54967/08_2026/9skk_54967.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9skk_54967/08_2026/9skk_54967.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9skk_54967/08_2026/9skk_54967.map" model { file = "/net/cci-nas-00/data/ceres_data/9skk_54967/08_2026/9skk_54967.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9skk_54967/08_2026/9skk_54967.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.001 sd= 0.011 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 50 5.16 5 C 14683 2.51 5 N 3800 2.21 5 O 4371 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22904 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2468 Classifications: {'peptide': 313} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 301} Chain breaks: 1 Chain: "B" Number of atoms: 2599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2599 Classifications: {'peptide': 330} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 316} Chain: "C" Number of atoms: 2599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2599 Classifications: {'peptide': 330} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 316} Chain: "D" Number of atoms: 2599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2599 Classifications: {'peptide': 330} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 316} Chain: "E" Number of atoms: 2599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2599 Classifications: {'peptide': 330} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 316} Chain: "F" Number of atoms: 2599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2599 Classifications: {'peptide': 330} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 316} Chain: "G" Number of atoms: 2599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2599 Classifications: {'peptide': 330} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 316} Chain: "H" Number of atoms: 2599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2599 Classifications: {'peptide': 330} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 316} Chain: "I" Number of atoms: 2243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2243 Classifications: {'peptide': 280} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 266} Time building chain proxies: 5.07, per 1000 atoms: 0.22 Number of scatterers: 22904 At special positions: 0 Unit cell: (139.932, 144.072, 182.16, 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 50 16.00 O 4371 8.00 N 3800 7.00 C 14683 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.81 Conformation dependent library (CDL) restraints added in 786.1 milliseconds 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5584 Finding SS restraints... Secondary structure from input PDB file: 122 helices and 9 sheets defined 67.2% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 27 through 61 removed outlier: 6.698A pdb=" N MET A 44 " --> pdb=" O LYS A 40 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ALA A 45 " --> pdb=" O LYS A 41 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL A 46 " --> pdb=" O THR A 42 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA A 49 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE A 50 " --> pdb=" O VAL A 46 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 55 " --> pdb=" O ALA A 51 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER A 58 " --> pdb=" O GLY A 54 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N PHE A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE A 60 " --> pdb=" O LEU A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 84 Processing helix chain 'A' and resid 86 through 92 removed outlier: 3.853A pdb=" N LEU A 92 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 112 Processing helix chain 'A' and resid 114 through 123 Processing helix chain 'A' and resid 126 through 135 removed outlier: 3.858A pdb=" N GLN A 130 " --> pdb=" O TYR A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 150 removed outlier: 3.711A pdb=" N HIS A 142 " --> pdb=" O GLU A 138 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLU A 150 " --> pdb=" O VAL A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 161 removed outlier: 3.729A pdb=" N LYS A 161 " --> pdb=" O ASP A 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 157 through 161' Processing helix chain 'A' and resid 180 through 251 removed outlier: 3.569A pdb=" N LYS A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 287 Processing helix chain 'A' and resid 288 through 289 No H-bonds generated for 'chain 'A' and resid 288 through 289' Processing helix chain 'A' and resid 290 through 294 Processing helix chain 'A' and resid 295 through 310 Processing helix chain 'A' and resid 344 through 356 removed outlier: 3.645A pdb=" N VAL A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLY A 356 " --> pdb=" O VAL A 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 39 removed outlier: 3.729A pdb=" N LEU B 32 " --> pdb=" O ASP B 28 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE B 33 " --> pdb=" O LEU B 29 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER B 34 " --> pdb=" O LEU B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 61 removed outlier: 3.548A pdb=" N PHE B 50 " --> pdb=" O VAL B 46 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU B 55 " --> pdb=" O ALA B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 78 Processing helix chain 'B' and resid 79 through 85 removed outlier: 3.639A pdb=" N SER B 85 " --> pdb=" O GLU B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 91 Processing helix chain 'B' and resid 99 through 112 Processing helix chain 'B' and resid 113 through 124 Processing helix chain 'B' and resid 124 through 135 Processing helix chain 'B' and resid 137 through 150 removed outlier: 3.902A pdb=" N HIS B 142 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ARG B 143 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLU B 150 " --> pdb=" O VAL B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 251 removed outlier: 3.544A pdb=" N ALA B 184 " --> pdb=" O THR B 180 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLN B 185 " --> pdb=" O SER B 181 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN B 206 " --> pdb=" O GLU B 202 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL B 207 " --> pdb=" O SER B 203 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN B 216 " --> pdb=" O GLU B 212 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS B 219 " --> pdb=" O THR B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 287 Processing helix chain 'B' and resid 290 through 295 removed outlier: 4.306A pdb=" N LEU B 294 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN B 295 " --> pdb=" O VAL B 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 290 through 295' Processing helix chain 'B' and resid 295 through 311 Processing helix chain 'B' and resid 337 through 349 removed outlier: 3.722A pdb=" N ILE B 343 " --> pdb=" O ALA B 339 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER B 345 " --> pdb=" O ILE B 341 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ALA B 346 " --> pdb=" O VAL B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 356 removed outlier: 3.869A pdb=" N GLY B 355 " --> pdb=" O MET B 351 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLY B 356 " --> pdb=" O VAL B 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 351 through 356' Processing helix chain 'C' and resid 28 through 39 removed outlier: 4.050A pdb=" N SER C 34 " --> pdb=" O LEU C 30 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL C 35 " --> pdb=" O ASN C 31 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU C 36 " --> pdb=" O LEU C 32 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TRP C 37 " --> pdb=" O ILE C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 61 removed outlier: 4.369A pdb=" N VAL C 46 " --> pdb=" O THR C 42 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N VAL C 47 " --> pdb=" O VAL C 43 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU C 55 " --> pdb=" O ALA C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 78 Processing helix chain 'C' and resid 79 through 85 Processing helix chain 'C' and resid 86 through 91 Processing helix chain 'C' and resid 99 through 112 Processing helix chain 'C' and resid 113 through 124 Processing helix chain 'C' and resid 124 through 135 Processing helix chain 'C' and resid 140 through 150 removed outlier: 3.940A pdb=" N GLU C 150 " --> pdb=" O VAL C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 251 removed outlier: 3.573A pdb=" N VAL C 207 " --> pdb=" O SER C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 287 removed outlier: 3.723A pdb=" N ARG C 280 " --> pdb=" O ASP C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 311 Processing helix chain 'C' and resid 337 through 356 removed outlier: 3.525A pdb=" N ILE C 341 " --> pdb=" O GLY C 337 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL C 342 " --> pdb=" O LYS C 338 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N MET C 351 " --> pdb=" O LEU C 347 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL C 352 " --> pdb=" O ILE C 348 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA C 353 " --> pdb=" O GLY C 349 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY C 355 " --> pdb=" O MET C 351 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLY C 356 " --> pdb=" O VAL C 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 40 removed outlier: 3.908A pdb=" N LEU D 32 " --> pdb=" O ASP D 28 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE D 33 " --> pdb=" O LEU D 29 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER D 34 " --> pdb=" O LEU D 30 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL D 35 " --> pdb=" O ASN D 31 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU D 36 " --> pdb=" O LEU D 32 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N TRP D 37 " --> pdb=" O ILE D 33 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LYS D 40 " --> pdb=" O LEU D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 61 removed outlier: 3.747A pdb=" N VAL D 46 " --> pdb=" O THR D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 85 removed outlier: 3.747A pdb=" N SER D 85 " --> pdb=" O GLU D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 91 Processing helix chain 'D' and resid 99 through 112 Processing helix chain 'D' and resid 113 through 124 removed outlier: 3.519A pdb=" N ARG D 122 " --> pdb=" O GLU D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 134 Processing helix chain 'D' and resid 137 through 151 removed outlier: 4.306A pdb=" N HIS D 142 " --> pdb=" O GLU D 138 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ARG D 143 " --> pdb=" O LEU D 139 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYS D 151 " --> pdb=" O ALA D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 251 removed outlier: 3.605A pdb=" N GLN D 185 " --> pdb=" O SER D 181 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL D 207 " --> pdb=" O SER D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 287 Processing helix chain 'D' and resid 295 through 310 removed outlier: 3.538A pdb=" N LYS D 310 " --> pdb=" O GLU D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 352 removed outlier: 3.679A pdb=" N VAL D 342 " --> pdb=" O LYS D 338 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE D 343 " --> pdb=" O ALA D 339 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU D 344 " --> pdb=" O ILE D 340 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY D 349 " --> pdb=" O SER D 345 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY D 350 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N MET D 351 " --> pdb=" O LEU D 347 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL D 352 " --> pdb=" O ILE D 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 39 removed outlier: 3.779A pdb=" N LEU E 32 " --> pdb=" O ASP E 28 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE E 33 " --> pdb=" O LEU E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 59 removed outlier: 3.529A pdb=" N VAL E 43 " --> pdb=" O ALA E 39 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N MET E 44 " --> pdb=" O LYS E 40 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL E 46 " --> pdb=" O THR E 42 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA E 49 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU E 55 " --> pdb=" O ALA E 51 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU E 56 " --> pdb=" O CYS E 52 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE E 57 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER E 58 " --> pdb=" O GLY E 54 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE E 59 " --> pdb=" O LEU E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 92 removed outlier: 4.628A pdb=" N LYS E 88 " --> pdb=" O LYS E 84 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N LEU E 89 " --> pdb=" O SER E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 112 Processing helix chain 'E' and resid 113 through 124 Processing helix chain 'E' and resid 124 through 134 removed outlier: 3.562A pdb=" N GLN E 130 " --> pdb=" O TYR E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 150 removed outlier: 4.303A pdb=" N GLU E 150 " --> pdb=" O VAL E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 164 removed outlier: 3.617A pdb=" N LYS E 163 " --> pdb=" O SER E 160 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASP E 164 " --> pdb=" O LYS E 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 160 through 164' Processing helix chain 'E' and resid 181 through 251 removed outlier: 3.562A pdb=" N VAL E 207 " --> pdb=" O SER E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 287 Processing helix chain 'E' and resid 290 through 294 removed outlier: 3.845A pdb=" N LEU E 294 " --> pdb=" O VAL E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 311 removed outlier: 3.526A pdb=" N ARG E 299 " --> pdb=" O ASN E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 349 removed outlier: 3.588A pdb=" N ILE E 343 " --> pdb=" O ALA E 339 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU E 344 " --> pdb=" O ILE E 340 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA E 346 " --> pdb=" O VAL E 342 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY E 349 " --> pdb=" O SER E 345 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 355 removed outlier: 4.149A pdb=" N ALA E 353 " --> pdb=" O GLY E 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 39 removed outlier: 3.555A pdb=" N SER F 34 " --> pdb=" O LEU F 30 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU F 36 " --> pdb=" O LEU F 32 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TRP F 37 " --> pdb=" O ILE F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 61 removed outlier: 3.739A pdb=" N PHE F 50 " --> pdb=" O VAL F 46 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU F 55 " --> pdb=" O ALA F 51 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU F 56 " --> pdb=" O CYS F 52 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER F 58 " --> pdb=" O GLY F 54 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE F 59 " --> pdb=" O LEU F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 92 removed outlier: 4.982A pdb=" N LYS F 88 " --> pdb=" O LYS F 84 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N LEU F 89 " --> pdb=" O SER F 85 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU F 92 " --> pdb=" O LYS F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 112 Processing helix chain 'F' and resid 113 through 124 Processing helix chain 'F' and resid 124 through 134 removed outlier: 3.861A pdb=" N MET F 128 " --> pdb=" O SER F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 150 removed outlier: 4.066A pdb=" N HIS F 142 " --> pdb=" O GLU F 138 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ARG F 143 " --> pdb=" O LEU F 139 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLU F 150 " --> pdb=" O VAL F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 162 removed outlier: 4.241A pdb=" N LYS F 161 " --> pdb=" O ASP F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 249 removed outlier: 3.507A pdb=" N GLY F 190 " --> pdb=" O THR F 186 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE F 227 " --> pdb=" O ALA F 223 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA F 249 " --> pdb=" O ASP F 245 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 259 removed outlier: 3.614A pdb=" N SER F 258 " --> pdb=" O PRO F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 287 Processing helix chain 'F' and resid 295 through 311 Processing helix chain 'F' and resid 337 through 356 removed outlier: 3.505A pdb=" N ILE F 341 " --> pdb=" O GLY F 337 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL F 342 " --> pdb=" O LYS F 338 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA F 346 " --> pdb=" O VAL F 342 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU F 347 " --> pdb=" O ILE F 343 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N MET F 351 " --> pdb=" O LEU F 347 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N VAL F 352 " --> pdb=" O ILE F 348 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLY F 356 " --> pdb=" O VAL F 352 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 40 removed outlier: 3.581A pdb=" N ILE G 33 " --> pdb=" O LEU G 29 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N SER G 34 " --> pdb=" O LEU G 30 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL G 35 " --> pdb=" O ASN G 31 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TRP G 37 " --> pdb=" O ILE G 33 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA G 39 " --> pdb=" O VAL G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 53 removed outlier: 3.535A pdb=" N VAL G 46 " --> pdb=" O THR G 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 61 removed outlier: 3.885A pdb=" N ILE G 57 " --> pdb=" O ALA G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 85 Processing helix chain 'G' and resid 86 through 91 Processing helix chain 'G' and resid 99 through 112 removed outlier: 3.528A pdb=" N GLN G 112 " --> pdb=" O ILE G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 124 Processing helix chain 'G' and resid 124 through 134 Processing helix chain 'G' and resid 140 through 150 removed outlier: 3.726A pdb=" N GLU G 150 " --> pdb=" O VAL G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 249 removed outlier: 3.642A pdb=" N GLN G 185 " --> pdb=" O SER G 181 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU G 204 " --> pdb=" O VAL G 200 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS G 219 " --> pdb=" O THR G 215 " (cutoff:3.500A) Processing helix chain 'G' and resid 255 through 259 removed outlier: 4.235A pdb=" N SER G 258 " --> pdb=" O PRO G 255 " (cutoff:3.500A) Processing helix chain 'G' and resid 274 through 287 removed outlier: 3.628A pdb=" N ARG G 280 " --> pdb=" O ASP G 276 " (cutoff:3.500A) Processing helix chain 'G' and resid 295 through 311 removed outlier: 3.609A pdb=" N LYS G 310 " --> pdb=" O GLU G 306 " (cutoff:3.500A) Processing helix chain 'G' and resid 341 through 356 removed outlier: 3.590A pdb=" N LEU G 347 " --> pdb=" O ILE G 343 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ILE G 348 " --> pdb=" O LEU G 344 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY G 349 " --> pdb=" O SER G 345 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLY G 350 " --> pdb=" O ALA G 346 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N MET G 351 " --> pdb=" O LEU G 347 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL G 352 " --> pdb=" O ILE G 348 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA G 353 " --> pdb=" O GLY G 349 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLY G 356 " --> pdb=" O VAL G 352 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 44 removed outlier: 3.565A pdb=" N ARG H 38 " --> pdb=" O SER H 34 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N MET H 44 " --> pdb=" O LYS H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 61 removed outlier: 4.159A pdb=" N PHE H 50 " --> pdb=" O VAL H 46 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA H 53 " --> pdb=" O ALA H 49 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY H 54 " --> pdb=" O PHE H 50 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU H 55 " --> pdb=" O ALA H 51 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU H 56 " --> pdb=" O CYS H 52 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 85 Processing helix chain 'H' and resid 86 through 91 Processing helix chain 'H' and resid 99 through 112 Processing helix chain 'H' and resid 113 through 124 Processing helix chain 'H' and resid 124 through 134 removed outlier: 4.088A pdb=" N MET H 128 " --> pdb=" O SER H 124 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASP H 129 " --> pdb=" O PRO H 125 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLN H 130 " --> pdb=" O TYR H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 150 removed outlier: 3.723A pdb=" N GLU H 150 " --> pdb=" O VAL H 146 " (cutoff:3.500A) Processing helix chain 'H' and resid 157 through 162 removed outlier: 4.226A pdb=" N LYS H 161 " --> pdb=" O ASP H 157 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LYS H 162 " --> pdb=" O ASN H 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 157 through 162' Processing helix chain 'H' and resid 180 through 249 removed outlier: 4.114A pdb=" N ALA H 184 " --> pdb=" O THR H 180 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN H 185 " --> pdb=" O SER H 181 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU H 204 " --> pdb=" O VAL H 200 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS H 219 " --> pdb=" O THR H 215 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA H 249 " --> pdb=" O ASP H 245 " (cutoff:3.500A) Processing helix chain 'H' and resid 256 through 260 removed outlier: 3.781A pdb=" N GLY H 260 " --> pdb=" O TYR H 257 " (cutoff:3.500A) Processing helix chain 'H' and resid 274 through 287 removed outlier: 3.796A pdb=" N ARG H 280 " --> pdb=" O ASP H 276 " (cutoff:3.500A) Processing helix chain 'H' and resid 290 through 294 Processing helix chain 'H' and resid 295 through 311 removed outlier: 3.592A pdb=" N LYS H 310 " --> pdb=" O GLU H 306 " (cutoff:3.500A) Processing helix chain 'H' and resid 340 through 356 removed outlier: 3.694A pdb=" N ALA H 353 " --> pdb=" O GLY H 349 " (cutoff:3.500A) Processing helix chain 'I' and resid 75 through 78 Processing helix chain 'I' and resid 79 through 92 removed outlier: 3.683A pdb=" N LYS I 84 " --> pdb=" O GLN I 80 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N SER I 85 " --> pdb=" O GLU I 81 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LYS I 88 " --> pdb=" O LYS I 84 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N LEU I 89 " --> pdb=" O SER I 85 " (cutoff:3.500A) Processing helix chain 'I' and resid 99 through 112 removed outlier: 3.510A pdb=" N ALA I 103 " --> pdb=" O ASP I 99 " (cutoff:3.500A) Processing helix chain 'I' and resid 113 through 122 removed outlier: 3.829A pdb=" N GLU I 118 " --> pdb=" O VAL I 114 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLU I 119 " --> pdb=" O SER I 115 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR I 120 " --> pdb=" O LEU I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 124 through 134 removed outlier: 4.223A pdb=" N MET I 128 " --> pdb=" O SER I 124 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLN I 130 " --> pdb=" O TYR I 126 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N LEU I 131 " --> pdb=" O VAL I 127 " (cutoff:3.500A) Processing helix chain 'I' and resid 138 through 140 No H-bonds generated for 'chain 'I' and resid 138 through 140' Processing helix chain 'I' and resid 141 through 150 removed outlier: 3.530A pdb=" N GLU I 150 " --> pdb=" O VAL I 146 " (cutoff:3.500A) Processing helix chain 'I' and resid 156 through 161 removed outlier: 3.584A pdb=" N LYS I 161 " --> pdb=" O ASP I 157 " (cutoff:3.500A) Processing helix chain 'I' and resid 180 through 250 removed outlier: 3.539A pdb=" N ILE I 192 " --> pdb=" O LEU I 188 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP I 193 " --> pdb=" O SER I 189 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA I 249 " --> pdb=" O ASP I 245 " (cutoff:3.500A) Processing helix chain 'I' and resid 273 through 288 removed outlier: 3.561A pdb=" N GLU I 283 " --> pdb=" O GLU I 279 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE I 284 " --> pdb=" O ARG I 280 " (cutoff:3.500A) Processing helix chain 'I' and resid 291 through 294 Processing helix chain 'I' and resid 295 through 310 removed outlier: 3.655A pdb=" N ARG I 299 " --> pdb=" O ASN I 295 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 153 through 156 removed outlier: 3.504A pdb=" N SER A 175 " --> pdb=" O LYS A 153 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL A 155 " --> pdb=" O THR A 173 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER A 67 " --> pdb=" O PHE A 176 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 152 through 156 removed outlier: 7.236A pdb=" N THR B 66 " --> pdb=" O SER B 328 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N SER B 328 " --> pdb=" O THR B 66 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ALA B 68 " --> pdb=" O SER B 326 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N SER B 326 " --> pdb=" O ALA B 68 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N VAL B 70 " --> pdb=" O GLN B 324 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 153 through 156 removed outlier: 6.020A pdb=" N VAL C 70 " --> pdb=" O GLN C 324 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 153 through 156 removed outlier: 6.046A pdb=" N VAL D 70 " --> pdb=" O GLN D 324 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 152 through 156 removed outlier: 7.247A pdb=" N THR E 66 " --> pdb=" O SER E 328 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N SER E 328 " --> pdb=" O THR E 66 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ALA E 68 " --> pdb=" O SER E 326 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N SER E 326 " --> pdb=" O ALA E 68 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N VAL E 70 " --> pdb=" O GLN E 324 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 153 through 156 removed outlier: 5.804A pdb=" N VAL F 70 " --> pdb=" O GLN F 324 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 65 through 71 Processing sheet with id=AA8, first strand: chain 'H' and resid 65 through 71 Processing sheet with id=AA9, first strand: chain 'I' and resid 153 through 155 removed outlier: 6.772A pdb=" N ALA I 68 " --> pdb=" O PRO I 327 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N THR I 72 " --> pdb=" O TYR I 323 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N TYR I 323 " --> pdb=" O THR I 72 " (cutoff:3.500A) 1409 hydrogen bonds defined for protein. 4086 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: 3.73 Time building geometry restraints manager: 2.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 7400 1.35 - 1.46: 4799 1.46 - 1.58: 11000 1.58 - 1.70: 0 1.70 - 1.82: 84 Bond restraints: 23283 Sorted by residual: bond pdb=" N ASP H 137 " pdb=" CA ASP H 137 " ideal model delta sigma weight residual 1.452 1.490 -0.038 1.22e-02 6.72e+03 9.65e+00 bond pdb=" N ILE G 96 " pdb=" CA ILE G 96 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.18e-02 7.18e+03 9.33e+00 bond pdb=" N VAL H 331 " pdb=" CA VAL H 331 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.97e+00 bond pdb=" N LYS H 332 " pdb=" CA LYS H 332 " ideal model delta sigma weight residual 1.452 1.486 -0.034 1.25e-02 6.40e+03 7.35e+00 bond pdb=" N ASP C 164 " pdb=" CA ASP C 164 " ideal model delta sigma weight residual 1.457 1.492 -0.034 1.29e-02 6.01e+03 7.12e+00 ... (remaining 23278 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 31035 2.02 - 4.05: 394 4.05 - 6.07: 48 6.07 - 8.10: 15 8.10 - 10.12: 9 Bond angle restraints: 31501 Sorted by residual: angle pdb=" CB LYS H 97 " pdb=" CG LYS H 97 " pdb=" CD LYS H 97 " ideal model delta sigma weight residual 111.30 119.74 -8.44 2.30e+00 1.89e-01 1.35e+01 angle pdb=" C LEU H 139 " pdb=" N ASP H 140 " pdb=" CA ASP H 140 " ideal model delta sigma weight residual 122.29 116.59 5.70 1.56e+00 4.11e-01 1.34e+01 angle pdb=" N ILE E 60 " pdb=" CA ILE E 60 " pdb=" C ILE E 60 " ideal model delta sigma weight residual 113.42 109.19 4.23 1.17e+00 7.31e-01 1.31e+01 angle pdb=" CB LYS D 264 " pdb=" CG LYS D 264 " pdb=" CD LYS D 264 " ideal model delta sigma weight residual 111.30 119.50 -8.20 2.30e+00 1.89e-01 1.27e+01 angle pdb=" N VAL D 331 " pdb=" CA VAL D 331 " pdb=" C VAL D 331 " ideal model delta sigma weight residual 113.22 108.86 4.36 1.23e+00 6.61e-01 1.25e+01 ... (remaining 31496 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 12308 17.74 - 35.49: 1587 35.49 - 53.23: 368 53.23 - 70.97: 100 70.97 - 88.72: 36 Dihedral angle restraints: 14399 sinusoidal: 5842 harmonic: 8557 Sorted by residual: dihedral pdb=" CA VAL D 263 " pdb=" C VAL D 263 " pdb=" N LYS D 264 " pdb=" CA LYS D 264 " ideal model delta harmonic sigma weight residual 180.00 162.14 17.86 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA TYR H 323 " pdb=" C TYR H 323 " pdb=" N GLN H 324 " pdb=" CA GLN H 324 " ideal model delta harmonic sigma weight residual 180.00 162.42 17.58 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA ASP I 266 " pdb=" CB ASP I 266 " pdb=" CG ASP I 266 " pdb=" OD1 ASP I 266 " ideal model delta sinusoidal sigma weight residual -30.00 -89.18 59.18 1 2.00e+01 2.50e-03 1.17e+01 ... (remaining 14396 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 3014 0.046 - 0.092: 586 0.092 - 0.138: 93 0.138 - 0.184: 8 0.184 - 0.230: 2 Chirality restraints: 3703 Sorted by residual: chirality pdb=" CA ILE G 96 " pdb=" N ILE G 96 " pdb=" C ILE G 96 " pdb=" CB ILE G 96 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CA ILE G 98 " pdb=" N ILE G 98 " pdb=" C ILE G 98 " pdb=" CB ILE G 98 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA LYS C 163 " pdb=" N LYS C 163 " pdb=" C LYS C 163 " pdb=" CB LYS C 163 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.17 2.00e-01 2.50e+01 7.65e-01 ... (remaining 3700 not shown) Planarity restraints: 3986 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU D 102 " 0.011 2.00e-02 2.50e+03 2.24e-02 5.02e+00 pdb=" CD GLU D 102 " -0.039 2.00e-02 2.50e+03 pdb=" OE1 GLU D 102 " 0.014 2.00e-02 2.50e+03 pdb=" OE2 GLU D 102 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP C 95 " -0.011 2.00e-02 2.50e+03 2.22e-02 4.91e+00 pdb=" CG ASP C 95 " 0.038 2.00e-02 2.50e+03 pdb=" OD1 ASP C 95 " -0.014 2.00e-02 2.50e+03 pdb=" OD2 ASP C 95 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 95 " 0.009 2.00e-02 2.50e+03 1.81e-02 3.29e+00 pdb=" C ASP C 95 " -0.031 2.00e-02 2.50e+03 pdb=" O ASP C 95 " 0.012 2.00e-02 2.50e+03 pdb=" N ILE C 96 " 0.010 2.00e-02 2.50e+03 ... (remaining 3983 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 6435 2.82 - 3.34: 23626 3.34 - 3.86: 37438 3.86 - 4.38: 41777 4.38 - 4.90: 69805 Nonbonded interactions: 179081 Sorted by model distance: nonbonded pdb=" O ASP H 140 " pdb=" N ARG H 143 " model vdw 2.295 3.120 nonbonded pdb=" O ASP B 95 " pdb=" OD1 ASP B 95 " model vdw 2.398 3.040 nonbonded pdb=" O ASP H 140 " pdb=" C LEU H 141 " model vdw 2.450 3.270 nonbonded pdb=" O ASP C 164 " pdb=" C GLU C 165 " model vdw 2.460 3.270 nonbonded pdb=" O ASP C 93 " pdb=" OD1 ASP C 93 " model vdw 2.491 3.040 ... (remaining 179076 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 27 through 251 or resid 269 through 356)) selection = (chain 'C' and (resid 27 through 251 or resid 269 through 356)) selection = (chain 'D' and (resid 27 through 251 or resid 269 through 356)) selection = (chain 'E' and (resid 27 through 251 or resid 269 through 356)) selection = (chain 'F' and (resid 27 through 251 or resid 269 through 356)) selection = (chain 'G' and (resid 27 through 251 or resid 269 through 356)) selection = (chain 'H' and (resid 27 through 251 or resid 269 through 356)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 19.300 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 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 : 0.003 0.038 23283 Z= 0.137 Angle : 0.561 10.123 31501 Z= 0.297 Chirality : 0.036 0.230 3703 Planarity : 0.003 0.050 3986 Dihedral : 17.280 88.715 8815 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.75 % Allowed : 28.52 % Favored : 70.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.83 % 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: 0.74 (0.16), residues: 2883 helix: 1.18 (0.12), residues: 1760 sheet: 1.95 (0.38), residues: 213 loop : -1.22 (0.21), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 280 TYR 0.018 0.001 TYR A 194 PHE 0.015 0.001 PHE I 104 TRP 0.023 0.001 TRP H 37 HIS 0.001 0.000 HIS G 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.14 (23283) covalent geometry : angle 0.56147 / 0.30 (31501) hydrogen bonds : bond 0.22161 / 14.75 ( 1409) hydrogen bonds : angle 6.59124 / 4.72 ( 4086) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 0.632 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 142 HIS cc_start: 0.9281 (m90) cc_final: 0.8780 (t-170) REVERT: A 194 TYR cc_start: 0.8521 (t80) cc_final: 0.8284 (t80) REVERT: A 323 TYR cc_start: 0.8386 (OUTLIER) cc_final: 0.7616 (t80) REVERT: C 59 PHE cc_start: 0.8670 (m-10) cc_final: 0.8311 (m-10) REVERT: D 60 ILE cc_start: 0.9278 (tp) cc_final: 0.9022 (pt) REVERT: D 157 ASP cc_start: 0.9324 (t0) cc_final: 0.9042 (t0) REVERT: E 44 MET cc_start: 0.6576 (ptt) cc_final: 0.6276 (tmm) REVERT: F 44 MET cc_start: 0.8101 (ttm) cc_final: 0.7775 (tmm) REVERT: F 297 GLU cc_start: 0.8761 (tm-30) cc_final: 0.8499 (tm-30) REVERT: F 344 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7822 (tt) REVERT: G 93 ASP cc_start: 0.8908 (m-30) cc_final: 0.8567 (t0) REVERT: G 351 MET cc_start: 0.8370 (mmp) cc_final: 0.7391 (ttm) REVERT: H 93 ASP cc_start: 0.9124 (t0) cc_final: 0.8860 (t0) REVERT: H 102 GLU cc_start: 0.9590 (mm-30) cc_final: 0.9196 (mp0) REVERT: I 172 TRP cc_start: 0.8715 (t-100) cc_final: 0.8330 (t-100) REVERT: I 191 TYR cc_start: 0.8260 (t80) cc_final: 0.7837 (t80) REVERT: I 208 ARG cc_start: 0.9461 (ttp-110) cc_final: 0.9216 (ptt180) REVERT: I 222 LEU cc_start: 0.9373 (tp) cc_final: 0.9086 (mp) REVERT: I 226 ARG cc_start: 0.9421 (mtt90) cc_final: 0.8979 (mpt180) outliers start: 19 outliers final: 15 residues processed: 149 average time/residue: 0.1572 time to fit residues: 36.6493 Evaluate side-chains 143 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 323 TYR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 264 LYS Chi-restraints excluded: chain G residue 269 PHE Chi-restraints excluded: chain G residue 280 ARG Chi-restraints excluded: chain I residue 111 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 40.0000 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.0770 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 overall best weight: 2.1944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 112 GLN E 324 GLN F 307 GLN ** H 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 185 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.087761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.053990 restraints weight = 77079.309| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 3.77 r_work: 0.2803 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 23283 Z= 0.194 Angle : 0.563 9.220 31501 Z= 0.291 Chirality : 0.038 0.170 3703 Planarity : 0.004 0.057 3986 Dihedral : 4.578 57.067 3102 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.53 % Allowed : 26.09 % Favored : 70.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.83 % 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: 1.30 (0.16), residues: 2883 helix: 1.73 (0.12), residues: 1831 sheet: 1.84 (0.37), residues: 218 loop : -1.42 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG I 299 TYR 0.016 0.002 TYR H 120 PHE 0.023 0.001 PHE I 104 TRP 0.015 0.001 TRP H 37 HIS 0.003 0.001 HIS G 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.19 (23283) covalent geometry : angle 0.56267 / 0.29 (31501) hydrogen bonds : bond 0.05176 / 3.48 ( 1409) hydrogen bonds : angle 4.26290 / 3.01 ( 4086) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 136 time to evaluate : 0.927 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 37 TRP cc_start: 0.7343 (m100) cc_final: 0.6674 (m100) REVERT: A 142 HIS cc_start: 0.9257 (m90) cc_final: 0.8749 (t-170) REVERT: A 194 TYR cc_start: 0.8678 (t80) cc_final: 0.8465 (t80) REVERT: A 242 TYR cc_start: 0.9526 (t80) cc_final: 0.9294 (t80) REVERT: C 44 MET cc_start: 0.7819 (pmm) cc_final: 0.7117 (ppp) REVERT: C 59 PHE cc_start: 0.8677 (m-10) cc_final: 0.8450 (m-10) REVERT: C 163 LYS cc_start: 0.8769 (mmtm) cc_final: 0.8329 (pptt) REVERT: C 174 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.9023 (mt) REVERT: C 224 GLN cc_start: 0.9106 (OUTLIER) cc_final: 0.8890 (tt0) REVERT: C 323 TYR cc_start: 0.9056 (OUTLIER) cc_final: 0.8810 (m-10) REVERT: D 60 ILE cc_start: 0.9306 (tp) cc_final: 0.8954 (pt) REVERT: D 102 GLU cc_start: 0.8918 (tm-30) cc_final: 0.8624 (tm-30) REVERT: D 157 ASP cc_start: 0.9360 (t0) cc_final: 0.9122 (t0) REVERT: E 44 MET cc_start: 0.6690 (ptt) cc_final: 0.6436 (tmm) REVERT: E 297 GLU cc_start: 0.8788 (tm-30) cc_final: 0.8511 (tm-30) REVERT: F 44 MET cc_start: 0.8004 (ttm) cc_final: 0.7646 (tmm) REVERT: F 297 GLU cc_start: 0.8899 (tm-30) cc_final: 0.8681 (tm-30) REVERT: F 304 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8807 (tt) REVERT: G 44 MET cc_start: 0.5504 (tmm) cc_final: 0.4625 (ptt) REVERT: G 93 ASP cc_start: 0.9072 (m-30) cc_final: 0.8705 (t0) REVERT: H 93 ASP cc_start: 0.9140 (t0) cc_final: 0.8874 (t0) REVERT: H 102 GLU cc_start: 0.9670 (mm-30) cc_final: 0.9385 (mp0) REVERT: H 152 MET cc_start: 0.8675 (tpp) cc_final: 0.8069 (tpp) REVERT: I 104 PHE cc_start: 0.9530 (t80) cc_final: 0.8900 (t80) REVERT: I 172 TRP cc_start: 0.8689 (t-100) cc_final: 0.8265 (t-100) REVERT: I 191 TYR cc_start: 0.8363 (t80) cc_final: 0.8094 (t80) REVERT: I 222 LEU cc_start: 0.9590 (tp) cc_final: 0.9320 (mt) REVERT: I 226 ARG cc_start: 0.9359 (mtt90) cc_final: 0.9025 (mmt-90) outliers start: 90 outliers final: 51 residues processed: 220 average time/residue: 0.1486 time to fit residues: 52.8056 Evaluate side-chains 172 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 117 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 323 TYR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 323 TYR Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 63 GLN Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 158 ASN Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 224 GLN Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 323 TYR Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 323 TYR Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 246 ILE Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain F residue 304 LEU Chi-restraints excluded: chain G residue 50 PHE Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 129 ASP Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 269 PHE Chi-restraints excluded: chain G residue 280 ARG Chi-restraints excluded: chain G residue 291 VAL Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 211 LEU Chi-restraints excluded: chain H residue 213 ILE Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 185 GLN Chi-restraints excluded: chain I residue 303 TYR Chi-restraints excluded: chain I residue 312 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 140 optimal weight: 1.9990 chunk 22 optimal weight: 30.0000 chunk 44 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 246 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 287 optimal weight: 7.9990 chunk 153 optimal weight: 0.3980 chunk 204 optimal weight: 0.9980 chunk 159 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 130 GLN ** H 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.087842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.053982 restraints weight = 77583.081| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 3.79 r_work: 0.2804 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 23283 Z= 0.165 Angle : 0.539 10.461 31501 Z= 0.272 Chirality : 0.037 0.167 3703 Planarity : 0.004 0.053 3986 Dihedral : 4.323 57.504 3089 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 3.30 % Allowed : 26.25 % Favored : 70.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.83 % 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: 1.48 (0.16), residues: 2883 helix: 1.92 (0.12), residues: 1824 sheet: 1.85 (0.37), residues: 218 loop : -1.43 (0.21), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 280 TYR 0.022 0.001 TYR A 126 PHE 0.013 0.001 PHE G 321 TRP 0.015 0.001 TRP H 37 HIS 0.002 0.001 HIS G 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 (23283) covalent geometry : angle 0.53861 / 0.27 (31501) hydrogen bonds : bond 0.04738 / 3.17 ( 1409) hydrogen bonds : angle 3.98618 / 2.81 ( 4086) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 124 time to evaluate : 0.928 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 37 TRP cc_start: 0.7297 (m100) cc_final: 0.6605 (m100) REVERT: A 128 MET cc_start: 0.9148 (pmm) cc_final: 0.8271 (pmm) REVERT: A 132 LYS cc_start: 0.9455 (OUTLIER) cc_final: 0.8896 (mmtm) REVERT: A 142 HIS cc_start: 0.9254 (m90) cc_final: 0.8754 (t-170) REVERT: A 194 TYR cc_start: 0.8661 (t80) cc_final: 0.8447 (t80) REVERT: C 44 MET cc_start: 0.7860 (pmm) cc_final: 0.7159 (ppp) REVERT: C 174 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9111 (mt) REVERT: C 323 TYR cc_start: 0.9051 (OUTLIER) cc_final: 0.8828 (m-10) REVERT: D 60 ILE cc_start: 0.9323 (tp) cc_final: 0.8980 (pt) REVERT: D 102 GLU cc_start: 0.8937 (tm-30) cc_final: 0.8631 (tm-30) REVERT: D 157 ASP cc_start: 0.9371 (t0) cc_final: 0.9129 (t0) REVERT: E 44 MET cc_start: 0.6669 (ptt) cc_final: 0.6439 (tmm) REVERT: E 297 GLU cc_start: 0.8769 (tm-30) cc_final: 0.8458 (tm-30) REVERT: F 44 MET cc_start: 0.8046 (ttm) cc_final: 0.7650 (tmm) REVERT: F 304 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8823 (tt) REVERT: G 44 MET cc_start: 0.5406 (tmm) cc_final: 0.4620 (ptt) REVERT: G 93 ASP cc_start: 0.9078 (m-30) cc_final: 0.8708 (t0) REVERT: G 136 ILE cc_start: 0.8711 (OUTLIER) cc_final: 0.8502 (tp) REVERT: H 37 TRP cc_start: 0.7364 (OUTLIER) cc_final: 0.6776 (p-90) REVERT: H 93 ASP cc_start: 0.9132 (t0) cc_final: 0.8857 (t0) REVERT: H 102 GLU cc_start: 0.9674 (mm-30) cc_final: 0.9356 (mp0) REVERT: H 152 MET cc_start: 0.8660 (tpp) cc_final: 0.8144 (tpp) REVERT: I 90 ARG cc_start: 0.9370 (tpp-160) cc_final: 0.8793 (mmm-85) REVERT: I 172 TRP cc_start: 0.8678 (t-100) cc_final: 0.8176 (t-100) REVERT: I 222 LEU cc_start: 0.9611 (tp) cc_final: 0.9305 (mp) REVERT: I 226 ARG cc_start: 0.9376 (mtt90) cc_final: 0.9083 (mmt-90) REVERT: I 301 ARG cc_start: 0.9118 (mtm-85) cc_final: 0.8879 (mtp180) outliers start: 84 outliers final: 52 residues processed: 202 average time/residue: 0.1509 time to fit residues: 49.0900 Evaluate side-chains 178 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 120 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 132 LYS Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 323 TYR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 323 TYR Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 63 GLN Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 158 ASN Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 238 GLN Chi-restraints excluded: chain C residue 323 TYR Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 323 TYR Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain F residue 304 LEU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 129 ASP Chi-restraints excluded: chain G residue 136 ILE Chi-restraints excluded: chain G residue 152 MET Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 264 LYS Chi-restraints excluded: chain G residue 269 PHE Chi-restraints excluded: chain G residue 280 ARG Chi-restraints excluded: chain G residue 291 VAL Chi-restraints excluded: chain G residue 340 ILE Chi-restraints excluded: chain H residue 37 TRP Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 213 ILE Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 303 TYR Chi-restraints excluded: chain I residue 312 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 217 optimal weight: 2.9990 chunk 230 optimal weight: 10.0000 chunk 129 optimal weight: 0.6980 chunk 262 optimal weight: 0.0770 chunk 136 optimal weight: 2.9990 chunk 235 optimal weight: 0.0670 chunk 90 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 181 optimal weight: 0.7980 chunk 246 optimal weight: 2.9990 overall best weight: 0.9278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.088890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.055049 restraints weight = 77153.554| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 3.83 r_work: 0.2844 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 23283 Z= 0.111 Angle : 0.501 12.391 31501 Z= 0.249 Chirality : 0.036 0.160 3703 Planarity : 0.004 0.043 3986 Dihedral : 4.097 55.749 3086 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.75 % Allowed : 26.28 % Favored : 70.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.83 % 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: 1.66 (0.16), residues: 2883 helix: 2.07 (0.12), residues: 1833 sheet: 2.00 (0.37), residues: 216 loop : -1.44 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 280 TYR 0.022 0.001 TYR A 126 PHE 0.021 0.001 PHE B 48 TRP 0.015 0.001 TRP H 37 HIS 0.001 0.000 HIS I 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (23283) covalent geometry : angle 0.50135 / 0.25 (31501) hydrogen bonds : bond 0.04096 / 2.74 ( 1409) hydrogen bonds : angle 3.66255 / 2.58 ( 4086) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 133 time to evaluate : 0.941 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 142 HIS cc_start: 0.9247 (m90) cc_final: 0.8768 (t-170) REVERT: A 242 TYR cc_start: 0.9578 (t80) cc_final: 0.9365 (t80) REVERT: B 150 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8451 (pm20) REVERT: B 334 ASP cc_start: 0.9025 (OUTLIER) cc_final: 0.8523 (t0) REVERT: C 44 MET cc_start: 0.7821 (pmm) cc_final: 0.7161 (ppp) REVERT: C 163 LYS cc_start: 0.8853 (mmtm) cc_final: 0.8581 (pptt) REVERT: C 174 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.9085 (mt) REVERT: C 323 TYR cc_start: 0.9064 (OUTLIER) cc_final: 0.8833 (m-10) REVERT: D 60 ILE cc_start: 0.9310 (tp) cc_final: 0.8954 (pt) REVERT: D 157 ASP cc_start: 0.9359 (t0) cc_final: 0.9091 (t0) REVERT: E 44 MET cc_start: 0.6773 (ptt) cc_final: 0.6568 (tmm) REVERT: E 297 GLU cc_start: 0.8620 (tm-30) cc_final: 0.8291 (tm-30) REVERT: F 44 MET cc_start: 0.8045 (ttm) cc_final: 0.7671 (tmm) REVERT: G 44 MET cc_start: 0.5341 (tmm) cc_final: 0.4661 (ptt) REVERT: G 93 ASP cc_start: 0.9097 (m-30) cc_final: 0.8706 (t0) REVERT: G 136 ILE cc_start: 0.8697 (OUTLIER) cc_final: 0.8481 (tp) REVERT: H 37 TRP cc_start: 0.7232 (OUTLIER) cc_final: 0.6686 (p-90) REVERT: H 93 ASP cc_start: 0.9126 (t0) cc_final: 0.8835 (t0) REVERT: H 102 GLU cc_start: 0.9656 (mm-30) cc_final: 0.9335 (mp0) REVERT: H 152 MET cc_start: 0.8600 (tpp) cc_final: 0.8354 (tpp) REVERT: I 90 ARG cc_start: 0.9364 (tpp-160) cc_final: 0.8788 (mmm-85) REVERT: I 104 PHE cc_start: 0.9542 (t80) cc_final: 0.9081 (t80) REVERT: I 152 MET cc_start: 0.8745 (tpt) cc_final: 0.7741 (ttt) REVERT: I 222 LEU cc_start: 0.9616 (tp) cc_final: 0.9372 (mm) REVERT: I 226 ARG cc_start: 0.9377 (mtt90) cc_final: 0.9043 (mmt-90) outliers start: 70 outliers final: 48 residues processed: 197 average time/residue: 0.1484 time to fit residues: 46.8008 Evaluate side-chains 176 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 122 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 323 TYR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 323 TYR Chi-restraints excluded: chain B residue 334 ASP Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 63 GLN Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 158 ASN Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 323 TYR Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 196 SER Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 129 ASP Chi-restraints excluded: chain G residue 136 ILE Chi-restraints excluded: chain G residue 171 SER Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 264 LYS Chi-restraints excluded: chain G residue 269 PHE Chi-restraints excluded: chain G residue 280 ARG Chi-restraints excluded: chain G residue 291 VAL Chi-restraints excluded: chain G residue 340 ILE Chi-restraints excluded: chain H residue 37 TRP Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 211 LEU Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 312 HIS Chi-restraints excluded: chain I residue 326 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 66 optimal weight: 9.9990 chunk 116 optimal weight: 1.9990 chunk 266 optimal weight: 0.7980 chunk 120 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 256 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 196 optimal weight: 30.0000 chunk 181 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 209 ASN G 112 GLN ** H 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 185 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.088324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.054557 restraints weight = 76803.190| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 3.80 r_work: 0.2827 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 23283 Z= 0.130 Angle : 0.522 12.361 31501 Z= 0.258 Chirality : 0.036 0.162 3703 Planarity : 0.004 0.044 3986 Dihedral : 4.031 54.980 3086 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.22 % Allowed : 26.13 % Favored : 70.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.83 % 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: 1.75 (0.16), residues: 2883 helix: 2.12 (0.12), residues: 1840 sheet: 2.05 (0.36), residues: 214 loop : -1.41 (0.21), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 208 TYR 0.022 0.001 TYR A 126 PHE 0.015 0.001 PHE G 321 TRP 0.016 0.001 TRP H 37 HIS 0.002 0.001 HIS C 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (23283) covalent geometry : angle 0.52164 / 0.26 (31501) hydrogen bonds : bond 0.04034 / 2.69 ( 1409) hydrogen bonds : angle 3.61408 / 2.54 ( 4086) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 126 time to evaluate : 0.869 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 142 HIS cc_start: 0.9236 (m90) cc_final: 0.8755 (t-170) REVERT: A 180 THR cc_start: 0.8438 (OUTLIER) cc_final: 0.8234 (t) REVERT: A 194 TYR cc_start: 0.8711 (t80) cc_final: 0.8490 (t80) REVERT: A 242 TYR cc_start: 0.9562 (t80) cc_final: 0.9331 (t80) REVERT: B 150 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8474 (pm20) REVERT: B 334 ASP cc_start: 0.9032 (OUTLIER) cc_final: 0.8535 (t0) REVERT: C 44 MET cc_start: 0.7883 (pmm) cc_final: 0.7088 (ppp) REVERT: C 163 LYS cc_start: 0.8812 (mmtm) cc_final: 0.8594 (pptt) REVERT: C 174 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9093 (mt) REVERT: C 224 GLN cc_start: 0.8972 (OUTLIER) cc_final: 0.8662 (tt0) REVERT: C 323 TYR cc_start: 0.9067 (OUTLIER) cc_final: 0.8837 (m-10) REVERT: D 102 GLU cc_start: 0.8870 (tm-30) cc_final: 0.8614 (tm-30) REVERT: D 157 ASP cc_start: 0.9363 (t0) cc_final: 0.9102 (t0) REVERT: F 44 MET cc_start: 0.7984 (ttm) cc_final: 0.7629 (tmm) REVERT: G 44 MET cc_start: 0.5306 (tmm) cc_final: 0.4674 (ptt) REVERT: G 93 ASP cc_start: 0.9128 (m-30) cc_final: 0.8728 (t0) REVERT: G 136 ILE cc_start: 0.8698 (OUTLIER) cc_final: 0.8479 (tp) REVERT: H 37 TRP cc_start: 0.7162 (OUTLIER) cc_final: 0.6622 (p-90) REVERT: H 93 ASP cc_start: 0.9063 (t0) cc_final: 0.8799 (t0) REVERT: H 102 GLU cc_start: 0.9658 (mm-30) cc_final: 0.9352 (mm-30) REVERT: I 104 PHE cc_start: 0.9536 (t80) cc_final: 0.9012 (t80) REVERT: I 152 MET cc_start: 0.8744 (tpt) cc_final: 0.7802 (ttm) REVERT: I 183 GLU cc_start: 0.8953 (OUTLIER) cc_final: 0.8595 (mp0) REVERT: I 191 TYR cc_start: 0.8261 (t80) cc_final: 0.7969 (t80) REVERT: I 222 LEU cc_start: 0.9640 (tp) cc_final: 0.9280 (mm) REVERT: I 226 ARG cc_start: 0.9365 (mtt90) cc_final: 0.9078 (mpt180) REVERT: I 299 ARG cc_start: 0.8968 (mmm160) cc_final: 0.8719 (mmp80) outliers start: 82 outliers final: 55 residues processed: 202 average time/residue: 0.1461 time to fit residues: 47.4738 Evaluate side-chains 183 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 119 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 323 TYR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 323 TYR Chi-restraints excluded: chain B residue 334 ASP Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 63 GLN Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 158 ASN Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 224 GLN Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 323 TYR Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 323 TYR Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 88 LYS Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 196 SER Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 129 ASP Chi-restraints excluded: chain G residue 136 ILE Chi-restraints excluded: chain G residue 152 MET Chi-restraints excluded: chain G residue 171 SER Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 264 LYS Chi-restraints excluded: chain G residue 269 PHE Chi-restraints excluded: chain G residue 280 ARG Chi-restraints excluded: chain G residue 291 VAL Chi-restraints excluded: chain G residue 340 ILE Chi-restraints excluded: chain H residue 37 TRP Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 118 GLU Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 183 GLU Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 312 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 88 optimal weight: 0.9980 chunk 213 optimal weight: 1.9990 chunk 176 optimal weight: 0.6980 chunk 253 optimal weight: 0.0980 chunk 2 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 149 optimal weight: 0.9980 chunk 200 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 258 optimal weight: 0.9990 chunk 63 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.089672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.056064 restraints weight = 76636.586| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 3.79 r_work: 0.2865 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 23283 Z= 0.099 Angle : 0.507 11.521 31501 Z= 0.248 Chirality : 0.036 0.156 3703 Planarity : 0.003 0.044 3986 Dihedral : 3.937 53.432 3086 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.90 % Allowed : 26.60 % Favored : 70.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.83 % 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: 1.87 (0.16), residues: 2883 helix: 2.23 (0.12), residues: 1835 sheet: 2.11 (0.36), residues: 217 loop : -1.39 (0.21), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 90 TYR 0.023 0.001 TYR A 126 PHE 0.025 0.001 PHE G 59 TRP 0.016 0.001 TRP H 37 HIS 0.001 0.000 HIS I 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.10 (23283) covalent geometry : angle 0.50657 / 0.25 (31501) hydrogen bonds : bond 0.03699 / 2.47 ( 1409) hydrogen bonds : angle 3.45355 / 2.43 ( 4086) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 131 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 HIS cc_start: 0.9214 (m90) cc_final: 0.8741 (t-170) REVERT: A 180 THR cc_start: 0.8435 (OUTLIER) cc_final: 0.8227 (t) REVERT: A 194 TYR cc_start: 0.8719 (t80) cc_final: 0.8498 (t80) REVERT: B 150 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.8483 (pm20) REVERT: B 334 ASP cc_start: 0.9018 (OUTLIER) cc_final: 0.8517 (t0) REVERT: C 44 MET cc_start: 0.7830 (pmm) cc_final: 0.7058 (ppp) REVERT: C 174 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.9013 (mt) REVERT: C 323 TYR cc_start: 0.9043 (OUTLIER) cc_final: 0.8808 (m-10) REVERT: D 60 ILE cc_start: 0.9323 (OUTLIER) cc_final: 0.8953 (pt) REVERT: D 157 ASP cc_start: 0.9359 (t0) cc_final: 0.9074 (t0) REVERT: F 44 MET cc_start: 0.8041 (ttm) cc_final: 0.7656 (tmm) REVERT: F 194 TYR cc_start: 0.8809 (t80) cc_final: 0.8480 (t80) REVERT: G 44 MET cc_start: 0.5253 (tmm) cc_final: 0.4629 (ptt) REVERT: G 93 ASP cc_start: 0.9072 (m-30) cc_final: 0.8678 (t0) REVERT: G 136 ILE cc_start: 0.8673 (OUTLIER) cc_final: 0.8455 (tp) REVERT: H 37 TRP cc_start: 0.7005 (OUTLIER) cc_final: 0.6525 (p-90) REVERT: H 93 ASP cc_start: 0.9062 (t0) cc_final: 0.8775 (t0) REVERT: H 97 LYS cc_start: 0.9365 (mmmt) cc_final: 0.9138 (mmmt) REVERT: H 102 GLU cc_start: 0.9638 (mm-30) cc_final: 0.9338 (mp0) REVERT: I 104 PHE cc_start: 0.9509 (t80) cc_final: 0.9045 (t80) REVERT: I 152 MET cc_start: 0.8703 (tpt) cc_final: 0.7921 (ttm) REVERT: I 183 GLU cc_start: 0.8958 (OUTLIER) cc_final: 0.8560 (mp0) REVERT: I 191 TYR cc_start: 0.8224 (t80) cc_final: 0.7929 (t80) REVERT: I 222 LEU cc_start: 0.9634 (tp) cc_final: 0.9281 (mm) REVERT: I 226 ARG cc_start: 0.9384 (mtt90) cc_final: 0.9074 (mmt-90) REVERT: I 301 ARG cc_start: 0.9070 (mtm-85) cc_final: 0.8665 (mtp180) outliers start: 74 outliers final: 54 residues processed: 198 average time/residue: 0.1567 time to fit residues: 49.7095 Evaluate side-chains 187 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 124 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 323 TYR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 323 TYR Chi-restraints excluded: chain B residue 334 ASP Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 63 GLN Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 257 TYR Chi-restraints excluded: chain C residue 323 TYR Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 323 TYR Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 88 LYS Chi-restraints excluded: chain E residue 196 SER Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 129 ASP Chi-restraints excluded: chain G residue 136 ILE Chi-restraints excluded: chain G residue 171 SER Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 269 PHE Chi-restraints excluded: chain G residue 280 ARG Chi-restraints excluded: chain G residue 340 ILE Chi-restraints excluded: chain H residue 37 TRP Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 276 ASP Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 100 ARG Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 118 GLU Chi-restraints excluded: chain I residue 126 TYR Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 183 GLU Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 312 HIS Chi-restraints excluded: chain I residue 326 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 49 optimal weight: 4.9990 chunk 276 optimal weight: 3.9990 chunk 252 optimal weight: 10.0000 chunk 79 optimal weight: 0.5980 chunk 130 optimal weight: 40.0000 chunk 223 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 155 optimal weight: 0.6980 chunk 62 optimal weight: 8.9990 chunk 183 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.088150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.054182 restraints weight = 77982.048| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 3.80 r_work: 0.2801 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 23283 Z= 0.162 Angle : 0.547 10.217 31501 Z= 0.272 Chirality : 0.037 0.166 3703 Planarity : 0.004 0.048 3986 Dihedral : 3.944 54.150 3084 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 3.53 % Allowed : 26.09 % Favored : 70.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.83 % 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: 1.85 (0.16), residues: 2883 helix: 2.21 (0.12), residues: 1828 sheet: 2.12 (0.36), residues: 215 loop : -1.36 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 143 TYR 0.023 0.001 TYR A 126 PHE 0.020 0.001 PHE G 59 TRP 0.016 0.001 TRP H 37 HIS 0.002 0.001 HIS C 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 (23283) covalent geometry : angle 0.54708 / 0.27 (31501) hydrogen bonds : bond 0.04000 / 2.68 ( 1409) hydrogen bonds : angle 3.57811 / 2.51 ( 4086) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 123 time to evaluate : 0.860 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 37 TRP cc_start: 0.7386 (m100) cc_final: 0.6753 (m100) REVERT: A 142 HIS cc_start: 0.9232 (m90) cc_final: 0.8740 (t-170) REVERT: A 180 THR cc_start: 0.8441 (OUTLIER) cc_final: 0.8232 (t) REVERT: A 194 TYR cc_start: 0.8723 (t80) cc_final: 0.8485 (t80) REVERT: B 150 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8504 (pm20) REVERT: B 334 ASP cc_start: 0.9048 (OUTLIER) cc_final: 0.8564 (t0) REVERT: C 44 MET cc_start: 0.7830 (pmm) cc_final: 0.7184 (ppp) REVERT: C 174 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.9115 (mt) REVERT: C 323 TYR cc_start: 0.9057 (OUTLIER) cc_final: 0.8776 (m-10) REVERT: D 60 ILE cc_start: 0.9319 (OUTLIER) cc_final: 0.8963 (pt) REVERT: D 102 GLU cc_start: 0.8871 (tm-30) cc_final: 0.8634 (tm-30) REVERT: D 157 ASP cc_start: 0.9380 (t0) cc_final: 0.9114 (t0) REVERT: F 44 MET cc_start: 0.8073 (ttm) cc_final: 0.7700 (tmm) REVERT: G 44 MET cc_start: 0.5224 (tmm) cc_final: 0.4628 (ptt) REVERT: G 93 ASP cc_start: 0.9082 (m-30) cc_final: 0.8708 (t0) REVERT: G 136 ILE cc_start: 0.8695 (OUTLIER) cc_final: 0.8471 (tp) REVERT: H 37 TRP cc_start: 0.6935 (OUTLIER) cc_final: 0.6475 (p-90) REVERT: H 93 ASP cc_start: 0.9059 (t0) cc_final: 0.8780 (t0) REVERT: H 97 LYS cc_start: 0.9366 (mmmt) cc_final: 0.9130 (mmmt) REVERT: H 102 GLU cc_start: 0.9662 (mm-30) cc_final: 0.9357 (mm-30) REVERT: H 152 MET cc_start: 0.8478 (tpp) cc_final: 0.8263 (tpp) REVERT: I 90 ARG cc_start: 0.9382 (tpp-160) cc_final: 0.8840 (mmm160) REVERT: I 104 PHE cc_start: 0.9520 (t80) cc_final: 0.8970 (t80) REVERT: I 152 MET cc_start: 0.8751 (tpt) cc_final: 0.8043 (ttm) REVERT: I 183 GLU cc_start: 0.8965 (OUTLIER) cc_final: 0.8579 (mp0) REVERT: I 191 TYR cc_start: 0.8233 (t80) cc_final: 0.7887 (t80) REVERT: I 222 LEU cc_start: 0.9674 (tp) cc_final: 0.9314 (mp) REVERT: I 226 ARG cc_start: 0.9429 (mtt90) cc_final: 0.9097 (mmt-90) REVERT: I 301 ARG cc_start: 0.9127 (mtm-85) cc_final: 0.8836 (mtm110) outliers start: 90 outliers final: 64 residues processed: 205 average time/residue: 0.1538 time to fit residues: 50.7358 Evaluate side-chains 191 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 118 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 323 TYR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 323 TYR Chi-restraints excluded: chain B residue 334 ASP Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 63 GLN Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 158 ASN Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 257 TYR Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 323 TYR Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 323 TYR Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 88 LYS Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 196 SER Chi-restraints excluded: chain E residue 237 ILE Chi-restraints excluded: chain E residue 272 SER Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 129 ASP Chi-restraints excluded: chain G residue 136 ILE Chi-restraints excluded: chain G residue 152 MET Chi-restraints excluded: chain G residue 171 SER Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 264 LYS Chi-restraints excluded: chain G residue 280 ARG Chi-restraints excluded: chain G residue 340 ILE Chi-restraints excluded: chain H residue 37 TRP Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 213 ILE Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 276 ASP Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 100 ARG Chi-restraints excluded: chain I residue 126 TYR Chi-restraints excluded: chain I residue 169 TYR Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 183 GLU Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 312 HIS Chi-restraints excluded: chain I residue 326 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 171 optimal weight: 2.9990 chunk 133 optimal weight: 8.9990 chunk 18 optimal weight: 0.9980 chunk 125 optimal weight: 3.9990 chunk 190 optimal weight: 0.5980 chunk 284 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 123 optimal weight: 0.0040 chunk 35 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 96 optimal weight: 10.0000 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 261 GLN ** H 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.089738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.055960 restraints weight = 77040.697| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 3.79 r_work: 0.2854 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 23283 Z= 0.102 Angle : 0.524 10.332 31501 Z= 0.257 Chirality : 0.036 0.198 3703 Planarity : 0.003 0.044 3986 Dihedral : 3.813 52.038 3082 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.82 % Allowed : 26.68 % Favored : 70.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.83 % 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: 1.93 (0.16), residues: 2883 helix: 2.26 (0.12), residues: 1831 sheet: 2.22 (0.35), residues: 215 loop : -1.32 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 299 TYR 0.021 0.001 TYR A 126 PHE 0.028 0.001 PHE B 48 TRP 0.016 0.001 TRP H 37 HIS 0.001 0.000 HIS I 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (23283) covalent geometry : angle 0.52420 / 0.26 (31501) hydrogen bonds : bond 0.03662 / 2.44 ( 1409) hydrogen bonds : angle 3.41014 / 2.40 ( 4086) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 128 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 TRP cc_start: 0.7390 (m100) cc_final: 0.6779 (m100) REVERT: A 142 HIS cc_start: 0.9220 (m90) cc_final: 0.8740 (t-170) REVERT: A 180 THR cc_start: 0.8394 (OUTLIER) cc_final: 0.8172 (t) REVERT: A 194 TYR cc_start: 0.8735 (t80) cc_final: 0.8508 (t80) REVERT: B 93 ASP cc_start: 0.9158 (t0) cc_final: 0.8716 (t0) REVERT: B 150 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8486 (pm20) REVERT: B 334 ASP cc_start: 0.9019 (OUTLIER) cc_final: 0.8540 (t0) REVERT: C 44 MET cc_start: 0.7817 (pmm) cc_final: 0.7060 (ppp) REVERT: C 174 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.9029 (mt) REVERT: C 245 ASP cc_start: 0.9227 (OUTLIER) cc_final: 0.8878 (t0) REVERT: C 323 TYR cc_start: 0.9038 (OUTLIER) cc_final: 0.8763 (m-80) REVERT: D 60 ILE cc_start: 0.9316 (OUTLIER) cc_final: 0.8947 (pt) REVERT: D 157 ASP cc_start: 0.9351 (t0) cc_final: 0.9062 (t0) REVERT: F 44 MET cc_start: 0.8082 (ttm) cc_final: 0.7709 (tmm) REVERT: G 44 MET cc_start: 0.5176 (tmm) cc_final: 0.4578 (ptt) REVERT: G 93 ASP cc_start: 0.9047 (m-30) cc_final: 0.8637 (t0) REVERT: G 119 GLU cc_start: 0.9463 (mm-30) cc_final: 0.9255 (tp30) REVERT: G 280 ARG cc_start: 0.9010 (OUTLIER) cc_final: 0.8493 (tpp-160) REVERT: H 37 TRP cc_start: 0.6829 (OUTLIER) cc_final: 0.6407 (p-90) REVERT: H 93 ASP cc_start: 0.9061 (t0) cc_final: 0.8767 (t0) REVERT: H 97 LYS cc_start: 0.9406 (mmmt) cc_final: 0.9190 (mmmt) REVERT: H 102 GLU cc_start: 0.9647 (mm-30) cc_final: 0.9359 (mm-30) REVERT: H 152 MET cc_start: 0.8448 (tpp) cc_final: 0.8226 (tpp) REVERT: I 90 ARG cc_start: 0.9404 (tpp-160) cc_final: 0.8834 (mmm160) REVERT: I 104 PHE cc_start: 0.9506 (t80) cc_final: 0.8946 (t80) REVERT: I 152 MET cc_start: 0.8615 (tpt) cc_final: 0.8043 (ttm) REVERT: I 183 GLU cc_start: 0.8953 (OUTLIER) cc_final: 0.8547 (mp0) REVERT: I 191 TYR cc_start: 0.8188 (t80) cc_final: 0.7803 (t80) REVERT: I 222 LEU cc_start: 0.9658 (tp) cc_final: 0.9389 (mm) REVERT: I 226 ARG cc_start: 0.9412 (mtt90) cc_final: 0.9123 (mmt-90) outliers start: 72 outliers final: 53 residues processed: 191 average time/residue: 0.1481 time to fit residues: 45.4977 Evaluate side-chains 184 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 121 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 323 TYR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 323 TYR Chi-restraints excluded: chain B residue 334 ASP Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 158 ASN Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 257 TYR Chi-restraints excluded: chain C residue 323 TYR Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 88 LYS Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 196 SER Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 129 ASP Chi-restraints excluded: chain G residue 152 MET Chi-restraints excluded: chain G residue 171 SER Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 264 LYS Chi-restraints excluded: chain G residue 269 PHE Chi-restraints excluded: chain G residue 280 ARG Chi-restraints excluded: chain G residue 340 ILE Chi-restraints excluded: chain H residue 37 TRP Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 276 ASP Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 118 GLU Chi-restraints excluded: chain I residue 126 TYR Chi-restraints excluded: chain I residue 169 TYR Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 183 GLU Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 312 HIS Chi-restraints excluded: chain I residue 326 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 259 optimal weight: 0.4980 chunk 51 optimal weight: 0.9980 chunk 288 optimal weight: 0.0770 chunk 236 optimal weight: 4.9990 chunk 146 optimal weight: 0.6980 chunk 186 optimal weight: 2.9990 chunk 166 optimal weight: 7.9990 chunk 174 optimal weight: 0.8980 chunk 270 optimal weight: 4.9990 chunk 237 optimal weight: 1.9990 chunk 268 optimal weight: 6.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 232 GLN ** H 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 80 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.089886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.056195 restraints weight = 77559.658| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 3.81 r_work: 0.2865 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 23283 Z= 0.102 Angle : 0.542 13.127 31501 Z= 0.263 Chirality : 0.036 0.212 3703 Planarity : 0.004 0.044 3986 Dihedral : 3.746 52.047 3082 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.71 % Allowed : 26.64 % Favored : 70.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.83 % 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: 1.96 (0.16), residues: 2883 helix: 2.32 (0.12), residues: 1826 sheet: 2.19 (0.35), residues: 217 loop : -1.39 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 208 TYR 0.021 0.001 TYR F 194 PHE 0.019 0.001 PHE I 318 TRP 0.016 0.001 TRP H 37 HIS 0.001 0.000 HIS I 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 (23283) covalent geometry : angle 0.54196 / 0.26 (31501) hydrogen bonds : bond 0.03527 / 2.36 ( 1409) hydrogen bonds : angle 3.32839 / 2.35 ( 4086) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 130 time to evaluate : 0.903 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 37 TRP cc_start: 0.7402 (m100) cc_final: 0.6808 (m100) REVERT: A 118 GLU cc_start: 0.9557 (mm-30) cc_final: 0.9355 (mm-30) REVERT: A 142 HIS cc_start: 0.9209 (m90) cc_final: 0.8837 (t70) REVERT: A 180 THR cc_start: 0.8355 (OUTLIER) cc_final: 0.8124 (t) REVERT: A 194 TYR cc_start: 0.8741 (t80) cc_final: 0.8524 (t80) REVERT: B 93 ASP cc_start: 0.9137 (t0) cc_final: 0.8693 (t0) REVERT: B 150 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8493 (pm20) REVERT: B 334 ASP cc_start: 0.9027 (OUTLIER) cc_final: 0.8555 (t0) REVERT: C 44 MET cc_start: 0.7778 (pmm) cc_final: 0.7029 (ppp) REVERT: C 174 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.9134 (mt) REVERT: C 245 ASP cc_start: 0.9220 (OUTLIER) cc_final: 0.8874 (t0) REVERT: C 323 TYR cc_start: 0.9029 (OUTLIER) cc_final: 0.8759 (m-10) REVERT: D 60 ILE cc_start: 0.9244 (OUTLIER) cc_final: 0.8885 (pt) REVERT: D 102 GLU cc_start: 0.8866 (tm-30) cc_final: 0.8638 (tp30) REVERT: D 157 ASP cc_start: 0.9342 (t0) cc_final: 0.9024 (t0) REVERT: F 44 MET cc_start: 0.8077 (ttm) cc_final: 0.7707 (tmm) REVERT: G 44 MET cc_start: 0.5205 (tmm) cc_final: 0.4615 (ptt) REVERT: G 93 ASP cc_start: 0.9066 (m-30) cc_final: 0.8641 (t0) REVERT: G 136 ILE cc_start: 0.8671 (OUTLIER) cc_final: 0.8429 (tp) REVERT: H 37 TRP cc_start: 0.6770 (OUTLIER) cc_final: 0.6387 (p-90) REVERT: H 93 ASP cc_start: 0.9056 (t0) cc_final: 0.8754 (t0) REVERT: H 97 LYS cc_start: 0.9375 (mmmt) cc_final: 0.9167 (mmmt) REVERT: H 102 GLU cc_start: 0.9634 (mm-30) cc_final: 0.9348 (mm-30) REVERT: I 79 TRP cc_start: 0.6786 (m-90) cc_final: 0.5640 (m-90) REVERT: I 90 ARG cc_start: 0.9375 (tpp-160) cc_final: 0.8757 (mmm160) REVERT: I 104 PHE cc_start: 0.9507 (t80) cc_final: 0.8962 (t80) REVERT: I 152 MET cc_start: 0.8600 (tpt) cc_final: 0.8154 (ttm) REVERT: I 183 GLU cc_start: 0.8968 (OUTLIER) cc_final: 0.8563 (mp0) REVERT: I 191 TYR cc_start: 0.8204 (t80) cc_final: 0.7808 (t80) REVERT: I 208 ARG cc_start: 0.9662 (mtm-85) cc_final: 0.9412 (mpp80) REVERT: I 222 LEU cc_start: 0.9662 (tp) cc_final: 0.9374 (mp) REVERT: I 226 ARG cc_start: 0.9415 (mtt90) cc_final: 0.9164 (mmt-90) REVERT: I 299 ARG cc_start: 0.8899 (mmp80) cc_final: 0.8661 (mmp80) outliers start: 69 outliers final: 53 residues processed: 191 average time/residue: 0.1460 time to fit residues: 44.9663 Evaluate side-chains 191 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 128 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 323 TYR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 323 TYR Chi-restraints excluded: chain B residue 334 ASP Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 63 GLN Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 158 ASN Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 323 TYR Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 323 TYR Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 88 LYS Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 196 SER Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 129 ASP Chi-restraints excluded: chain G residue 136 ILE Chi-restraints excluded: chain G residue 171 SER Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 264 LYS Chi-restraints excluded: chain G residue 340 ILE Chi-restraints excluded: chain H residue 37 TRP Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 276 ASP Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 118 GLU Chi-restraints excluded: chain I residue 126 TYR Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 183 GLU Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 312 HIS Chi-restraints excluded: chain I residue 326 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 205 optimal weight: 0.9980 chunk 264 optimal weight: 3.9990 chunk 164 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 252 optimal weight: 6.9990 chunk 150 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 142 optimal weight: 0.9990 chunk 207 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.117215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.083112 restraints weight = 88164.246| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 4.39 r_work: 0.2828 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 23283 Z= 0.133 Angle : 0.556 11.217 31501 Z= 0.273 Chirality : 0.037 0.193 3703 Planarity : 0.004 0.044 3986 Dihedral : 3.679 52.159 3077 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.55 % Allowed : 26.76 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.83 % 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: 1.98 (0.16), residues: 2883 helix: 2.34 (0.12), residues: 1823 sheet: 2.24 (0.35), residues: 215 loop : -1.37 (0.21), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 208 TYR 0.027 0.001 TYR I 169 PHE 0.031 0.001 PHE B 48 TRP 0.016 0.001 TRP H 37 HIS 0.002 0.000 HIS D 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (23283) covalent geometry : angle 0.55604 / 0.27 (31501) hydrogen bonds : bond 0.03707 / 2.48 ( 1409) hydrogen bonds : angle 3.40209 / 2.39 ( 4086) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 126 time to evaluate : 0.882 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 37 TRP cc_start: 0.7454 (m100) cc_final: 0.6918 (m100) REVERT: A 118 GLU cc_start: 0.9571 (mm-30) cc_final: 0.9359 (mm-30) REVERT: A 142 HIS cc_start: 0.9214 (m90) cc_final: 0.8840 (t-170) REVERT: A 180 THR cc_start: 0.8335 (OUTLIER) cc_final: 0.8124 (t) REVERT: A 194 TYR cc_start: 0.8713 (t80) cc_final: 0.8484 (t80) REVERT: B 93 ASP cc_start: 0.9201 (t0) cc_final: 0.8780 (t0) REVERT: B 150 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8502 (pm20) REVERT: B 334 ASP cc_start: 0.9029 (OUTLIER) cc_final: 0.8567 (t0) REVERT: C 44 MET cc_start: 0.7735 (pmm) cc_final: 0.7099 (ppp) REVERT: C 174 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.9127 (mt) REVERT: C 245 ASP cc_start: 0.9214 (OUTLIER) cc_final: 0.8868 (t0) REVERT: C 323 TYR cc_start: 0.9019 (OUTLIER) cc_final: 0.8717 (m-80) REVERT: D 60 ILE cc_start: 0.9261 (OUTLIER) cc_final: 0.8913 (pt) REVERT: D 157 ASP cc_start: 0.9351 (t0) cc_final: 0.9078 (t0) REVERT: F 44 MET cc_start: 0.8091 (ttm) cc_final: 0.7734 (tmm) REVERT: G 44 MET cc_start: 0.5275 (tmm) cc_final: 0.4642 (ptt) REVERT: G 93 ASP cc_start: 0.9047 (m-30) cc_final: 0.8628 (t0) REVERT: G 136 ILE cc_start: 0.8615 (OUTLIER) cc_final: 0.8355 (tp) REVERT: H 37 TRP cc_start: 0.6779 (OUTLIER) cc_final: 0.6341 (p-90) REVERT: H 93 ASP cc_start: 0.9070 (t0) cc_final: 0.8784 (t0) REVERT: H 97 LYS cc_start: 0.9380 (mmmt) cc_final: 0.9170 (mmmt) REVERT: H 102 GLU cc_start: 0.9628 (mm-30) cc_final: 0.9326 (mm-30) REVERT: I 79 TRP cc_start: 0.7004 (m-90) cc_final: 0.5807 (m-90) REVERT: I 90 ARG cc_start: 0.9382 (tpp-160) cc_final: 0.8785 (mmm160) REVERT: I 104 PHE cc_start: 0.9554 (t80) cc_final: 0.9099 (t80) REVERT: I 152 MET cc_start: 0.8601 (tpt) cc_final: 0.8181 (ttm) REVERT: I 183 GLU cc_start: 0.8896 (OUTLIER) cc_final: 0.8479 (mp0) REVERT: I 191 TYR cc_start: 0.8199 (t80) cc_final: 0.7882 (t80) REVERT: I 208 ARG cc_start: 0.9648 (mtm-85) cc_final: 0.9396 (mpp80) REVERT: I 222 LEU cc_start: 0.9669 (tp) cc_final: 0.9305 (mp) REVERT: I 226 ARG cc_start: 0.9471 (mtt90) cc_final: 0.9148 (mmt-90) outliers start: 65 outliers final: 52 residues processed: 184 average time/residue: 0.1527 time to fit residues: 44.5291 Evaluate side-chains 186 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 124 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 323 TYR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 323 TYR Chi-restraints excluded: chain B residue 334 ASP Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 158 ASN Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 323 TYR Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 323 TYR Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 88 LYS Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 196 SER Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 129 ASP Chi-restraints excluded: chain G residue 136 ILE Chi-restraints excluded: chain G residue 171 SER Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 264 LYS Chi-restraints excluded: chain G residue 340 ILE Chi-restraints excluded: chain H residue 37 TRP Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 276 ASP Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 126 TYR Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 183 GLU Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 312 HIS Chi-restraints excluded: chain I residue 326 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 19 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 137 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 63 optimal weight: 30.0000 chunk 195 optimal weight: 20.0000 chunk 276 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 31 optimal weight: 40.0000 chunk 80 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.089833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.055927 restraints weight = 77020.523| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 3.76 r_work: 0.2840 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 23283 Z= 0.119 Angle : 0.542 10.121 31501 Z= 0.265 Chirality : 0.036 0.185 3703 Planarity : 0.004 0.044 3986 Dihedral : 3.657 51.597 3077 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.71 % Allowed : 26.48 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.83 % 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: 2.01 (0.16), residues: 2883 helix: 2.34 (0.12), residues: 1825 sheet: 2.31 (0.35), residues: 215 loop : -1.33 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 208 TYR 0.028 0.001 TYR I 169 PHE 0.017 0.001 PHE G 59 TRP 0.016 0.001 TRP H 37 HIS 0.001 0.000 HIS I 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (23283) covalent geometry : angle 0.54203 / 0.27 (31501) hydrogen bonds : bond 0.03637 / 2.43 ( 1409) hydrogen bonds : angle 3.36342 / 2.37 ( 4086) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6208.51 seconds wall clock time: 106 minutes 52.78 seconds (6412.78 seconds total)