Starting phenix.real_space_refine on Fri Aug 7 00:16:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/12bi_76279/08_2026/12bi_76279.cif Found real_map, /net/cci-nas-00/data/ceres_data/12bi_76279/08_2026/12bi_76279.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/12bi_76279/08_2026/12bi_76279.cif" } default_model = "/net/cci-nas-00/data/ceres_data/12bi_76279/08_2026/12bi_76279.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/12bi_76279/08_2026/12bi_76279.map" default_real_map = "/net/cci-nas-00/data/ceres_data/12bi_76279/08_2026/12bi_76279.map" } resolution = 3.97 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= 0.018 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 82 5.16 5 C 11239 2.51 5 N 3029 2.21 5 O 3293 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17643 Number of models: 1 Model: "" Number of chains: 6 Chain: "D" Number of atoms: 2853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 2853 Classifications: {'peptide': 383} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 360} Chain breaks: 1 Chain: "E" Number of atoms: 2969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 2969 Classifications: {'peptide': 398} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 373} Chain: "B" Number of atoms: 2955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 2955 Classifications: {'peptide': 396} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 371} Chain: "C" Number of atoms: 3009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3009 Classifications: {'peptide': 402} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 377} Chain: "A" Number of atoms: 2848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 2848 Classifications: {'peptide': 382} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 359} Chain breaks: 1 Chain: "F" Number of atoms: 3009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3009 Classifications: {'peptide': 402} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 377} Time building chain proxies: 4.02, per 1000 atoms: 0.23 Number of scatterers: 17643 At special positions: 0 Unit cell: (92.5083, 120.515, 187.563, 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 82 16.00 O 3293 8.00 N 3029 7.00 C 11239 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: 1.37 Conformation dependent library (CDL) restraints added in 683.4 milliseconds 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4284 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 32 sheets defined 41.1% alpha, 26.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'D' and resid 13 through 25 removed outlier: 3.826A pdb=" N CYS D 24 " --> pdb=" O ALA D 20 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLY D 25 " --> pdb=" O LEU D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 37 removed outlier: 3.814A pdb=" N GLY D 37 " --> pdb=" O SER D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 82 Processing helix chain 'D' and resid 86 through 109 Processing helix chain 'D' and resid 111 through 115 Processing helix chain 'D' and resid 122 through 139 removed outlier: 3.667A pdb=" N ILE D 126 " --> pdb=" O ALA D 122 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU D 139 " --> pdb=" O GLY D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 174 Processing helix chain 'D' and resid 190 through 201 Processing helix chain 'D' and resid 259 through 261 No H-bonds generated for 'chain 'D' and resid 259 through 261' Processing helix chain 'D' and resid 262 through 273 Processing helix chain 'D' and resid 286 through 288 No H-bonds generated for 'chain 'D' and resid 286 through 288' Processing helix chain 'D' and resid 302 through 314 removed outlier: 3.701A pdb=" N VAL D 306 " --> pdb=" O LYS D 302 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER D 314 " --> pdb=" O ILE D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 376 Processing helix chain 'D' and resid 378 through 394 removed outlier: 3.747A pdb=" N VAL D 382 " --> pdb=" O PRO D 378 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 24 removed outlier: 3.586A pdb=" N CYS E 24 " --> pdb=" O ALA E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 36 removed outlier: 3.576A pdb=" N LYS E 36 " --> pdb=" O THR E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 39 No H-bonds generated for 'chain 'E' and resid 37 through 39' Processing helix chain 'E' and resid 72 through 82 Processing helix chain 'E' and resid 86 through 109 Processing helix chain 'E' and resid 111 through 115 removed outlier: 3.594A pdb=" N VAL E 115 " --> pdb=" O ALA E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 139 removed outlier: 3.737A pdb=" N ILE E 126 " --> pdb=" O ALA E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 174 removed outlier: 3.527A pdb=" N LEU E 171 " --> pdb=" O ALA E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 201 Processing helix chain 'E' and resid 259 through 261 No H-bonds generated for 'chain 'E' and resid 259 through 261' Processing helix chain 'E' and resid 262 through 273 Processing helix chain 'E' and resid 285 through 289 removed outlier: 3.668A pdb=" N GLY E 288 " --> pdb=" O MET E 285 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG E 289 " --> pdb=" O LYS E 286 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 285 through 289' Processing helix chain 'E' and resid 299 through 301 No H-bonds generated for 'chain 'E' and resid 299 through 301' Processing helix chain 'E' and resid 302 through 313 Processing helix chain 'E' and resid 364 through 376 removed outlier: 3.614A pdb=" N CYS E 368 " --> pdb=" O GLU E 364 " (cutoff:3.500A) Processing helix chain 'E' and resid 378 through 395 removed outlier: 3.610A pdb=" N VAL E 382 " --> pdb=" O PRO E 378 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA E 395 " --> pdb=" O ARG E 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 25 removed outlier: 3.573A pdb=" N GLY B 25 " --> pdb=" O LEU B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 37 removed outlier: 3.886A pdb=" N GLY B 37 " --> pdb=" O SER B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 82 Processing helix chain 'B' and resid 86 through 109 Processing helix chain 'B' and resid 122 through 139 removed outlier: 3.689A pdb=" N ILE B 126 " --> pdb=" O ALA B 122 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU B 139 " --> pdb=" O GLY B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 175 removed outlier: 3.640A pdb=" N GLN B 175 " --> pdb=" O LEU B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 201 Processing helix chain 'B' and resid 259 through 261 No H-bonds generated for 'chain 'B' and resid 259 through 261' Processing helix chain 'B' and resid 262 through 273 Processing helix chain 'B' and resid 299 through 301 No H-bonds generated for 'chain 'B' and resid 299 through 301' Processing helix chain 'B' and resid 302 through 313 Processing helix chain 'B' and resid 364 through 376 removed outlier: 3.713A pdb=" N CYS B 368 " --> pdb=" O GLU B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 395 removed outlier: 3.666A pdb=" N VAL B 382 " --> pdb=" O PRO B 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 24 Processing helix chain 'C' and resid 27 through 37 removed outlier: 3.688A pdb=" N LEU C 31 " --> pdb=" O SER C 27 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLY C 37 " --> pdb=" O SER C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 82 Processing helix chain 'C' and resid 86 through 109 Processing helix chain 'C' and resid 111 through 115 removed outlier: 3.535A pdb=" N VAL C 115 " --> pdb=" O ALA C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 139 removed outlier: 3.697A pdb=" N ILE C 126 " --> pdb=" O ALA C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 174 Processing helix chain 'C' and resid 190 through 200 Processing helix chain 'C' and resid 259 through 261 No H-bonds generated for 'chain 'C' and resid 259 through 261' Processing helix chain 'C' and resid 262 through 274 removed outlier: 3.701A pdb=" N GLY C 274 " --> pdb=" O THR C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 301 No H-bonds generated for 'chain 'C' and resid 299 through 301' Processing helix chain 'C' and resid 302 through 314 Processing helix chain 'C' and resid 364 through 376 Processing helix chain 'C' and resid 378 through 395 removed outlier: 3.660A pdb=" N VAL C 382 " --> pdb=" O PRO C 378 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ALA C 395 " --> pdb=" O ARG C 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 24 Processing helix chain 'A' and resid 27 through 35 removed outlier: 3.530A pdb=" N LEU A 31 " --> pdb=" O SER A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 39 Processing helix chain 'A' and resid 72 through 82 Processing helix chain 'A' and resid 86 through 109 Processing helix chain 'A' and resid 122 through 139 removed outlier: 4.092A pdb=" N ILE A 126 " --> pdb=" O ALA A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 174 Processing helix chain 'A' and resid 190 through 201 Processing helix chain 'A' and resid 259 through 261 No H-bonds generated for 'chain 'A' and resid 259 through 261' Processing helix chain 'A' and resid 262 through 273 Processing helix chain 'A' and resid 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 302 through 313 removed outlier: 3.501A pdb=" N VAL A 306 " --> pdb=" O LYS A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 376 removed outlier: 3.727A pdb=" N CYS A 368 " --> pdb=" O GLU A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 395 removed outlier: 3.631A pdb=" N VAL A 382 " --> pdb=" O PRO A 378 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 24 Processing helix chain 'F' and resid 27 through 36 Processing helix chain 'F' and resid 37 through 39 No H-bonds generated for 'chain 'F' and resid 37 through 39' Processing helix chain 'F' and resid 72 through 82 Processing helix chain 'F' and resid 86 through 109 Processing helix chain 'F' and resid 122 through 139 removed outlier: 3.651A pdb=" N ILE F 126 " --> pdb=" O ALA F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 174 Processing helix chain 'F' and resid 190 through 201 removed outlier: 3.710A pdb=" N ALA F 201 " --> pdb=" O ILE F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 261 No H-bonds generated for 'chain 'F' and resid 259 through 261' Processing helix chain 'F' and resid 262 through 274 removed outlier: 3.552A pdb=" N GLY F 274 " --> pdb=" O THR F 270 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 288 No H-bonds generated for 'chain 'F' and resid 286 through 288' Processing helix chain 'F' and resid 302 through 314 Processing helix chain 'F' and resid 364 through 376 removed outlier: 3.550A pdb=" N CYS F 368 " --> pdb=" O GLU F 364 " (cutoff:3.500A) Processing helix chain 'F' and resid 378 through 395 removed outlier: 3.672A pdb=" N VAL F 382 " --> pdb=" O PRO F 378 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA F 395 " --> pdb=" O ARG F 391 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 203 through 204 removed outlier: 3.813A pdb=" N SER D 203 " --> pdb=" O VAL D 144 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS D 143 " --> pdb=" O LYS D 2 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE D 145 " --> pdb=" O ALA D 4 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA D 233 " --> pdb=" O TYR D 5 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ARG D 214 " --> pdb=" O LEU D 234 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLU D 236 " --> pdb=" O LEU D 212 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU D 212 " --> pdb=" O GLU D 236 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU E 149 " --> pdb=" O PRO E 178 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TYR E 180 " --> pdb=" O LEU E 149 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 46 through 52 removed outlier: 3.583A pdb=" N VAL D 50 " --> pdb=" O ALA D 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 149 through 151 Processing sheet with id=AA4, first strand: chain 'D' and resid 277 through 278 removed outlier: 3.806A pdb=" N ASP D 277 " --> pdb=" O LEU D 297 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE D 251 " --> pdb=" O ALA D 296 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL D 250 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 9.195A pdb=" N ARG D 323 " --> pdb=" O ARG E 323 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ARG E 323 " --> pdb=" O ARG D 323 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN D 325 " --> pdb=" O PHE E 321 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N CYS E 298 " --> pdb=" O LEU E 249 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE E 251 " --> pdb=" O ALA E 296 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASP E 277 " --> pdb=" O LEU E 297 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 282 through 284 removed outlier: 3.650A pdb=" N VAL D 283 " --> pdb=" O GLY D 291 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE D 251 " --> pdb=" O ALA D 296 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL D 250 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU F 327 " --> pdb=" O LEU D 319 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE D 321 " --> pdb=" O GLN F 325 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLN F 325 " --> pdb=" O PHE D 321 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 330 through 337 removed outlier: 3.513A pdb=" N ALA D 334 " --> pdb=" O VAL D 345 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL D 343 " --> pdb=" O VAL D 336 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 203 through 204 removed outlier: 3.967A pdb=" N SER E 203 " --> pdb=" O VAL E 144 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER E 146 " --> pdb=" O SER E 203 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N ILE E 145 " --> pdb=" O LYS E 2 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ALA E 4 " --> pdb=" O ILE E 145 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG E 231 " --> pdb=" O ASP E 7 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LEU E 232 " --> pdb=" O VAL E 215 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N VAL E 215 " --> pdb=" O LEU E 232 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N LEU E 234 " --> pdb=" O THR E 213 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET E 210 " --> pdb=" O VAL F 179 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU F 149 " --> pdb=" O PRO F 178 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR F 180 " --> pdb=" O LEU F 149 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 43 through 52 removed outlier: 3.514A pdb=" N ALA E 57 " --> pdb=" O VAL E 50 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 154 through 158 removed outlier: 4.083A pdb=" N GLY E 154 " --> pdb=" O VAL E 165 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL E 165 " --> pdb=" O GLY E 154 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL E 156 " --> pdb=" O LEU E 163 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 327 through 328 removed outlier: 6.588A pdb=" N GLY F 318 " --> pdb=" O THR F 254 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N THR F 254 " --> pdb=" O GLY F 318 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N CYS F 298 " --> pdb=" O LEU F 249 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ILE F 251 " --> pdb=" O ALA F 296 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N PHE F 279 " --> pdb=" O THR F 295 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASP F 277 " --> pdb=" O LEU F 297 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 327 through 328 removed outlier: 6.588A pdb=" N GLY F 318 " --> pdb=" O THR F 254 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N THR F 254 " --> pdb=" O GLY F 318 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N CYS F 298 " --> pdb=" O LEU F 249 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ILE F 251 " --> pdb=" O ALA F 296 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 330 through 338 Processing sheet with id=AB4, first strand: chain 'B' and resid 203 through 204 removed outlier: 3.911A pdb=" N SER B 203 " --> pdb=" O VAL B 144 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER B 146 " --> pdb=" O SER B 203 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LYS B 143 " --> pdb=" O LYS B 2 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA B 4 " --> pdb=" O LYS B 143 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARG B 231 " --> pdb=" O ASP B 7 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU B 232 " --> pdb=" O VAL B 215 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N VAL B 215 " --> pdb=" O LEU B 232 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LEU B 234 " --> pdb=" O THR B 213 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU B 236 " --> pdb=" O ASN B 211 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET B 210 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEU C 149 " --> pdb=" O TYR C 180 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 43 through 51 removed outlier: 3.515A pdb=" N ARG B 48 " --> pdb=" O ASP B 59 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 149 through 151 removed outlier: 3.903A pdb=" N TYR B 180 " --> pdb=" O LEU B 149 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 155 through 158 removed outlier: 3.596A pdb=" N VAL B 156 " --> pdb=" O LEU B 163 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 327 through 328 removed outlier: 6.391A pdb=" N GLY C 318 " --> pdb=" O THR C 254 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N THR C 254 " --> pdb=" O GLY C 318 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG C 322 " --> pdb=" O VAL C 250 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE C 251 " --> pdb=" O ALA C 296 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE C 294 " --> pdb=" O THR C 253 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN C 284 " --> pdb=" O PHE B 280 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 327 through 328 removed outlier: 6.391A pdb=" N GLY C 318 " --> pdb=" O THR C 254 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N THR C 254 " --> pdb=" O GLY C 318 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG C 322 " --> pdb=" O VAL C 250 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE C 251 " --> pdb=" O ALA C 296 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE C 294 " --> pdb=" O THR C 253 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 290 through 297 current: chain 'A' and resid 290 through 298 removed outlier: 3.594A pdb=" N CYS A 298 " --> pdb=" O LEU A 249 " (cutoff:3.500A) removed outlier: 9.368A pdb=" N ARG A 323 " --> pdb=" O ARG B 323 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ARG B 323 " --> pdb=" O ARG A 323 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN A 325 " --> pdb=" O PHE B 321 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N GLY B 318 " --> pdb=" O THR B 254 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N THR B 254 " --> pdb=" O GLY B 318 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N CYS B 298 " --> pdb=" O LEU B 249 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU B 293 " --> pdb=" O THR B 281 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASP B 277 " --> pdb=" O LEU B 297 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 330 through 338 removed outlier: 3.843A pdb=" N VAL B 336 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL B 343 " --> pdb=" O VAL B 336 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN B 360 " --> pdb=" O GLY B 348 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N TYR B 350 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE B 358 " --> pdb=" O TYR B 350 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 143 through 146 removed outlier: 3.683A pdb=" N LEU C 232 " --> pdb=" O GLY C 216 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ARG C 214 " --> pdb=" O LEU C 234 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLU C 236 " --> pdb=" O LEU C 212 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N LEU C 212 " --> pdb=" O GLU C 236 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 43 through 51 Processing sheet with id=AC4, first strand: chain 'C' and resid 155 through 157 removed outlier: 3.706A pdb=" N VAL C 156 " --> pdb=" O LEU C 163 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 330 through 338 Processing sheet with id=AC6, first strand: chain 'A' and resid 203 through 204 removed outlier: 3.730A pdb=" N SER A 203 " --> pdb=" O VAL A 144 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER A 146 " --> pdb=" O SER A 203 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LYS A 2 " --> pdb=" O LYS A 143 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N ILE A 145 " --> pdb=" O LYS A 2 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ALA A 4 " --> pdb=" O ILE A 145 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG A 231 " --> pdb=" O ASP A 7 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N GLU A 236 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N LEU A 212 " --> pdb=" O GLU A 236 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 43 through 52 Processing sheet with id=AC8, first strand: chain 'A' and resid 149 through 153 removed outlier: 4.431A pdb=" N SER A 153 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ASP A 184 " --> pdb=" O SER A 153 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 330 through 338 removed outlier: 3.750A pdb=" N ALA A 334 " --> pdb=" O VAL A 345 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL A 345 " --> pdb=" O ALA A 334 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL A 336 " --> pdb=" O VAL A 343 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL A 343 " --> pdb=" O VAL A 336 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY A 348 " --> pdb=" O ASN A 360 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN A 360 " --> pdb=" O GLY A 348 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 143 through 146 removed outlier: 6.801A pdb=" N LYS F 2 " --> pdb=" O LYS F 143 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N ILE F 145 " --> pdb=" O LYS F 2 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ALA F 4 " --> pdb=" O ILE F 145 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR F 5 " --> pdb=" O ALA F 233 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA F 233 " --> pdb=" O TYR F 5 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG F 231 " --> pdb=" O ASP F 7 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 143 through 146 removed outlier: 6.801A pdb=" N LYS F 2 " --> pdb=" O LYS F 143 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N ILE F 145 " --> pdb=" O LYS F 2 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ALA F 4 " --> pdb=" O ILE F 145 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 43 through 48 Processing sheet with id=AD4, first strand: chain 'F' and resid 155 through 158 removed outlier: 3.512A pdb=" N VAL F 156 " --> pdb=" O LEU F 163 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY F 161 " --> pdb=" O CYS F 158 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 330 through 338 removed outlier: 3.535A pdb=" N GLN F 330 " --> pdb=" O LEU F 349 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR F 350 " --> pdb=" O ILE F 358 " (cutoff:3.500A) 932 hydrogen bonds defined for protein. 2679 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.31 Time building geometry restraints manager: 1.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.06 - 1.21: 3 1.21 - 1.36: 5954 1.36 - 1.51: 5747 1.51 - 1.67: 6170 1.67 - 1.82: 124 Bond restraints: 17998 Sorted by residual: bond pdb=" CG PRO B 378 " pdb=" CD PRO B 378 " ideal model delta sigma weight residual 1.503 1.202 0.301 3.40e-02 8.65e+02 7.83e+01 bond pdb=" CB PRO B 378 " pdb=" CG PRO B 378 " ideal model delta sigma weight residual 1.492 1.057 0.435 5.00e-02 4.00e+02 7.58e+01 bond pdb=" C PRO C 208 " pdb=" O PRO C 208 " ideal model delta sigma weight residual 1.235 1.165 0.070 1.30e-02 5.92e+03 2.89e+01 bond pdb=" N PRO B 378 " pdb=" CA PRO B 378 " ideal model delta sigma weight residual 1.466 1.525 -0.060 1.19e-02 7.06e+03 2.52e+01 bond pdb=" N ALA C 209 " pdb=" CA ALA C 209 " ideal model delta sigma weight residual 1.457 1.500 -0.042 1.29e-02 6.01e+03 1.07e+01 ... (remaining 17993 not shown) Histogram of bond angle deviations from ideal: 0.00 - 12.59: 24455 12.59 - 25.17: 2 25.17 - 37.76: 2 37.76 - 50.34: 0 50.34 - 62.93: 1 Bond angle restraints: 24460 Sorted by residual: angle pdb=" N PRO B 378 " pdb=" CD PRO B 378 " pdb=" CG PRO B 378 " ideal model delta sigma weight residual 103.20 73.64 29.56 1.50e+00 4.44e-01 3.88e+02 angle pdb=" CB PRO B 378 " pdb=" CG PRO B 378 " pdb=" CD PRO B 378 " ideal model delta sigma weight residual 106.10 169.03 -62.93 3.20e+00 9.77e-02 3.87e+02 angle pdb=" CA PRO B 378 " pdb=" CB PRO B 378 " pdb=" CG PRO B 378 " ideal model delta sigma weight residual 104.50 69.24 35.26 1.90e+00 2.77e-01 3.44e+02 angle pdb=" CA PRO B 378 " pdb=" N PRO B 378 " pdb=" CD PRO B 378 " ideal model delta sigma weight residual 112.00 100.52 11.48 1.40e+00 5.10e-01 6.72e+01 angle pdb=" C GLN C -2 " pdb=" CA GLN C -2 " pdb=" CB GLN C -2 " ideal model delta sigma weight residual 116.54 109.93 6.61 1.15e+00 7.56e-01 3.31e+01 ... (remaining 24455 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.02: 9447 18.02 - 36.04: 1071 36.04 - 54.05: 232 54.05 - 72.07: 53 72.07 - 90.09: 22 Dihedral angle restraints: 10825 sinusoidal: 4136 harmonic: 6689 Sorted by residual: dihedral pdb=" N PRO B 378 " pdb=" CG PRO B 378 " pdb=" CD PRO B 378 " pdb=" CB PRO B 378 " ideal model delta sinusoidal sigma weight residual -30.00 -93.20 63.20 1 1.50e+01 4.44e-03 2.34e+01 dihedral pdb=" CA PRO B 378 " pdb=" CB PRO B 378 " pdb=" CG PRO B 378 " pdb=" CD PRO B 378 " ideal model delta sinusoidal sigma weight residual -38.00 -119.36 81.36 1 2.00e+01 2.50e-03 2.04e+01 dihedral pdb=" CA MET D 210 " pdb=" C MET D 210 " pdb=" N ASN D 211 " pdb=" CA ASN D 211 " ideal model delta harmonic sigma weight residual 180.00 162.19 17.81 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 10822 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 2326 0.055 - 0.111: 467 0.111 - 0.166: 56 0.166 - 0.222: 1 0.222 - 0.277: 2 Chirality restraints: 2852 Sorted by residual: chirality pdb=" CB VAL C 130 " pdb=" CA VAL C 130 " pdb=" CG1 VAL C 130 " pdb=" CG2 VAL C 130 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CG LEU B 173 " pdb=" CB LEU B 173 " pdb=" CD1 LEU B 173 " pdb=" CD2 LEU B 173 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CG LEU B 35 " pdb=" CB LEU B 35 " pdb=" CD1 LEU B 35 " pdb=" CD2 LEU B 35 " both_signs ideal model delta sigma weight residual False -2.59 -2.76 0.17 2.00e-01 2.50e+01 7.23e-01 ... (remaining 2849 not shown) Planarity restraints: 3185 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 377 " 0.072 5.00e-02 4.00e+02 1.01e-01 1.63e+01 pdb=" N PRO B 378 " -0.174 5.00e-02 4.00e+02 pdb=" CA PRO B 378 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 378 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 338 " -0.037 5.00e-02 4.00e+02 5.55e-02 4.92e+00 pdb=" N PRO A 339 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 339 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 339 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 43 " -0.012 2.00e-02 2.50e+03 1.39e-02 4.85e+00 pdb=" CG TRP D 43 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP D 43 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP D 43 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP D 43 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 43 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 43 " -0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 43 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 43 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP D 43 " -0.000 2.00e-02 2.50e+03 ... (remaining 3182 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1702 2.74 - 3.28: 16759 3.28 - 3.82: 27590 3.82 - 4.36: 29052 4.36 - 4.90: 53107 Nonbonded interactions: 128210 Sorted by model distance: nonbonded pdb=" O ALA E 167 " pdb=" OG1 THR E 170 " model vdw 2.199 3.040 nonbonded pdb=" O SER B 315 " pdb=" OG SER B 315 " model vdw 2.208 3.040 nonbonded pdb=" O GLY F -1 " pdb=" ND2 ASN F 238 " model vdw 2.211 3.120 nonbonded pdb=" OG SER B 13 " pdb=" OD1 ASP B 15 " model vdw 2.219 3.040 nonbonded pdb=" O ILE D 80 " pdb=" OG SER D 83 " model vdw 2.230 3.040 ... (remaining 128205 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 1 through 153 or resid 168 through 396)) selection = (chain 'C' and (resid 1 through 153 or resid 168 through 396)) selection = (chain 'D' and (resid 1 through 153 or resid 168 through 396)) selection = (chain 'E' and (resid 1 through 153 or resid 168 through 396)) selection = (chain 'F' and (resid 1 through 153 or resid 168 through 396)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.500 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 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 : 0.006 0.435 17998 Z= 0.223 Angle : 0.863 62.931 24460 Z= 0.416 Chirality : 0.044 0.277 2852 Planarity : 0.005 0.101 3185 Dihedral : 16.385 90.090 6541 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.18 % Favored : 95.57 % Rotamer: Outliers : 0.76 % Allowed : 25.04 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % 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: -0.01 (0.18), residues: 2347 helix: 1.72 (0.18), residues: 862 sheet: -0.88 (0.20), residues: 690 loop : -1.00 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 231 TYR 0.015 0.001 TYR F 383 PHE 0.014 0.002 PHE C 9 TRP 0.037 0.002 TRP D 43 HIS 0.003 0.001 HIS E 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00587 / 0.22 (17998) covalent geometry : angle 0.86262 / 0.42 (24460) hydrogen bonds : bond 0.20654 / 14.20 ( 901) hydrogen bonds : angle 7.36931 / 5.22 ( 2679) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 167 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 333 MET cc_start: 0.8181 (mmt) cc_final: 0.7918 (mmt) REVERT: E 1 MET cc_start: 0.7753 (ttt) cc_final: 0.7545 (ttt) REVERT: F 271 MET cc_start: 0.8630 (ttm) cc_final: 0.8306 (mtp) outliers start: 14 outliers final: 8 residues processed: 177 average time/residue: 0.1159 time to fit residues: 33.2956 Evaluate side-chains 168 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 160 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain C residue 207 PHE Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 383 TYR Chi-restraints excluded: chain F residue 328 VAL Chi-restraints excluded: chain F residue 383 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 0.7980 chunk 227 optimal weight: 0.9990 chunk 107 optimal weight: 0.3980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.0980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 200 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 160 HIS F 118 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.139494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.095847 restraints weight = 30077.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.094157 restraints weight = 23536.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.094858 restraints weight = 26195.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.095448 restraints weight = 19310.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.095614 restraints weight = 17232.149| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17998 Z= 0.110 Angle : 0.591 12.858 24460 Z= 0.287 Chirality : 0.042 0.232 2852 Planarity : 0.005 0.051 3185 Dihedral : 4.545 53.984 2525 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.07 % Favored : 96.89 % Rotamer: Outliers : 2.54 % Allowed : 21.47 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % 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: 0.30 (0.18), residues: 2347 helix: 1.93 (0.18), residues: 882 sheet: -0.59 (0.20), residues: 707 loop : -1.00 (0.21), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 214 TYR 0.012 0.001 TYR F 177 PHE 0.027 0.001 PHE A 97 TRP 0.021 0.001 TRP D 43 HIS 0.003 0.001 HIS F 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (17998) covalent geometry : angle 0.59109 / 0.29 (24460) hydrogen bonds : bond 0.03556 / 2.43 ( 901) hydrogen bonds : angle 4.91924 / 3.52 ( 2679) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 198 time to evaluate : 0.492 Fit side-chains revert: symmetry clash REVERT: D 48 ARG cc_start: 0.7251 (ptp90) cc_final: 0.6774 (mtm-85) REVERT: D 72 HIS cc_start: 0.7908 (OUTLIER) cc_final: 0.7426 (t70) REVERT: D 97 PHE cc_start: 0.7975 (m-80) cc_final: 0.7752 (m-80) REVERT: E 284 GLN cc_start: 0.8594 (tm-30) cc_final: 0.7825 (tm-30) REVERT: B 345 VAL cc_start: 0.7024 (OUTLIER) cc_final: 0.6798 (m) REVERT: C 130 VAL cc_start: 0.8960 (m) cc_final: 0.8735 (t) REVERT: C 211 ASN cc_start: 0.8548 (OUTLIER) cc_final: 0.8098 (t0) REVERT: A 15 ASP cc_start: 0.8773 (m-30) cc_final: 0.8427 (m-30) REVERT: A 35 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.7622 (tp) REVERT: A 97 PHE cc_start: 0.7841 (m-80) cc_final: 0.7519 (m-80) REVERT: F 82 ASN cc_start: 0.8339 (m-40) cc_final: 0.8120 (p0) REVERT: F 300 GLU cc_start: 0.7924 (tm-30) cc_final: 0.7609 (tm-30) outliers start: 47 outliers final: 16 residues processed: 234 average time/residue: 0.1027 time to fit residues: 40.0373 Evaluate side-chains 189 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 169 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 72 HIS Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 383 TYR Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain C residue 0 HIS Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain C residue 383 TYR Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 118 HIS Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 160 HIS Chi-restraints excluded: chain F residue 211 ASN Chi-restraints excluded: chain F residue 383 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 165 optimal weight: 7.9990 chunk 45 optimal weight: 0.0970 chunk 29 optimal weight: 0.7980 chunk 20 optimal weight: 9.9990 chunk 123 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 84 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 228 optimal weight: 0.0870 overall best weight: 0.9960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 160 HIS ** F 68 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 = 0.3800 r_free = 0.3800 target = 0.138776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.094954 restraints weight = 30484.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.093328 restraints weight = 24630.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.094357 restraints weight = 25525.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.094710 restraints weight = 19002.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.094931 restraints weight = 16850.349| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17998 Z= 0.118 Angle : 0.571 12.889 24460 Z= 0.273 Chirality : 0.041 0.181 2852 Planarity : 0.005 0.052 3185 Dihedral : 4.125 58.177 2517 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.07 % Favored : 96.89 % Rotamer: Outliers : 3.14 % Allowed : 22.55 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % 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: 0.48 (0.18), residues: 2347 helix: 2.05 (0.17), residues: 882 sheet: -0.44 (0.20), residues: 707 loop : -0.92 (0.21), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 46 TYR 0.008 0.001 TYR B 180 PHE 0.020 0.001 PHE A 97 TRP 0.016 0.001 TRP D 43 HIS 0.002 0.000 HIS C 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (17998) covalent geometry : angle 0.57074 / 0.27 (24460) hydrogen bonds : bond 0.03393 / 2.32 ( 901) hydrogen bonds : angle 4.55764 / 3.24 ( 2679) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 187 time to evaluate : 0.689 Fit side-chains revert: symmetry clash REVERT: D 48 ARG cc_start: 0.7243 (ptp90) cc_final: 0.6785 (mtm-85) REVERT: D 72 HIS cc_start: 0.7993 (OUTLIER) cc_final: 0.7475 (t70) REVERT: E 90 LYS cc_start: 0.8067 (tttt) cc_final: 0.7706 (tttt) REVERT: E 284 GLN cc_start: 0.8574 (tm-30) cc_final: 0.7792 (tm-30) REVERT: B 132 SER cc_start: 0.8843 (m) cc_final: 0.8158 (p) REVERT: C 160 HIS cc_start: 0.7242 (OUTLIER) cc_final: 0.6995 (t70) REVERT: A 15 ASP cc_start: 0.8847 (m-30) cc_final: 0.8436 (m-30) REVERT: A 35 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.7694 (tp) REVERT: A 97 PHE cc_start: 0.7817 (m-80) cc_final: 0.7370 (m-80) REVERT: A 349 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7495 (mt) REVERT: F 76 ILE cc_start: 0.9195 (mm) cc_final: 0.8876 (mt) REVERT: F 300 GLU cc_start: 0.7921 (tm-30) cc_final: 0.7634 (tm-30) REVERT: F 324 ASP cc_start: 0.7934 (m-30) cc_final: 0.7616 (m-30) outliers start: 58 outliers final: 33 residues processed: 230 average time/residue: 0.1096 time to fit residues: 41.6329 Evaluate side-chains 212 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 175 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 72 HIS Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 310 ILE Chi-restraints excluded: chain E residue 338 THR Chi-restraints excluded: chain E residue 383 TYR Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain C residue 0 HIS Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 160 HIS Chi-restraints excluded: chain C residue 238 ASN Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain C residue 383 TYR Chi-restraints excluded: chain A residue 17 CYS Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 118 HIS Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 160 HIS Chi-restraints excluded: chain F residue 211 ASN Chi-restraints excluded: chain F residue 383 TYR Chi-restraints excluded: chain F residue 387 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 171 optimal weight: 30.0000 chunk 191 optimal weight: 0.8980 chunk 221 optimal weight: 0.9990 chunk 187 optimal weight: 1.9990 chunk 89 optimal weight: 0.0370 chunk 81 optimal weight: 8.9990 chunk 1 optimal weight: 20.0000 chunk 140 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 chunk 154 optimal weight: 0.0770 chunk 43 optimal weight: 3.9990 overall best weight: 0.8020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 160 HIS C 81 ASN ** F 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 284 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.139921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.095447 restraints weight = 30110.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.094007 restraints weight = 24430.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.094979 restraints weight = 25779.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.095372 restraints weight = 19650.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.095699 restraints weight = 17073.445| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17998 Z= 0.105 Angle : 0.548 12.247 24460 Z= 0.260 Chirality : 0.041 0.150 2852 Planarity : 0.005 0.052 3185 Dihedral : 3.828 56.040 2515 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.73 % Favored : 97.23 % Rotamer: Outliers : 3.30 % Allowed : 22.07 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % 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: 0.63 (0.18), residues: 2347 helix: 2.13 (0.18), residues: 886 sheet: -0.30 (0.20), residues: 703 loop : -0.86 (0.22), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 331 TYR 0.018 0.001 TYR D 180 PHE 0.019 0.001 PHE C 280 TRP 0.017 0.001 TRP D 43 HIS 0.002 0.000 HIS C 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.10 (17998) covalent geometry : angle 0.54791 / 0.26 (24460) hydrogen bonds : bond 0.03032 / 2.08 ( 901) hydrogen bonds : angle 4.29431 / 3.05 ( 2679) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 188 time to evaluate : 0.739 Fit side-chains REVERT: D 48 ARG cc_start: 0.7200 (ptp90) cc_final: 0.6774 (mtm-85) REVERT: D 72 HIS cc_start: 0.8017 (OUTLIER) cc_final: 0.7478 (t70) REVERT: E 284 GLN cc_start: 0.8570 (tm-30) cc_final: 0.7742 (tm-30) REVERT: B 132 SER cc_start: 0.8846 (m) cc_final: 0.8136 (p) REVERT: B 173 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8560 (mm) REVERT: C 160 HIS cc_start: 0.7311 (OUTLIER) cc_final: 0.7066 (t70) REVERT: A 15 ASP cc_start: 0.8784 (m-30) cc_final: 0.8386 (m-30) REVERT: A 35 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.7654 (tp) REVERT: A 97 PHE cc_start: 0.7958 (m-80) cc_final: 0.7523 (m-80) REVERT: A 349 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7618 (mt) outliers start: 61 outliers final: 36 residues processed: 233 average time/residue: 0.1058 time to fit residues: 41.0272 Evaluate side-chains 218 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 177 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 72 HIS Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 207 PHE Chi-restraints excluded: chain E residue 310 ILE Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 338 THR Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain C residue 0 HIS Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 24 CYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 160 HIS Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 238 ASN Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 383 TYR Chi-restraints excluded: chain A residue 17 CYS Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 118 HIS Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 160 HIS Chi-restraints excluded: chain F residue 211 ASN Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 383 TYR Chi-restraints excluded: chain F residue 387 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 144 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 85 optimal weight: 8.9990 chunk 196 optimal weight: 0.1980 chunk 191 optimal weight: 0.7980 chunk 117 optimal weight: 2.9990 chunk 41 optimal weight: 10.0000 chunk 125 optimal weight: 8.9990 chunk 133 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 160 HIS ** F 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 175 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.140522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.095740 restraints weight = 30107.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.095313 restraints weight = 25571.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.096038 restraints weight = 22377.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.096247 restraints weight = 17528.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.096328 restraints weight = 17088.389| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 17998 Z= 0.101 Angle : 0.541 12.014 24460 Z= 0.257 Chirality : 0.040 0.144 2852 Planarity : 0.005 0.053 3185 Dihedral : 3.765 57.277 2515 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.64 % Favored : 97.32 % Rotamer: Outliers : 3.46 % Allowed : 22.12 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.18), residues: 2347 helix: 2.19 (0.18), residues: 888 sheet: -0.20 (0.20), residues: 703 loop : -0.82 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 159 TYR 0.016 0.001 TYR E 365 PHE 0.011 0.001 PHE A 97 TRP 0.018 0.001 TRP D 43 HIS 0.005 0.000 HIS B 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.10 (17998) covalent geometry : angle 0.54052 / 0.26 (24460) hydrogen bonds : bond 0.02894 / 1.96 ( 901) hydrogen bonds : angle 4.16102 / 2.97 ( 2679) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 194 time to evaluate : 0.492 Fit side-chains REVERT: D 48 ARG cc_start: 0.7217 (ptp90) cc_final: 0.6795 (mtm-85) REVERT: D 72 HIS cc_start: 0.8032 (OUTLIER) cc_final: 0.7219 (t70) REVERT: E 80 ILE cc_start: 0.8936 (mt) cc_final: 0.8674 (mm) REVERT: E 90 LYS cc_start: 0.8020 (tttt) cc_final: 0.7747 (tttt) REVERT: B 132 SER cc_start: 0.8850 (m) cc_final: 0.8159 (p) REVERT: B 173 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8520 (mm) REVERT: B 243 GLU cc_start: 0.2668 (OUTLIER) cc_final: 0.1260 (pm20) REVERT: C 160 HIS cc_start: 0.7322 (OUTLIER) cc_final: 0.7038 (t70) REVERT: A 15 ASP cc_start: 0.8764 (m-30) cc_final: 0.8272 (m-30) REVERT: A 35 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7636 (tp) REVERT: A 97 PHE cc_start: 0.7993 (m-80) cc_final: 0.7574 (m-80) REVERT: A 349 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7566 (mt) REVERT: F -5 LEU cc_start: 0.3222 (OUTLIER) cc_final: 0.1680 (tp) REVERT: F 300 GLU cc_start: 0.7727 (tm-30) cc_final: 0.7428 (tm-30) outliers start: 64 outliers final: 43 residues processed: 244 average time/residue: 0.0980 time to fit residues: 40.3668 Evaluate side-chains 229 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 179 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 72 HIS Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 207 PHE Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 338 THR Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain C residue 0 HIS Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 160 HIS Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 238 ASN Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 383 TYR Chi-restraints excluded: chain A residue 17 CYS Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 118 HIS Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain F residue -5 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 160 HIS Chi-restraints excluded: chain F residue 211 ASN Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 383 TYR Chi-restraints excluded: chain F residue 387 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 70 optimal weight: 1.9990 chunk 159 optimal weight: 9.9990 chunk 30 optimal weight: 0.9980 chunk 200 optimal weight: 1.9990 chunk 151 optimal weight: 0.9980 chunk 172 optimal weight: 9.9990 chunk 195 optimal weight: 0.0040 chunk 39 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 overall best weight: 0.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 160 HIS B 160 HIS ** F 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 72 HIS F 175 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.139750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.095188 restraints weight = 30277.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.094582 restraints weight = 27588.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.095383 restraints weight = 24173.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.095645 restraints weight = 18948.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.095815 restraints weight = 17500.715| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17998 Z= 0.114 Angle : 0.548 12.553 24460 Z= 0.261 Chirality : 0.041 0.188 2852 Planarity : 0.005 0.053 3185 Dihedral : 3.799 59.647 2515 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.77 % Favored : 97.19 % Rotamer: Outliers : 4.06 % Allowed : 21.90 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % 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: 0.77 (0.18), residues: 2347 helix: 2.18 (0.18), residues: 889 sheet: -0.16 (0.20), residues: 703 loop : -0.79 (0.22), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 159 TYR 0.019 0.001 TYR D 180 PHE 0.011 0.001 PHE F 6 TRP 0.022 0.002 TRP E 43 HIS 0.003 0.000 HIS B 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.11 (17998) covalent geometry : angle 0.54838 / 0.26 (24460) hydrogen bonds : bond 0.03037 / 2.07 ( 901) hydrogen bonds : angle 4.11644 / 2.93 ( 2679) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 190 time to evaluate : 0.641 Fit side-chains REVERT: D 48 ARG cc_start: 0.7222 (ptp90) cc_final: 0.6801 (mtm-85) REVERT: D 72 HIS cc_start: 0.7972 (OUTLIER) cc_final: 0.7180 (t70) REVERT: E 80 ILE cc_start: 0.8987 (mt) cc_final: 0.8696 (mm) REVERT: E 90 LYS cc_start: 0.8038 (tttt) cc_final: 0.7690 (tttt) REVERT: B 132 SER cc_start: 0.8853 (m) cc_final: 0.8151 (p) REVERT: B 173 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8505 (mm) REVERT: B 243 GLU cc_start: 0.2507 (OUTLIER) cc_final: 0.1306 (pm20) REVERT: B 271 MET cc_start: 0.8982 (tpp) cc_final: 0.8482 (ttm) REVERT: C -4 TYR cc_start: 0.7763 (m-80) cc_final: 0.7551 (m-80) REVERT: A 15 ASP cc_start: 0.8804 (m-30) cc_final: 0.8374 (m-30) REVERT: A 35 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7645 (tp) REVERT: A 97 PHE cc_start: 0.8028 (m-80) cc_final: 0.7604 (m-80) REVERT: A 223 GLU cc_start: 0.7065 (tp30) cc_final: 0.6793 (tp30) REVERT: A 349 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7723 (mt) REVERT: F -5 LEU cc_start: 0.3396 (OUTLIER) cc_final: 0.1850 (tp) REVERT: F 76 ILE cc_start: 0.9208 (mm) cc_final: 0.8854 (mt) outliers start: 75 outliers final: 57 residues processed: 248 average time/residue: 0.1093 time to fit residues: 44.6914 Evaluate side-chains 240 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 177 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 72 HIS Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 338 THR Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 207 PHE Chi-restraints excluded: chain E residue 310 ILE Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 338 THR Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain C residue 0 HIS Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 24 CYS Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 238 ASN Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 325 GLN Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 383 TYR Chi-restraints excluded: chain A residue 17 CYS Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 118 HIS Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain F residue -5 LEU Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 160 HIS Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 211 ASN Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 258 MET Chi-restraints excluded: chain F residue 383 TYR Chi-restraints excluded: chain F residue 387 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 168 optimal weight: 0.0030 chunk 89 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 chunk 159 optimal weight: 10.0000 chunk 92 optimal weight: 8.9990 chunk 114 optimal weight: 8.9990 chunk 125 optimal weight: 3.9990 chunk 199 optimal weight: 8.9990 chunk 87 optimal weight: 1.9990 chunk 190 optimal weight: 6.9990 chunk 217 optimal weight: 0.1980 overall best weight: 1.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 160 HIS ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 175 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.137507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.094199 restraints weight = 30522.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.091132 restraints weight = 26976.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.092210 restraints weight = 27984.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.092777 restraints weight = 20296.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.093106 restraints weight = 18132.606| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17998 Z= 0.158 Angle : 0.591 12.542 24460 Z= 0.284 Chirality : 0.042 0.156 2852 Planarity : 0.005 0.053 3185 Dihedral : 4.001 59.224 2515 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.05 % Favored : 95.91 % Rotamer: Outliers : 4.00 % Allowed : 22.55 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % 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: 0.67 (0.18), residues: 2347 helix: 2.14 (0.18), residues: 886 sheet: -0.23 (0.19), residues: 709 loop : -0.87 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 231 TYR 0.012 0.001 TYR F 180 PHE 0.016 0.001 PHE F 6 TRP 0.024 0.002 TRP E 43 HIS 0.003 0.001 HIS C 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.16 (17998) covalent geometry : angle 0.59091 / 0.28 (24460) hydrogen bonds : bond 0.03510 / 2.39 ( 901) hydrogen bonds : angle 4.27943 / 3.05 ( 2679) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 182 time to evaluate : 0.630 Fit side-chains REVERT: D 48 ARG cc_start: 0.7276 (ptp90) cc_final: 0.6859 (mtm-85) REVERT: D 72 HIS cc_start: 0.7976 (OUTLIER) cc_final: 0.7501 (t70) REVERT: D 333 MET cc_start: 0.8329 (mmt) cc_final: 0.8089 (mmt) REVERT: E 80 ILE cc_start: 0.9025 (mt) cc_final: 0.8771 (mm) REVERT: E 90 LYS cc_start: 0.8102 (tttt) cc_final: 0.7774 (tttt) REVERT: B 132 SER cc_start: 0.8874 (m) cc_final: 0.8192 (p) REVERT: B 173 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8545 (mm) REVERT: B 243 GLU cc_start: 0.2613 (OUTLIER) cc_final: 0.1345 (pm20) REVERT: B 271 MET cc_start: 0.9016 (tpp) cc_final: 0.8476 (ttm) REVERT: C -4 TYR cc_start: 0.7823 (m-80) cc_final: 0.7572 (m-80) REVERT: C 172 TYR cc_start: 0.8470 (m-80) cc_final: 0.8267 (m-80) REVERT: A 15 ASP cc_start: 0.8935 (m-30) cc_final: 0.8456 (m-30) REVERT: A 35 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.7673 (tp) REVERT: A 97 PHE cc_start: 0.8174 (m-80) cc_final: 0.7794 (m-80) REVERT: A 349 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7851 (mt) REVERT: F -5 LEU cc_start: 0.3392 (OUTLIER) cc_final: 0.1787 (tp) outliers start: 74 outliers final: 52 residues processed: 240 average time/residue: 0.1027 time to fit residues: 41.7981 Evaluate side-chains 238 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 180 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 72 HIS Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 338 THR Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 207 PHE Chi-restraints excluded: chain E residue 310 ILE Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 338 THR Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain C residue 0 HIS Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 24 CYS Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 238 ASN Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 325 GLN Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 383 TYR Chi-restraints excluded: chain A residue 17 CYS Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 118 HIS Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain F residue -5 LEU Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 118 HIS Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 160 HIS Chi-restraints excluded: chain F residue 211 ASN Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 383 TYR Chi-restraints excluded: chain F residue 387 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 97 optimal weight: 3.9990 chunk 219 optimal weight: 4.9990 chunk 166 optimal weight: 9.9990 chunk 182 optimal weight: 0.9980 chunk 212 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 149 optimal weight: 0.0570 chunk 15 optimal weight: 9.9990 chunk 177 optimal weight: 0.0170 chunk 33 optimal weight: 5.9990 overall best weight: 0.5936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 160 HIS ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 175 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.140445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.096122 restraints weight = 30076.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.094499 restraints weight = 26337.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.095657 restraints weight = 23724.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.095934 restraints weight = 18817.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.096094 restraints weight = 17310.656| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 17998 Z= 0.097 Angle : 0.553 11.825 24460 Z= 0.260 Chirality : 0.040 0.157 2852 Planarity : 0.005 0.053 3185 Dihedral : 3.742 58.605 2515 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.13 % Favored : 97.83 % Rotamer: Outliers : 3.03 % Allowed : 23.09 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % 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: 0.80 (0.18), residues: 2347 helix: 2.20 (0.18), residues: 889 sheet: -0.13 (0.20), residues: 702 loop : -0.78 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 214 TYR 0.019 0.001 TYR E 365 PHE 0.010 0.001 PHE F 97 TRP 0.028 0.002 TRP E 43 HIS 0.002 0.000 HIS B 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 (17998) covalent geometry : angle 0.55300 / 0.26 (24460) hydrogen bonds : bond 0.02726 / 1.86 ( 901) hydrogen bonds : angle 4.00979 / 2.86 ( 2679) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 188 time to evaluate : 0.659 Fit side-chains REVERT: D 21 LEU cc_start: 0.9298 (mt) cc_final: 0.9042 (mt) REVERT: D 48 ARG cc_start: 0.7224 (ptp90) cc_final: 0.6821 (mtm-85) REVERT: D 72 HIS cc_start: 0.7996 (OUTLIER) cc_final: 0.7291 (t70) REVERT: E 80 ILE cc_start: 0.9003 (mt) cc_final: 0.8714 (mm) REVERT: E 90 LYS cc_start: 0.8042 (tttt) cc_final: 0.7748 (tttt) REVERT: B 132 SER cc_start: 0.8840 (m) cc_final: 0.8162 (p) REVERT: B 173 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8474 (mm) REVERT: B 243 GLU cc_start: 0.2579 (OUTLIER) cc_final: 0.1349 (pm20) REVERT: B 271 MET cc_start: 0.8945 (tpp) cc_final: 0.8435 (ttm) REVERT: C -4 TYR cc_start: 0.7803 (m-80) cc_final: 0.7543 (m-80) REVERT: C 329 CYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8115 (m) REVERT: A 15 ASP cc_start: 0.8925 (m-30) cc_final: 0.8438 (m-30) REVERT: A 35 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7674 (tp) REVERT: A 97 PHE cc_start: 0.8112 (m-80) cc_final: 0.7773 (m-80) REVERT: F -5 LEU cc_start: 0.3376 (OUTLIER) cc_final: 0.1773 (tp) outliers start: 56 outliers final: 41 residues processed: 230 average time/residue: 0.0994 time to fit residues: 38.6987 Evaluate side-chains 222 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 175 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 6 PHE Chi-restraints excluded: chain D residue 72 HIS Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 338 THR Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 207 PHE Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 338 THR Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain C residue 0 HIS Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 24 CYS Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 238 ASN Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 383 TYR Chi-restraints excluded: chain A residue 17 CYS Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 118 HIS Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain F residue -5 LEU Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 160 HIS Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 383 TYR Chi-restraints excluded: chain F residue 387 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 209 optimal weight: 0.5980 chunk 34 optimal weight: 5.9990 chunk 165 optimal weight: 9.9990 chunk 166 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 138 optimal weight: 4.9990 chunk 227 optimal weight: 0.8980 chunk 13 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 105 optimal weight: 0.9980 chunk 108 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 160 HIS ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 175 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.139775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.096421 restraints weight = 30156.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.093708 restraints weight = 25140.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.094807 restraints weight = 28491.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.095297 restraints weight = 19949.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.095593 restraints weight = 17311.232| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17998 Z= 0.107 Angle : 0.557 15.515 24460 Z= 0.263 Chirality : 0.041 0.196 2852 Planarity : 0.005 0.053 3185 Dihedral : 3.703 59.479 2515 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.77 % Favored : 97.19 % Rotamer: Outliers : 2.60 % Allowed : 23.69 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % 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: 0.84 (0.18), residues: 2347 helix: 2.21 (0.18), residues: 891 sheet: -0.12 (0.19), residues: 711 loop : -0.72 (0.22), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 231 TYR 0.010 0.001 TYR D 172 PHE 0.013 0.001 PHE F 97 TRP 0.029 0.002 TRP E 43 HIS 0.002 0.000 HIS B 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (17998) covalent geometry : angle 0.55700 / 0.26 (24460) hydrogen bonds : bond 0.02883 / 1.96 ( 901) hydrogen bonds : angle 4.01915 / 2.88 ( 2679) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 182 time to evaluate : 0.664 Fit side-chains REVERT: D 21 LEU cc_start: 0.9315 (mt) cc_final: 0.9066 (mt) REVERT: D 48 ARG cc_start: 0.7256 (ptp90) cc_final: 0.6826 (mtm-85) REVERT: D 72 HIS cc_start: 0.8027 (OUTLIER) cc_final: 0.7272 (t70) REVERT: E 80 ILE cc_start: 0.9037 (mt) cc_final: 0.8752 (mm) REVERT: E 90 LYS cc_start: 0.8098 (tttt) cc_final: 0.7793 (tttt) REVERT: B 132 SER cc_start: 0.8869 (m) cc_final: 0.8208 (p) REVERT: B 173 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8467 (mm) REVERT: B 243 GLU cc_start: 0.2499 (OUTLIER) cc_final: 0.1301 (pm20) REVERT: B 271 MET cc_start: 0.8969 (tpp) cc_final: 0.8482 (ttm) REVERT: C -4 TYR cc_start: 0.7834 (m-80) cc_final: 0.7554 (m-80) REVERT: A 15 ASP cc_start: 0.8972 (m-30) cc_final: 0.8561 (m-30) REVERT: A 35 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7672 (tp) REVERT: A 97 PHE cc_start: 0.8136 (m-80) cc_final: 0.7813 (m-80) REVERT: F -5 LEU cc_start: 0.3409 (OUTLIER) cc_final: 0.2451 (tp) outliers start: 48 outliers final: 37 residues processed: 219 average time/residue: 0.0964 time to fit residues: 35.4911 Evaluate side-chains 223 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 181 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 72 HIS Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 338 THR Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 207 PHE Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 338 THR Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain C residue 0 HIS Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 24 CYS Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 238 ASN Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 383 TYR Chi-restraints excluded: chain A residue 17 CYS Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 118 HIS Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain F residue -5 LEU Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 160 HIS Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 383 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 4 optimal weight: 6.9990 chunk 153 optimal weight: 0.9980 chunk 89 optimal weight: 10.0000 chunk 148 optimal weight: 0.0970 chunk 226 optimal weight: 0.9990 chunk 1 optimal weight: 20.0000 chunk 86 optimal weight: 2.9990 chunk 187 optimal weight: 0.9990 chunk 206 optimal weight: 0.9980 chunk 188 optimal weight: 1.9990 chunk 152 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 160 HIS ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 68 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 = 0.3822 r_free = 0.3822 target = 0.140170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.096282 restraints weight = 30080.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.094868 restraints weight = 26581.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.096326 restraints weight = 25750.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.096192 restraints weight = 19284.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.096556 restraints weight = 17213.258| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17998 Z= 0.105 Angle : 0.559 14.711 24460 Z= 0.264 Chirality : 0.041 0.200 2852 Planarity : 0.005 0.053 3185 Dihedral : 3.667 59.749 2515 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.39 % Favored : 97.57 % Rotamer: Outliers : 2.54 % Allowed : 23.69 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % 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: 0.90 (0.18), residues: 2347 helix: 2.23 (0.18), residues: 891 sheet: -0.05 (0.19), residues: 722 loop : -0.70 (0.22), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 214 TYR 0.023 0.001 TYR E 365 PHE 0.012 0.001 PHE F 97 TRP 0.031 0.002 TRP E 43 HIS 0.004 0.000 HIS E 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (17998) covalent geometry : angle 0.55945 / 0.26 (24460) hydrogen bonds : bond 0.02862 / 1.94 ( 901) hydrogen bonds : angle 3.99613 / 2.86 ( 2679) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 187 time to evaluate : 0.549 Fit side-chains REVERT: D 21 LEU cc_start: 0.9308 (mt) cc_final: 0.9060 (mt) REVERT: D 48 ARG cc_start: 0.7218 (ptp90) cc_final: 0.6809 (mtm-85) REVERT: D 72 HIS cc_start: 0.7963 (OUTLIER) cc_final: 0.7249 (t70) REVERT: E 80 ILE cc_start: 0.9010 (mt) cc_final: 0.8726 (mm) REVERT: E 90 LYS cc_start: 0.8099 (tttt) cc_final: 0.7798 (tttt) REVERT: B 132 SER cc_start: 0.8858 (m) cc_final: 0.8183 (p) REVERT: B 173 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8444 (mm) REVERT: B 243 GLU cc_start: 0.2514 (OUTLIER) cc_final: 0.1343 (pm20) REVERT: B 271 MET cc_start: 0.8945 (tpp) cc_final: 0.8445 (ttm) REVERT: C -4 TYR cc_start: 0.7852 (m-80) cc_final: 0.7562 (m-80) REVERT: C 285 MET cc_start: 0.8394 (ttm) cc_final: 0.7860 (ttt) REVERT: A 15 ASP cc_start: 0.8957 (m-30) cc_final: 0.8563 (m-30) REVERT: A 35 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7628 (tp) REVERT: A 97 PHE cc_start: 0.8148 (m-80) cc_final: 0.7839 (m-80) REVERT: F -5 LEU cc_start: 0.2986 (OUTLIER) cc_final: 0.2110 (tp) outliers start: 47 outliers final: 40 residues processed: 222 average time/residue: 0.1029 time to fit residues: 38.3178 Evaluate side-chains 226 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 181 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 72 HIS Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 338 THR Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 207 PHE Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 338 THR Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain C residue 0 HIS Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 24 CYS Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 238 ASN Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 383 TYR Chi-restraints excluded: chain A residue 17 CYS Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 118 HIS Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain F residue -5 LEU Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 160 HIS Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 383 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 138 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 210 optimal weight: 0.3980 chunk 87 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 145 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 181 optimal weight: 0.7980 chunk 189 optimal weight: 6.9990 chunk 119 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 HIS ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 68 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 = 0.3821 r_free = 0.3821 target = 0.140096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.095936 restraints weight = 30046.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.094712 restraints weight = 26864.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.095486 restraints weight = 23604.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.095946 restraints weight = 19200.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.096063 restraints weight = 17310.985| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 17998 Z= 0.103 Angle : 0.556 14.114 24460 Z= 0.262 Chirality : 0.041 0.195 2852 Planarity : 0.005 0.053 3185 Dihedral : 3.636 59.920 2515 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.56 % Favored : 97.40 % Rotamer: Outliers : 2.65 % Allowed : 23.63 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % 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: 0.93 (0.18), residues: 2347 helix: 2.23 (0.18), residues: 890 sheet: 0.00 (0.19), residues: 714 loop : -0.67 (0.22), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 231 TYR 0.010 0.001 TYR D 172 PHE 0.012 0.001 PHE F 97 TRP 0.030 0.002 TRP E 43 HIS 0.005 0.000 HIS E 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.10 (17998) covalent geometry : angle 0.55597 / 0.26 (24460) hydrogen bonds : bond 0.02778 / 1.89 ( 901) hydrogen bonds : angle 3.96689 / 2.84 ( 2679) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2347.62 seconds wall clock time: 41 minutes 35.67 seconds (2495.67 seconds total)