Starting phenix.real_space_refine on Fri Jun 5 02:48:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/30gh_57756/06_2026/30gh_57756.cif Found real_map, /net/cci-nas-00/data/ceres_data/30gh_57756/06_2026/30gh_57756.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/30gh_57756/06_2026/30gh_57756.cif" } default_model = "/net/cci-nas-00/data/ceres_data/30gh_57756/06_2026/30gh_57756.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/30gh_57756/06_2026/30gh_57756.map" default_real_map = "/net/cci-nas-00/data/ceres_data/30gh_57756/06_2026/30gh_57756.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.030 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 66 5.16 5 C 10615 2.51 5 N 2953 2.21 5 O 3149 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16783 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2885 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 355} Chain breaks: 1 Chain: "A" Number of atoms: 2878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2878 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 355} Chain breaks: 1 Chain: "C" Number of atoms: 2894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2894 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 356} Chain breaks: 1 Chain: "D" Number of atoms: 2894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2894 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 356} Chain breaks: 1 Chain: "E" Number of atoms: 2616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2616 Classifications: {'peptide': 330} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 310} Chain: "F" Number of atoms: 2616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2616 Classifications: {'peptide': 330} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 310} Time building chain proxies: 4.47, per 1000 atoms: 0.27 Number of scatterers: 16783 At special positions: 0 Unit cell: (81.4, 100.64, 197.58, 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 66 16.00 O 3149 8.00 N 2953 7.00 C 10615 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: 1.32 Conformation dependent library (CDL) restraints added in 675.8 milliseconds 4250 Ramachandran restraints generated. 2125 Oldfield, 0 Emsley, 2125 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3950 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 28 sheets defined 40.3% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'B' and resid 29 through 49 removed outlier: 3.914A pdb=" N GLN B 48 " --> pdb=" O ALA B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 91 Processing helix chain 'B' and resid 95 through 98 Processing helix chain 'B' and resid 151 through 170 removed outlier: 3.561A pdb=" N ALA B 157 " --> pdb=" O THR B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 226 removed outlier: 3.597A pdb=" N LYS B 223 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 236 Processing helix chain 'B' and resid 253 through 258 removed outlier: 3.517A pdb=" N ASP B 258 " --> pdb=" O GLY B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 270 Processing helix chain 'B' and resid 289 through 308 Processing helix chain 'B' and resid 341 through 353 Processing helix chain 'B' and resid 356 through 364 removed outlier: 3.528A pdb=" N ILE B 360 " --> pdb=" O ARG B 356 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL B 361 " --> pdb=" O PRO B 357 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG B 362 " --> pdb=" O GLY B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 375 removed outlier: 3.553A pdb=" N ARG B 373 " --> pdb=" O ILE B 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 49 removed outlier: 3.639A pdb=" N CYS A 34 " --> pdb=" O PRO A 30 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP A 35 " --> pdb=" O ASP A 31 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN A 48 " --> pdb=" O ALA A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 91 Processing helix chain 'A' and resid 151 through 170 removed outlier: 3.601A pdb=" N ASN A 161 " --> pdb=" O ALA A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 226 removed outlier: 3.980A pdb=" N LYS A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 231 Processing helix chain 'A' and resid 232 through 236 Processing helix chain 'A' and resid 253 through 258 Processing helix chain 'A' and resid 265 through 271 Processing helix chain 'A' and resid 289 through 308 removed outlier: 4.179A pdb=" N ALA A 295 " --> pdb=" O ASP A 291 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA A 298 " --> pdb=" O ALA A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 353 Processing helix chain 'A' and resid 356 through 365 removed outlier: 3.742A pdb=" N ARG A 362 " --> pdb=" O GLY A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 389 Processing helix chain 'C' and resid 29 through 49 removed outlier: 4.026A pdb=" N GLN C 48 " --> pdb=" O ALA C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 91 Processing helix chain 'C' and resid 95 through 98 Processing helix chain 'C' and resid 151 through 170 Processing helix chain 'C' and resid 214 through 226 removed outlier: 3.568A pdb=" N VAL C 226 " --> pdb=" O LEU C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 231 Processing helix chain 'C' and resid 232 through 236 Processing helix chain 'C' and resid 253 through 257 removed outlier: 3.887A pdb=" N GLN C 256 " --> pdb=" O GLY C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 271 Processing helix chain 'C' and resid 289 through 308 removed outlier: 5.010A pdb=" N ALA C 295 " --> pdb=" O ASP C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 353 Processing helix chain 'C' and resid 356 through 365 Processing helix chain 'C' and resid 370 through 375 removed outlier: 3.876A pdb=" N THR C 374 " --> pdb=" O ILE C 370 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA C 375 " --> pdb=" O TYR C 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 370 through 375' Processing helix chain 'C' and resid 385 through 389 removed outlier: 3.562A pdb=" N VAL C 389 " --> pdb=" O PRO C 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 49 removed outlier: 3.701A pdb=" N CYS D 34 " --> pdb=" O PRO D 30 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLN D 48 " --> pdb=" O ALA D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 91 Processing helix chain 'D' and resid 151 through 170 removed outlier: 3.754A pdb=" N ALA D 157 " --> pdb=" O THR D 153 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N HIS D 158 " --> pdb=" O ILE D 154 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG D 169 " --> pdb=" O ALA D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 225 Processing helix chain 'D' and resid 226 through 231 Processing helix chain 'D' and resid 232 through 236 Processing helix chain 'D' and resid 253 through 258 Processing helix chain 'D' and resid 265 through 270 Processing helix chain 'D' and resid 289 through 308 Processing helix chain 'D' and resid 341 through 353 Processing helix chain 'D' and resid 356 through 365 Processing helix chain 'D' and resid 370 through 374 Processing helix chain 'D' and resid 385 through 389 Processing helix chain 'E' and resid 38 through 50 Processing helix chain 'E' and resid 74 through 86 removed outlier: 4.168A pdb=" N HIS E 83 " --> pdb=" O HIS E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 103 Processing helix chain 'E' and resid 105 through 124 removed outlier: 3.855A pdb=" N ALA E 109 " --> pdb=" O GLN E 105 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL E 114 " --> pdb=" O SER E 110 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA E 116 " --> pdb=" O LEU E 112 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N SER E 117 " --> pdb=" O ASN E 113 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA E 121 " --> pdb=" O SER E 117 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS E 122 " --> pdb=" O GLY E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 127 No H-bonds generated for 'chain 'E' and resid 125 through 127' Processing helix chain 'E' and resid 138 through 140 No H-bonds generated for 'chain 'E' and resid 138 through 140' Processing helix chain 'E' and resid 157 through 174 Processing helix chain 'E' and resid 191 through 194 removed outlier: 3.703A pdb=" N GLU E 194 " --> pdb=" O LYS E 191 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 191 through 194' Processing helix chain 'E' and resid 195 through 200 removed outlier: 4.446A pdb=" N MET E 200 " --> pdb=" O ALA E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 200 through 206 Processing helix chain 'E' and resid 224 through 239 Processing helix chain 'E' and resid 257 through 269 removed outlier: 3.670A pdb=" N ALA E 266 " --> pdb=" O ALA E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 303 removed outlier: 3.654A pdb=" N LEU E 303 " --> pdb=" O LYS E 299 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 320 removed outlier: 4.191A pdb=" N LYS E 316 " --> pdb=" O ARG E 312 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER E 318 " --> pdb=" O GLY E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 328 Processing helix chain 'F' and resid 38 through 50 Processing helix chain 'F' and resid 74 through 86 Processing helix chain 'F' and resid 98 through 103 Processing helix chain 'F' and resid 105 through 114 Processing helix chain 'F' and resid 114 through 128 Processing helix chain 'F' and resid 138 through 140 No H-bonds generated for 'chain 'F' and resid 138 through 140' Processing helix chain 'F' and resid 157 through 174 Processing helix chain 'F' and resid 191 through 194 Processing helix chain 'F' and resid 195 through 200 Processing helix chain 'F' and resid 200 through 206 Processing helix chain 'F' and resid 224 through 241 removed outlier: 3.665A pdb=" N LEU F 240 " --> pdb=" O GLU F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 257 through 269 Processing helix chain 'F' and resid 297 through 303 Processing helix chain 'F' and resid 310 through 320 removed outlier: 4.546A pdb=" N LYS F 316 " --> pdb=" O ARG F 312 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N TRP F 320 " --> pdb=" O LYS F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 328 removed outlier: 3.532A pdb=" N TRP F 328 " --> pdb=" O ILE F 324 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 17 through 25 removed outlier: 6.049A pdb=" N ARG B 177 " --> pdb=" O HIS B 209 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N HIS B 209 " --> pdb=" O ARG B 177 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ASP B 179 " --> pdb=" O VAL B 207 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL B 207 " --> pdb=" O ASP B 179 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LYS B 181 " --> pdb=" O ILE B 205 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ILE B 205 " --> pdb=" O LYS B 181 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLN B 183 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ILE B 203 " --> pdb=" O GLN B 183 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N THR B 185 " --> pdb=" O HIS B 201 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ARG B 199 " --> pdb=" O GLN B 187 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N MET B 189 " --> pdb=" O PRO B 197 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ASP B 191 " --> pdb=" O VAL B 195 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N VAL B 195 " --> pdb=" O ASP B 191 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N ILE B 241 " --> pdb=" O ARG B 199 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N HIS B 201 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N HIS B 243 " --> pdb=" O HIS B 201 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ILE B 203 " --> pdb=" O HIS B 243 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 107 through 108 removed outlier: 6.327A pdb=" N ILE B 65 " --> pdb=" O LEU B 107 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 107 through 108 removed outlier: 6.327A pdb=" N ILE B 65 " --> pdb=" O LEU B 107 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 93 through 94 removed outlier: 3.746A pdb=" N PHE B 99 " --> pdb=" O ASP B 94 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 136 through 143 removed outlier: 3.684A pdb=" N VAL B 314 " --> pdb=" O ALA B 142 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER B 329 " --> pdb=" O SER B 319 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 17 through 25 removed outlier: 3.667A pdb=" N VAL A 184 " --> pdb=" O SER A 22 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ASP A 179 " --> pdb=" O GLN A 208 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N GLN A 187 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N VAL A 200 " --> pdb=" O GLN A 187 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N MET A 189 " --> pdb=" O ILE A 198 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE A 198 " --> pdb=" O MET A 189 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ASP A 191 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LEU A 196 " --> pdb=" O ASP A 191 " (cutoff:3.500A) removed outlier: 9.323A pdb=" N ILE A 241 " --> pdb=" O ARG A 199 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N HIS A 201 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N HIS A 243 " --> pdb=" O HIS A 201 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ILE A 203 " --> pdb=" O HIS A 243 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 105 through 113 removed outlier: 3.744A pdb=" N GLY A 69 " --> pdb=" O ALA A 109 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE A 71 " --> pdb=" O GLU A 111 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 93 through 94 removed outlier: 3.626A pdb=" N PHE A 99 " --> pdb=" O ASP A 94 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 136 through 143 removed outlier: 3.939A pdb=" N SER A 329 " --> pdb=" O SER A 319 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 17 through 25 removed outlier: 3.670A pdb=" N SER C 24 " --> pdb=" O THR C 182 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 17 through 25 removed outlier: 3.670A pdb=" N SER C 24 " --> pdb=" O THR C 182 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ARG C 177 " --> pdb=" O HIS C 209 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N HIS C 209 " --> pdb=" O ARG C 177 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N ASP C 179 " --> pdb=" O VAL C 207 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N VAL C 207 " --> pdb=" O ASP C 179 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LYS C 181 " --> pdb=" O ILE C 205 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ILE C 205 " --> pdb=" O LYS C 181 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N GLN C 183 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ILE C 203 " --> pdb=" O GLN C 183 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N THR C 185 " --> pdb=" O HIS C 201 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG C 199 " --> pdb=" O GLN C 187 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 53 through 54 removed outlier: 6.236A pdb=" N ILE C 71 " --> pdb=" O GLN C 113 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 64 through 68 Processing sheet with id=AB5, first strand: chain 'C' and resid 93 through 94 Processing sheet with id=AB6, first strand: chain 'C' and resid 136 through 143 Processing sheet with id=AB7, first strand: chain 'D' and resid 17 through 25 removed outlier: 3.650A pdb=" N PHE D 20 " --> pdb=" O VAL D 186 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LYS D 181 " --> pdb=" O VAL D 204 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL D 204 " --> pdb=" O LYS D 181 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLN D 183 " --> pdb=" O THR D 202 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N THR D 202 " --> pdb=" O GLN D 183 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N THR D 185 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N VAL D 200 " --> pdb=" O THR D 185 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N GLN D 187 " --> pdb=" O ILE D 198 " (cutoff:3.500A) removed outlier: 9.099A pdb=" N ILE D 241 " --> pdb=" O ARG D 199 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N HIS D 201 " --> pdb=" O ILE D 241 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N HIS D 243 " --> pdb=" O HIS D 201 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ILE D 203 " --> pdb=" O HIS D 243 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 105 through 108 removed outlier: 5.916A pdb=" N ILE D 65 " --> pdb=" O LEU D 107 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 105 through 108 removed outlier: 5.916A pdb=" N ILE D 65 " --> pdb=" O LEU D 107 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 93 through 94 Processing sheet with id=AC2, first strand: chain 'D' and resid 136 through 143 removed outlier: 3.658A pdb=" N GLY D 136 " --> pdb=" O TYR D 320 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER D 319 " --> pdb=" O SER D 329 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER D 329 " --> pdb=" O SER D 319 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 8 through 13 Processing sheet with id=AC4, first strand: chain 'E' and resid 68 through 69 removed outlier: 8.775A pdb=" N GLU E 68 " --> pdb=" O ALA E 55 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N GLY E 57 " --> pdb=" O GLU E 68 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ARG E 30 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N VAL E 91 " --> pdb=" O ARG E 30 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LEU E 32 " --> pdb=" O VAL E 91 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE E 134 " --> pdb=" O HIS E 92 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 185 through 186 Processing sheet with id=AC6, first strand: chain 'E' and resid 211 through 214 Processing sheet with id=AC7, first strand: chain 'F' and resid 8 through 13 Processing sheet with id=AC8, first strand: chain 'F' and resid 68 through 69 removed outlier: 6.240A pdb=" N VAL F 179 " --> pdb=" O PHE F 248 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 185 through 186 Processing sheet with id=AD1, first strand: chain 'F' and resid 211 through 214 removed outlier: 6.406A pdb=" N ALA F 211 " --> pdb=" O ARG F 277 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE F 279 " --> pdb=" O ALA F 211 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N MET F 213 " --> pdb=" O ILE F 279 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 734 hydrogen bonds defined for protein. 2052 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.84 Time building geometry restraints manager: 1.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3338 1.33 - 1.45: 4003 1.45 - 1.57: 9697 1.57 - 1.69: 0 1.69 - 1.81: 96 Bond restraints: 17134 Sorted by residual: bond pdb=" CA SER A 24 " pdb=" CB SER A 24 " ideal model delta sigma weight residual 1.533 1.438 0.095 1.66e-02 3.63e+03 3.30e+01 bond pdb=" CA SER A 283 " pdb=" CB SER A 283 " ideal model delta sigma weight residual 1.529 1.435 0.093 1.66e-02 3.63e+03 3.17e+01 bond pdb=" CA SER A 22 " pdb=" CB SER A 22 " ideal model delta sigma weight residual 1.531 1.457 0.074 1.83e-02 2.99e+03 1.65e+01 bond pdb=" N THR F 331 " pdb=" CA THR F 331 " ideal model delta sigma weight residual 1.455 1.498 -0.043 1.21e-02 6.83e+03 1.24e+01 bond pdb=" N PHE A 20 " pdb=" CA PHE A 20 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.20e-02 6.94e+03 1.16e+01 ... (remaining 17129 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 22792 2.30 - 4.59: 369 4.59 - 6.89: 31 6.89 - 9.18: 7 9.18 - 11.48: 1 Bond angle restraints: 23200 Sorted by residual: angle pdb=" C THR A 21 " pdb=" CA THR A 21 " pdb=" CB THR A 21 " ideal model delta sigma weight residual 109.48 100.43 9.05 1.68e+00 3.54e-01 2.90e+01 angle pdb=" CA TYR A 377 " pdb=" C TYR A 377 " pdb=" O TYR A 377 " ideal model delta sigma weight residual 121.28 114.92 6.36 1.19e+00 7.06e-01 2.85e+01 angle pdb=" C GLU A 23 " pdb=" CA GLU A 23 " pdb=" CB GLU A 23 " ideal model delta sigma weight residual 111.78 100.30 11.48 2.20e+00 2.07e-01 2.72e+01 angle pdb=" C ASN A 161 " pdb=" CA ASN A 161 " pdb=" CB ASN A 161 " ideal model delta sigma weight residual 110.81 118.97 -8.16 1.60e+00 3.91e-01 2.60e+01 angle pdb=" N THR C 288 " pdb=" CA THR C 288 " pdb=" C THR C 288 " ideal model delta sigma weight residual 111.07 106.15 4.92 1.07e+00 8.73e-01 2.11e+01 ... (remaining 23195 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 9260 17.64 - 35.28: 818 35.28 - 52.92: 171 52.92 - 70.55: 38 70.55 - 88.19: 23 Dihedral angle restraints: 10310 sinusoidal: 4153 harmonic: 6157 Sorted by residual: dihedral pdb=" C THR A 21 " pdb=" N THR A 21 " pdb=" CA THR A 21 " pdb=" CB THR A 21 " ideal model delta harmonic sigma weight residual -122.00 -109.20 -12.80 0 2.50e+00 1.60e-01 2.62e+01 dihedral pdb=" N THR A 21 " pdb=" C THR A 21 " pdb=" CA THR A 21 " pdb=" CB THR A 21 " ideal model delta harmonic sigma weight residual 123.40 113.25 10.15 0 2.50e+00 1.60e-01 1.65e+01 dihedral pdb=" CA LYS E 66 " pdb=" C LYS E 66 " pdb=" N PHE E 67 " pdb=" CA PHE E 67 " ideal model delta harmonic sigma weight residual -180.00 -161.49 -18.51 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 10307 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2168 0.064 - 0.127: 376 0.127 - 0.190: 19 0.190 - 0.254: 5 0.254 - 0.317: 1 Chirality restraints: 2569 Sorted by residual: chirality pdb=" CA THR A 21 " pdb=" N THR A 21 " pdb=" C THR A 21 " pdb=" CB THR A 21 " both_signs ideal model delta sigma weight residual False 2.53 2.84 -0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" CG LEU C 137 " pdb=" CB LEU C 137 " pdb=" CD1 LEU C 137 " pdb=" CD2 LEU C 137 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.22 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA SER A 22 " pdb=" N SER A 22 " pdb=" C SER A 22 " pdb=" CB SER A 22 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 2566 not shown) Planarity restraints: 3022 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 19 " -0.017 2.00e-02 2.50e+03 3.34e-02 1.11e+01 pdb=" C LEU A 19 " 0.058 2.00e-02 2.50e+03 pdb=" O LEU A 19 " -0.022 2.00e-02 2.50e+03 pdb=" N PHE A 20 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 286 " -0.011 2.00e-02 2.50e+03 2.29e-02 5.26e+00 pdb=" C ASP C 286 " 0.040 2.00e-02 2.50e+03 pdb=" O ASP C 286 " -0.015 2.00e-02 2.50e+03 pdb=" N TYR C 287 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 365 " -0.011 2.00e-02 2.50e+03 2.25e-02 5.06e+00 pdb=" C ASP C 365 " 0.039 2.00e-02 2.50e+03 pdb=" O ASP C 365 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU C 366 " -0.013 2.00e-02 2.50e+03 ... (remaining 3019 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1782 2.74 - 3.28: 17536 3.28 - 3.82: 29117 3.82 - 4.36: 35023 4.36 - 4.90: 59290 Nonbonded interactions: 142748 Sorted by model distance: nonbonded pdb=" NZ LYS C 285 " pdb=" OD2 ASP C 291 " model vdw 2.200 3.120 nonbonded pdb=" O ASP E 100 " pdb=" ND2 ASN E 104 " model vdw 2.210 3.120 nonbonded pdb=" O ASN C 352 " pdb=" NZ LYS C 391 " model vdw 2.220 3.120 nonbonded pdb=" OG1 THR B 21 " pdb=" OG1 THR B 185 " model vdw 2.227 3.040 nonbonded pdb=" OD1 ASP E 141 " pdb=" OH TYR E 147 " model vdw 2.245 3.040 ... (remaining 142743 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 13 through 114 or resid 128 through 395)) selection = (chain 'C' and (resid 13 through 114 or resid 128 through 395)) selection = (chain 'D' and (resid 13 through 114 or resid 128 through 395)) } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.270 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: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 16.980 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.030 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:1.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 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 : 0.005 0.095 17134 Z= 0.247 Angle : 0.714 11.477 23200 Z= 0.420 Chirality : 0.046 0.317 2569 Planarity : 0.004 0.045 3022 Dihedral : 14.825 88.192 6360 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.39 % Favored : 96.56 % Rotamer: Outliers : 2.00 % Allowed : 13.97 % Favored : 84.03 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 4.12 % 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: -0.33 (0.18), residues: 2125 helix: 0.36 (0.19), residues: 684 sheet: -0.28 (0.26), residues: 414 loop : -0.48 (0.19), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 74 TYR 0.018 0.002 TYR A 141 PHE 0.017 0.002 PHE E 67 TRP 0.015 0.002 TRP F 216 HIS 0.006 0.001 HIS D 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.25 (17134) covalent geometry : angle 0.71380 / 0.42 (23200) hydrogen bonds : bond 0.23535 / 15.81 ( 727) hydrogen bonds : angle 8.05694 / 5.65 ( 2052) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4250 Ramachandran restraints generated. 2125 Oldfield, 0 Emsley, 2125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4250 Ramachandran restraints generated. 2125 Oldfield, 0 Emsley, 2125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 165 time to evaluate : 0.634 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 58 THR cc_start: 0.9279 (m) cc_final: 0.8979 (m) REVERT: D 245 GLN cc_start: 0.7181 (OUTLIER) cc_final: 0.6687 (tm-30) REVERT: F 61 ARG cc_start: 0.3044 (mtt-85) cc_final: 0.2783 (ttp-170) REVERT: F 256 MET cc_start: 0.6974 (ppp) cc_final: 0.6609 (ppp) REVERT: F 328 TRP cc_start: 0.7280 (m100) cc_final: 0.6665 (m100) outliers start: 36 outliers final: 25 residues processed: 188 average time/residue: 0.1337 time to fit residues: 38.6265 Evaluate side-chains 186 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 160 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 161 ASN Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain C residue 218 MET Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 245 GLN Chi-restraints excluded: chain D residue 303 LYS Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 213 MET Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain F residue 5 GLU Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 280 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 20.0000 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 6.9990 chunk 212 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN A 161 ASN A 379 HIS ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.168486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.123743 restraints weight = 38091.252| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 5.60 r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.1009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17134 Z= 0.181 Angle : 0.610 8.813 23200 Z= 0.327 Chirality : 0.046 0.153 2569 Planarity : 0.004 0.043 3022 Dihedral : 6.235 58.479 2381 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.45 % Allowed : 12.47 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.12 % 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: -0.20 (0.18), residues: 2125 helix: 0.65 (0.19), residues: 703 sheet: -0.31 (0.25), residues: 427 loop : -0.51 (0.19), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 362 TYR 0.017 0.002 TYR F 259 PHE 0.014 0.002 PHE D 250 TRP 0.016 0.001 TRP A 300 HIS 0.007 0.001 HIS D 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.18 (17134) covalent geometry : angle 0.60953 / 0.33 (23200) hydrogen bonds : bond 0.04837 / 3.16 ( 727) hydrogen bonds : angle 5.70856 / 4.03 ( 2052) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4250 Ramachandran restraints generated. 2125 Oldfield, 0 Emsley, 2125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4250 Ramachandran restraints generated. 2125 Oldfield, 0 Emsley, 2125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 175 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 THR cc_start: 0.9276 (m) cc_final: 0.9009 (m) REVERT: C 240 THR cc_start: 0.6640 (m) cc_final: 0.6298 (p) REVERT: C 249 ARG cc_start: 0.7281 (OUTLIER) cc_final: 0.7062 (tpp-160) REVERT: D 57 GLU cc_start: 0.7512 (mm-30) cc_final: 0.7120 (mm-30) REVERT: D 245 GLN cc_start: 0.7509 (OUTLIER) cc_final: 0.6799 (tm-30) REVERT: E 21 GLU cc_start: 0.8935 (OUTLIER) cc_final: 0.8613 (pm20) REVERT: F 61 ARG cc_start: 0.3074 (mtt-85) cc_final: 0.2829 (ttp-170) REVERT: F 213 MET cc_start: 0.8879 (mmt) cc_final: 0.8504 (ptp) REVERT: F 218 GLN cc_start: 0.7082 (OUTLIER) cc_final: 0.6606 (tp40) REVERT: F 256 MET cc_start: 0.6926 (ppp) cc_final: 0.6229 (pmm) REVERT: F 257 THR cc_start: 0.7588 (p) cc_final: 0.7383 (t) REVERT: F 328 TRP cc_start: 0.7306 (m100) cc_final: 0.6682 (m100) outliers start: 44 outliers final: 20 residues processed: 208 average time/residue: 0.1342 time to fit residues: 42.9545 Evaluate side-chains 181 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 157 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 317 GLN Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 249 ARG Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 245 GLN Chi-restraints excluded: chain D residue 256 GLN Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 213 MET Chi-restraints excluded: chain F residue 218 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 118 optimal weight: 4.9990 chunk 90 optimal weight: 0.7980 chunk 74 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 77 optimal weight: 8.9990 chunk 86 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 213 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 ASN ** E 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 119 ASN ** F 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.170434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.126183 restraints weight = 38691.125| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 5.59 r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17134 Z= 0.118 Angle : 0.546 8.654 23200 Z= 0.288 Chirality : 0.044 0.153 2569 Planarity : 0.004 0.047 3022 Dihedral : 5.256 57.715 2352 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.34 % Allowed : 13.19 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.12 % 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: 0.03 (0.18), residues: 2125 helix: 0.84 (0.19), residues: 711 sheet: -0.15 (0.26), residues: 419 loop : -0.40 (0.20), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 362 TYR 0.019 0.001 TYR F 259 PHE 0.013 0.001 PHE F 12 TRP 0.013 0.001 TRP A 300 HIS 0.004 0.001 HIS D 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (17134) covalent geometry : angle 0.54555 / 0.29 (23200) hydrogen bonds : bond 0.03877 / 2.55 ( 727) hydrogen bonds : angle 5.19297 / 3.66 ( 2052) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4250 Ramachandran restraints generated. 2125 Oldfield, 0 Emsley, 2125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4250 Ramachandran restraints generated. 2125 Oldfield, 0 Emsley, 2125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 195 time to evaluate : 0.804 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 58 THR cc_start: 0.9260 (m) cc_final: 0.9001 (m) REVERT: A 189 MET cc_start: 0.7926 (mtp) cc_final: 0.7519 (mtp) REVERT: C 160 LEU cc_start: 0.8941 (mp) cc_final: 0.8715 (tt) REVERT: C 188 TYR cc_start: 0.6920 (m-80) cc_final: 0.6579 (m-80) REVERT: C 249 ARG cc_start: 0.7341 (OUTLIER) cc_final: 0.7101 (tpp-160) REVERT: C 392 LYS cc_start: 0.8942 (mmtm) cc_final: 0.8351 (tptt) REVERT: D 245 GLN cc_start: 0.7517 (OUTLIER) cc_final: 0.6788 (tm-30) REVERT: F 61 ARG cc_start: 0.3112 (mtt-85) cc_final: 0.2793 (ttp-170) REVERT: F 218 GLN cc_start: 0.6871 (OUTLIER) cc_final: 0.6235 (tp40) REVERT: F 256 MET cc_start: 0.6919 (OUTLIER) cc_final: 0.6573 (pmm) REVERT: F 328 TRP cc_start: 0.7305 (m100) cc_final: 0.6657 (m100) outliers start: 42 outliers final: 22 residues processed: 218 average time/residue: 0.1320 time to fit residues: 44.3911 Evaluate side-chains 194 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 168 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 317 GLN Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain C residue 218 MET Chi-restraints excluded: chain C residue 249 ARG Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 245 GLN Chi-restraints excluded: chain D residue 256 GLN Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 213 MET Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 218 GLN Chi-restraints excluded: chain F residue 256 MET Chi-restraints excluded: chain F residue 280 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 4 optimal weight: 4.9990 chunk 199 optimal weight: 20.0000 chunk 132 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 134 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 80 optimal weight: 6.9990 chunk 117 optimal weight: 9.9990 chunk 33 optimal weight: 0.8980 chunk 146 optimal weight: 8.9990 chunk 211 optimal weight: 9.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 372 GLN ** E 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 11 HIS ** F 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 233 GLN ** F 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.162517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.116534 restraints weight = 36816.140| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 5.57 r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 17134 Z= 0.331 Angle : 0.705 8.365 23200 Z= 0.376 Chirality : 0.048 0.166 2569 Planarity : 0.005 0.053 3022 Dihedral : 5.803 54.766 2349 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.56 % Allowed : 14.36 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.12 % 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: -0.49 (0.18), residues: 2125 helix: 0.39 (0.19), residues: 704 sheet: -0.40 (0.25), residues: 425 loop : -0.72 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 362 TYR 0.025 0.002 TYR A 141 PHE 0.019 0.002 PHE D 353 TRP 0.019 0.002 TRP D 274 HIS 0.013 0.002 HIS C 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00742 / 0.33 (17134) covalent geometry : angle 0.70455 / 0.38 (23200) hydrogen bonds : bond 0.04923 / 3.19 ( 727) hydrogen bonds : angle 5.60447 / 3.96 ( 2052) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4250 Ramachandran restraints generated. 2125 Oldfield, 0 Emsley, 2125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4250 Ramachandran restraints generated. 2125 Oldfield, 0 Emsley, 2125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 166 time to evaluate : 0.676 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: B 128 GLU cc_start: 0.7040 (OUTLIER) cc_final: 0.6138 (mm-30) REVERT: A 58 THR cc_start: 0.9290 (m) cc_final: 0.9076 (m) REVERT: A 70 GLU cc_start: 0.8121 (mp0) cc_final: 0.7909 (mp0) REVERT: A 145 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.8096 (pp20) REVERT: A 189 MET cc_start: 0.8112 (mtp) cc_final: 0.7647 (mtp) REVERT: A 258 ASP cc_start: 0.6978 (t0) cc_final: 0.6680 (t0) REVERT: C 249 ARG cc_start: 0.7347 (OUTLIER) cc_final: 0.7054 (tpp-160) REVERT: C 392 LYS cc_start: 0.9000 (mmtm) cc_final: 0.8747 (mmtm) REVERT: D 57 GLU cc_start: 0.7697 (mm-30) cc_final: 0.7327 (mm-30) REVERT: D 150 MET cc_start: 0.8141 (tpp) cc_final: 0.7733 (tpp) REVERT: D 245 GLN cc_start: 0.7645 (OUTLIER) cc_final: 0.6880 (tm-30) REVERT: D 271 TYR cc_start: 0.8754 (OUTLIER) cc_final: 0.8442 (m-80) REVERT: E 21 GLU cc_start: 0.8977 (OUTLIER) cc_final: 0.8569 (pm20) REVERT: E 188 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7532 (tp30) REVERT: F 61 ARG cc_start: 0.2964 (mtt-85) cc_final: 0.2719 (ttp-170) REVERT: F 213 MET cc_start: 0.8743 (mmt) cc_final: 0.8447 (ptp) REVERT: F 259 TYR cc_start: 0.8179 (t80) cc_final: 0.7343 (t80) REVERT: F 328 TRP cc_start: 0.7379 (m100) cc_final: 0.6728 (m100) outliers start: 64 outliers final: 36 residues processed: 213 average time/residue: 0.1258 time to fit residues: 41.7662 Evaluate side-chains 196 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 154 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 317 GLN Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain C residue 104 CYS Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 218 MET Chi-restraints excluded: chain C residue 249 ARG Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 245 GLN Chi-restraints excluded: chain D residue 256 GLN Chi-restraints excluded: chain D residue 271 TYR Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 218 GLN Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 280 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 213 optimal weight: 0.9980 chunk 210 optimal weight: 5.9990 chunk 68 optimal weight: 0.0980 chunk 151 optimal weight: 9.9990 chunk 85 optimal weight: 0.9990 chunk 209 optimal weight: 6.9990 chunk 144 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 93 optimal weight: 7.9990 chunk 208 optimal weight: 20.0000 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 255 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 = 0.4420 r_free = 0.4420 target = 0.169592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.123776 restraints weight = 38078.101| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 5.50 r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17134 Z= 0.123 Angle : 0.573 11.424 23200 Z= 0.297 Chirality : 0.044 0.188 2569 Planarity : 0.004 0.050 3022 Dihedral : 5.213 57.134 2346 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.34 % Allowed : 15.14 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.12 % 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: -0.04 (0.18), residues: 2125 helix: 0.84 (0.19), residues: 712 sheet: -0.15 (0.26), residues: 419 loop : -0.53 (0.20), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 219 TYR 0.015 0.001 TYR D 320 PHE 0.025 0.001 PHE F 220 TRP 0.016 0.001 TRP F 216 HIS 0.005 0.001 HIS D 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (17134) covalent geometry : angle 0.57268 / 0.30 (23200) hydrogen bonds : bond 0.03689 / 2.42 ( 727) hydrogen bonds : angle 5.11980 / 3.62 ( 2052) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4250 Ramachandran restraints generated. 2125 Oldfield, 0 Emsley, 2125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4250 Ramachandran restraints generated. 2125 Oldfield, 0 Emsley, 2125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 173 time to evaluate : 0.664 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 58 THR cc_start: 0.9244 (m) cc_final: 0.9016 (m) REVERT: A 150 MET cc_start: 0.6360 (mmm) cc_final: 0.6142 (mmm) REVERT: A 189 MET cc_start: 0.7930 (mtp) cc_final: 0.7511 (mtp) REVERT: C 240 THR cc_start: 0.6503 (m) cc_final: 0.6095 (p) REVERT: C 249 ARG cc_start: 0.7355 (OUTLIER) cc_final: 0.7145 (tpp-160) REVERT: C 392 LYS cc_start: 0.8930 (mmtm) cc_final: 0.8676 (mmtm) REVERT: D 57 GLU cc_start: 0.7515 (mm-30) cc_final: 0.7196 (mm-30) REVERT: D 245 GLN cc_start: 0.7628 (OUTLIER) cc_final: 0.6822 (tm-30) REVERT: D 334 HIS cc_start: 0.7204 (p90) cc_final: 0.6694 (p90) REVERT: D 342 GLU cc_start: 0.8845 (tm-30) cc_final: 0.8621 (tm-30) REVERT: E 21 GLU cc_start: 0.8949 (OUTLIER) cc_final: 0.8537 (pm20) REVERT: E 188 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7585 (tp30) REVERT: E 213 MET cc_start: 0.7537 (mpp) cc_final: 0.6696 (pmm) REVERT: F 12 PHE cc_start: 0.5083 (t80) cc_final: 0.4660 (t80) REVERT: F 61 ARG cc_start: 0.3016 (mtt-85) cc_final: 0.2773 (ttp-170) REVERT: F 328 TRP cc_start: 0.7324 (m100) cc_final: 0.6623 (m100) outliers start: 42 outliers final: 24 residues processed: 200 average time/residue: 0.1338 time to fit residues: 41.0052 Evaluate side-chains 194 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 167 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 317 GLN Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 218 MET Chi-restraints excluded: chain C residue 249 ARG Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 245 GLN Chi-restraints excluded: chain D residue 256 GLN Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 280 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 121 optimal weight: 0.0020 chunk 57 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 181 optimal weight: 8.9990 chunk 210 optimal weight: 8.9990 chunk 183 optimal weight: 5.9990 chunk 142 optimal weight: 5.9990 chunk 163 optimal weight: 40.0000 chunk 179 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 overall best weight: 2.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 255 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 = 0.4401 r_free = 0.4401 target = 0.168088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.122724 restraints weight = 38659.164| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 5.83 r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17134 Z= 0.186 Angle : 0.597 13.062 23200 Z= 0.311 Chirality : 0.045 0.174 2569 Planarity : 0.004 0.059 3022 Dihedral : 5.267 59.119 2346 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.56 % Allowed : 15.03 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.12 % 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: -0.09 (0.18), residues: 2125 helix: 0.86 (0.19), residues: 710 sheet: -0.24 (0.25), residues: 429 loop : -0.57 (0.20), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 362 TYR 0.015 0.002 TYR E 138 PHE 0.012 0.001 PHE F 220 TRP 0.016 0.001 TRP F 216 HIS 0.006 0.001 HIS C 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.19 (17134) covalent geometry : angle 0.59684 / 0.31 (23200) hydrogen bonds : bond 0.03829 / 2.49 ( 727) hydrogen bonds : angle 5.14259 / 3.64 ( 2052) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4250 Ramachandran restraints generated. 2125 Oldfield, 0 Emsley, 2125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4250 Ramachandran restraints generated. 2125 Oldfield, 0 Emsley, 2125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 174 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 128 GLU cc_start: 0.6938 (OUTLIER) cc_final: 0.6113 (mm-30) REVERT: A 58 THR cc_start: 0.9249 (m) cc_final: 0.9038 (m) REVERT: A 189 MET cc_start: 0.7999 (mtp) cc_final: 0.7229 (mmm) REVERT: A 258 ASP cc_start: 0.6873 (t70) cc_final: 0.6616 (t0) REVERT: C 240 THR cc_start: 0.6546 (m) cc_final: 0.6167 (p) REVERT: C 392 LYS cc_start: 0.8989 (mmtm) cc_final: 0.8415 (tptt) REVERT: D 57 GLU cc_start: 0.7569 (mm-30) cc_final: 0.7160 (mm-30) REVERT: D 245 GLN cc_start: 0.7627 (OUTLIER) cc_final: 0.6796 (tm-30) REVERT: D 342 GLU cc_start: 0.8919 (tm-30) cc_final: 0.8672 (tm-30) REVERT: E 21 GLU cc_start: 0.8974 (OUTLIER) cc_final: 0.8419 (pm20) REVERT: E 188 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7666 (tp30) REVERT: F 12 PHE cc_start: 0.5243 (t80) cc_final: 0.4888 (t80) REVERT: F 61 ARG cc_start: 0.2958 (mtt-85) cc_final: 0.2725 (ttp-170) REVERT: F 328 TRP cc_start: 0.7328 (m100) cc_final: 0.6621 (m100) outliers start: 46 outliers final: 29 residues processed: 205 average time/residue: 0.1323 time to fit residues: 42.2505 Evaluate side-chains 193 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 161 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 317 GLN Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 218 MET Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 245 GLN Chi-restraints excluded: chain D residue 256 GLN Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 280 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 190 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 209 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 111 optimal weight: 6.9990 chunk 61 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 133 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 188 optimal weight: 4.9990 chunk 137 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 372 GLN ** E 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 255 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 = 0.4425 r_free = 0.4425 target = 0.169971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.122685 restraints weight = 38622.328| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 6.50 r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17134 Z= 0.122 Angle : 0.572 14.222 23200 Z= 0.294 Chirality : 0.044 0.177 2569 Planarity : 0.004 0.056 3022 Dihedral : 5.070 57.907 2345 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.00 % Allowed : 15.75 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.12 % 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: 0.14 (0.18), residues: 2125 helix: 1.08 (0.20), residues: 711 sheet: -0.05 (0.26), residues: 421 loop : -0.49 (0.20), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 362 TYR 0.015 0.001 TYR E 259 PHE 0.024 0.001 PHE F 206 TRP 0.017 0.001 TRP F 216 HIS 0.004 0.001 HIS D 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (17134) covalent geometry : angle 0.57196 / 0.29 (23200) hydrogen bonds : bond 0.03433 / 2.26 ( 727) hydrogen bonds : angle 4.98260 / 3.52 ( 2052) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4250 Ramachandran restraints generated. 2125 Oldfield, 0 Emsley, 2125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4250 Ramachandran restraints generated. 2125 Oldfield, 0 Emsley, 2125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 177 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 128 GLU cc_start: 0.6912 (OUTLIER) cc_final: 0.6130 (mm-30) REVERT: A 58 THR cc_start: 0.9245 (m) cc_final: 0.9017 (m) REVERT: A 188 TYR cc_start: 0.7882 (m-80) cc_final: 0.7666 (m-80) REVERT: A 189 MET cc_start: 0.7844 (mtp) cc_final: 0.7137 (mmm) REVERT: C 240 THR cc_start: 0.6533 (m) cc_final: 0.6183 (p) REVERT: C 392 LYS cc_start: 0.8968 (mmtm) cc_final: 0.8452 (tptt) REVERT: D 57 GLU cc_start: 0.7544 (mm-30) cc_final: 0.7105 (mm-30) REVERT: D 334 HIS cc_start: 0.7197 (p90) cc_final: 0.6679 (p90) REVERT: D 342 GLU cc_start: 0.8967 (tm-30) cc_final: 0.8739 (tm-30) REVERT: E 21 GLU cc_start: 0.8932 (OUTLIER) cc_final: 0.8553 (pm20) REVERT: E 188 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7509 (tp30) REVERT: F 12 PHE cc_start: 0.5140 (t80) cc_final: 0.4761 (t80) REVERT: F 261 MET cc_start: 0.9363 (ppp) cc_final: 0.8891 (pmm) REVERT: F 328 TRP cc_start: 0.7350 (m100) cc_final: 0.6660 (m100) outliers start: 36 outliers final: 24 residues processed: 199 average time/residue: 0.1390 time to fit residues: 42.0349 Evaluate side-chains 192 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 166 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 317 GLN Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 256 GLN Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 213 MET Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 280 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 114 optimal weight: 0.9990 chunk 161 optimal weight: 50.0000 chunk 126 optimal weight: 10.0000 chunk 138 optimal weight: 9.9990 chunk 100 optimal weight: 4.9990 chunk 89 optimal weight: 0.3980 chunk 22 optimal weight: 5.9990 chunk 111 optimal weight: 6.9990 chunk 152 optimal weight: 7.9990 chunk 95 optimal weight: 0.2980 chunk 55 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 255 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 = 0.4408 r_free = 0.4408 target = 0.168320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.121642 restraints weight = 38913.312| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 5.75 r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17134 Z= 0.160 Angle : 0.592 11.956 23200 Z= 0.306 Chirality : 0.044 0.223 2569 Planarity : 0.004 0.053 3022 Dihedral : 4.911 54.169 2342 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.00 % Allowed : 15.75 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.12 % 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: 0.11 (0.18), residues: 2125 helix: 1.03 (0.20), residues: 710 sheet: -0.04 (0.26), residues: 419 loop : -0.50 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 362 TYR 0.013 0.001 TYR F 259 PHE 0.017 0.001 PHE F 140 TRP 0.017 0.001 TRP F 216 HIS 0.005 0.001 HIS C 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (17134) covalent geometry : angle 0.59243 / 0.31 (23200) hydrogen bonds : bond 0.03599 / 2.37 ( 727) hydrogen bonds : angle 5.01406 / 3.54 ( 2052) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4250 Ramachandran restraints generated. 2125 Oldfield, 0 Emsley, 2125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4250 Ramachandran restraints generated. 2125 Oldfield, 0 Emsley, 2125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 171 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 128 GLU cc_start: 0.6832 (OUTLIER) cc_final: 0.6011 (mm-30) REVERT: A 58 THR cc_start: 0.9242 (m) cc_final: 0.9028 (m) REVERT: A 189 MET cc_start: 0.7900 (mtp) cc_final: 0.7144 (mmm) REVERT: C 240 THR cc_start: 0.6519 (m) cc_final: 0.6166 (p) REVERT: C 392 LYS cc_start: 0.8977 (mmtm) cc_final: 0.8509 (tptt) REVERT: D 57 GLU cc_start: 0.7543 (mm-30) cc_final: 0.7077 (mm-30) REVERT: D 342 GLU cc_start: 0.8956 (tm-30) cc_final: 0.8687 (tm-30) REVERT: E 21 GLU cc_start: 0.8897 (OUTLIER) cc_final: 0.8505 (pm20) REVERT: E 188 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7526 (tp30) REVERT: E 213 MET cc_start: 0.7309 (mpp) cc_final: 0.6649 (pmm) REVERT: E 259 TYR cc_start: 0.9014 (t80) cc_final: 0.8763 (t80) REVERT: F 12 PHE cc_start: 0.5228 (t80) cc_final: 0.4870 (t80) REVERT: F 213 MET cc_start: 0.8581 (mmt) cc_final: 0.8105 (ptp) REVERT: F 328 TRP cc_start: 0.7358 (m100) cc_final: 0.6663 (m100) outliers start: 36 outliers final: 26 residues processed: 196 average time/residue: 0.1306 time to fit residues: 40.0444 Evaluate side-chains 194 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 166 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 317 GLN Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 256 GLN Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 280 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 102 optimal weight: 7.9990 chunk 184 optimal weight: 40.0000 chunk 172 optimal weight: 20.0000 chunk 174 optimal weight: 40.0000 chunk 73 optimal weight: 0.9980 chunk 209 optimal weight: 9.9990 chunk 166 optimal weight: 5.9990 chunk 200 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 62 optimal weight: 0.4980 chunk 131 optimal weight: 0.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 255 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 = 0.4413 r_free = 0.4413 target = 0.168922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.123104 restraints weight = 38682.970| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 5.53 r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17134 Z= 0.146 Angle : 0.597 12.668 23200 Z= 0.304 Chirality : 0.045 0.231 2569 Planarity : 0.004 0.066 3022 Dihedral : 4.837 49.863 2342 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.89 % Allowed : 15.97 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.12 % 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: 0.13 (0.18), residues: 2125 helix: 1.07 (0.20), residues: 713 sheet: -0.04 (0.26), residues: 419 loop : -0.51 (0.20), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 219 TYR 0.016 0.001 TYR F 259 PHE 0.021 0.001 PHE F 140 TRP 0.021 0.001 TRP F 216 HIS 0.005 0.001 HIS B 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (17134) covalent geometry : angle 0.59678 / 0.30 (23200) hydrogen bonds : bond 0.03486 / 2.30 ( 727) hydrogen bonds : angle 4.98140 / 3.52 ( 2052) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4250 Ramachandran restraints generated. 2125 Oldfield, 0 Emsley, 2125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4250 Ramachandran restraints generated. 2125 Oldfield, 0 Emsley, 2125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 175 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 128 GLU cc_start: 0.6733 (OUTLIER) cc_final: 0.5902 (mm-30) REVERT: A 58 THR cc_start: 0.9230 (m) cc_final: 0.9015 (m) REVERT: A 189 MET cc_start: 0.7822 (mtp) cc_final: 0.7099 (mmm) REVERT: A 394 LYS cc_start: 0.8828 (tppt) cc_final: 0.8496 (tppt) REVERT: C 240 THR cc_start: 0.6488 (m) cc_final: 0.6145 (p) REVERT: C 392 LYS cc_start: 0.8984 (mmtm) cc_final: 0.8518 (tptt) REVERT: D 57 GLU cc_start: 0.7573 (mm-30) cc_final: 0.7089 (mm-30) REVERT: D 150 MET cc_start: 0.7167 (mmm) cc_final: 0.5936 (mmm) REVERT: D 334 HIS cc_start: 0.7246 (p90) cc_final: 0.6788 (p90) REVERT: D 342 GLU cc_start: 0.8955 (tm-30) cc_final: 0.8673 (tm-30) REVERT: E 21 GLU cc_start: 0.8883 (OUTLIER) cc_final: 0.8476 (pm20) REVERT: E 188 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7530 (tp30) REVERT: E 213 MET cc_start: 0.7611 (mpp) cc_final: 0.6744 (pmm) REVERT: F 259 TYR cc_start: 0.7557 (t80) cc_final: 0.7290 (t80) REVERT: F 328 TRP cc_start: 0.7350 (m100) cc_final: 0.6651 (m100) outliers start: 34 outliers final: 26 residues processed: 198 average time/residue: 0.1302 time to fit residues: 39.6827 Evaluate side-chains 201 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 173 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 317 GLN Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 256 GLN Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 175 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 89 optimal weight: 0.9990 chunk 134 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 108 optimal weight: 0.4980 chunk 44 optimal weight: 9.9990 chunk 30 optimal weight: 7.9990 chunk 128 optimal weight: 8.9990 chunk 181 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 175 optimal weight: 3.9990 overall best weight: 1.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 161 ASN ** E 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 255 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 = 0.4424 r_free = 0.4424 target = 0.169734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.123698 restraints weight = 38438.646| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 5.67 r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17134 Z= 0.130 Angle : 0.590 12.246 23200 Z= 0.300 Chirality : 0.044 0.224 2569 Planarity : 0.005 0.130 3022 Dihedral : 4.747 44.429 2342 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.67 % Allowed : 16.64 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.12 % 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: 0.21 (0.18), residues: 2125 helix: 1.17 (0.20), residues: 712 sheet: -0.01 (0.26), residues: 419 loop : -0.47 (0.20), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 219 TYR 0.015 0.001 TYR F 259 PHE 0.031 0.001 PHE F 206 TRP 0.021 0.001 TRP F 216 HIS 0.005 0.001 HIS B 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (17134) covalent geometry : angle 0.59006 / 0.30 (23200) hydrogen bonds : bond 0.03351 / 2.21 ( 727) hydrogen bonds : angle 4.91169 / 3.47 ( 2052) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4250 Ramachandran restraints generated. 2125 Oldfield, 0 Emsley, 2125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4250 Ramachandran restraints generated. 2125 Oldfield, 0 Emsley, 2125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 181 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 128 GLU cc_start: 0.6716 (OUTLIER) cc_final: 0.5900 (mm-30) REVERT: A 58 THR cc_start: 0.9212 (m) cc_final: 0.9002 (m) REVERT: A 189 MET cc_start: 0.7817 (mtp) cc_final: 0.7100 (mmm) REVERT: A 394 LYS cc_start: 0.8836 (tppt) cc_final: 0.8508 (tppt) REVERT: C 240 THR cc_start: 0.6485 (m) cc_final: 0.6143 (p) REVERT: C 392 LYS cc_start: 0.8948 (mmtm) cc_final: 0.8499 (tptt) REVERT: D 57 GLU cc_start: 0.7545 (mm-30) cc_final: 0.7050 (mm-30) REVERT: D 150 MET cc_start: 0.7065 (mmm) cc_final: 0.5958 (mmm) REVERT: D 334 HIS cc_start: 0.7252 (p90) cc_final: 0.6778 (p90) REVERT: D 342 GLU cc_start: 0.8967 (tm-30) cc_final: 0.8672 (tm-30) REVERT: E 21 GLU cc_start: 0.8853 (OUTLIER) cc_final: 0.8452 (pm20) REVERT: E 188 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7467 (tp30) REVERT: E 213 MET cc_start: 0.7309 (mpp) cc_final: 0.6679 (pmm) REVERT: E 259 TYR cc_start: 0.8965 (t80) cc_final: 0.8704 (t80) REVERT: F 12 PHE cc_start: 0.5265 (t80) cc_final: 0.4910 (t80) REVERT: F 259 TYR cc_start: 0.7564 (t80) cc_final: 0.7339 (t80) REVERT: F 328 TRP cc_start: 0.7340 (m100) cc_final: 0.6627 (m100) outliers start: 30 outliers final: 26 residues processed: 202 average time/residue: 0.1323 time to fit residues: 40.9715 Evaluate side-chains 199 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 171 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 317 GLN Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 256 GLN Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 175 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 110 optimal weight: 0.4980 chunk 107 optimal weight: 1.9990 chunk 173 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 158 optimal weight: 5.9990 chunk 108 optimal weight: 0.4980 chunk 185 optimal weight: 2.9990 chunk 183 optimal weight: 20.0000 chunk 87 optimal weight: 1.9990 chunk 209 optimal weight: 50.0000 chunk 10 optimal weight: 8.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 255 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 = 0.4419 r_free = 0.4419 target = 0.169046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.122642 restraints weight = 38353.756| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 5.78 r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17134 Z= 0.143 Angle : 0.599 12.587 23200 Z= 0.305 Chirality : 0.044 0.217 2569 Planarity : 0.004 0.085 3022 Dihedral : 4.715 39.884 2342 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.73 % Allowed : 16.86 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.12 % 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: 0.19 (0.18), residues: 2125 helix: 1.15 (0.19), residues: 713 sheet: 0.03 (0.26), residues: 413 loop : -0.52 (0.20), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 219 TYR 0.014 0.001 TYR F 259 PHE 0.019 0.001 PHE F 140 TRP 0.019 0.001 TRP F 216 HIS 0.006 0.001 HIS B 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (17134) covalent geometry : angle 0.59916 / 0.30 (23200) hydrogen bonds : bond 0.03405 / 2.24 ( 727) hydrogen bonds : angle 4.91172 / 3.47 ( 2052) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4279.29 seconds wall clock time: 74 minutes 22.28 seconds (4462.28 seconds total)