Starting phenix.real_space_refine on Thu Feb 5 16:52:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e77_47660/02_2026/9e77_47660_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e77_47660/02_2026/9e77_47660.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9e77_47660/02_2026/9e77_47660_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e77_47660/02_2026/9e77_47660_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9e77_47660/02_2026/9e77_47660.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e77_47660/02_2026/9e77_47660.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.028 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 S 107 5.16 5 C 11835 2.51 5 N 3184 2.21 5 O 3507 1.98 5 F 2 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18636 Number of models: 1 Model: "" Number of chains: 10 Chain: "B" Number of atoms: 1722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1722 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 205} Chain: "H" Number of atoms: 1391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1391 Classifications: {'peptide': 174} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 163} Chain breaks: 1 Chain: "A" Number of atoms: 3284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3284 Classifications: {'peptide': 411} Link IDs: {'PTRANS': 9, 'TRANS': 401} Chain breaks: 1 Chain: "C" Number of atoms: 3216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3216 Classifications: {'peptide': 404} Link IDs: {'PTRANS': 13, 'TRANS': 390} Chain: "D" Number of atoms: 2143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2143 Classifications: {'peptide': 266} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 260} Chain: "E" Number of atoms: 2366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2366 Classifications: {'peptide': 298} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 287} Chain breaks: 1 Chain: "F" Number of atoms: 2190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2190 Classifications: {'peptide': 273} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 262} Chain breaks: 1 Chain: "G" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1687 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 4, 'TRANS': 208} Chain: "I" Number of atoms: 599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 599 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "E" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Unusual residues: {' ZN': 1, '6LT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.64, per 1000 atoms: 0.20 Number of scatterers: 18636 At special positions: 0 Unit cell: (123.48, 151.2, 174.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 107 16.00 F 2 9.00 O 3507 8.00 N 3184 7.00 C 11835 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: 1.84 Conformation dependent library (CDL) restraints added in 672.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E 402 " pdb="ZN ZN E 402 " - pdb=" NE2 HIS E 138 " pdb="ZN ZN E 402 " - pdb=" NE2 HIS E 140 " 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4446 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 8 sheets defined 68.4% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'B' and resid 231 through 248 removed outlier: 3.674A pdb=" N VAL B 236 " --> pdb=" O LEU B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 268 Processing helix chain 'B' and resid 269 through 271 No H-bonds generated for 'chain 'B' and resid 269 through 271' Processing helix chain 'B' and resid 272 through 288 removed outlier: 5.075A pdb=" N LYS B 278 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N TYR B 279 " --> pdb=" O THR B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 304 removed outlier: 4.366A pdb=" N TYR B 302 " --> pdb=" O GLU B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 321 Processing helix chain 'B' and resid 322 through 333 removed outlier: 3.809A pdb=" N PHE B 326 " --> pdb=" O ASP B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 345 Processing helix chain 'B' and resid 346 through 363 removed outlier: 3.566A pdb=" N LEU B 350 " --> pdb=" O HIS B 346 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE B 354 " --> pdb=" O LEU B 350 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG B 355 " --> pdb=" O LEU B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 379 Processing helix chain 'B' and resid 381 through 395 Processing helix chain 'B' and resid 417 through 442 removed outlier: 4.250A pdb=" N TYR B 421 " --> pdb=" O GLY B 417 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU B 442 " --> pdb=" O VAL B 438 " (cutoff:3.500A) Processing helix chain 'H' and resid 13 through 27 Processing helix chain 'H' and resid 33 through 47 Processing helix chain 'H' and resid 49 through 60 Processing helix chain 'H' and resid 61 through 68 Processing helix chain 'H' and resid 69 through 83 removed outlier: 3.624A pdb=" N GLY H 73 " --> pdb=" O SER H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 94 removed outlier: 3.803A pdb=" N ASN H 94 " --> pdb=" O TYR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 124 Processing helix chain 'H' and resid 130 through 138 Processing helix chain 'H' and resid 140 through 150 removed outlier: 3.607A pdb=" N ALA H 144 " --> pdb=" O PRO H 140 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LEU H 149 " --> pdb=" O VAL H 145 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N GLU H 150 " --> pdb=" O LYS H 146 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 209 Processing helix chain 'A' and resid 43 through 51 removed outlier: 3.956A pdb=" N TYR A 51 " --> pdb=" O TYR A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 67 removed outlier: 4.109A pdb=" N GLU A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 82 Processing helix chain 'A' and resid 83 through 87 removed outlier: 4.184A pdb=" N PHE A 86 " --> pdb=" O GLN A 83 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ASN A 87 " --> pdb=" O ARG A 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 83 through 87' Processing helix chain 'A' and resid 88 through 102 Processing helix chain 'A' and resid 127 through 156 Processing helix chain 'A' and resid 157 through 176 Processing helix chain 'A' and resid 178 through 189 Processing helix chain 'A' and resid 190 through 192 No H-bonds generated for 'chain 'A' and resid 190 through 192' Processing helix chain 'A' and resid 194 through 213 Processing helix chain 'A' and resid 214 through 228 removed outlier: 4.097A pdb=" N SER A 220 " --> pdb=" O SER A 216 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TYR A 221 " --> pdb=" O HIS A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 234 Processing helix chain 'A' and resid 245 through 260 Processing helix chain 'A' and resid 262 through 271 Processing helix chain 'A' and resid 272 through 273 No H-bonds generated for 'chain 'A' and resid 272 through 273' Processing helix chain 'A' and resid 274 through 278 Processing helix chain 'A' and resid 285 through 301 removed outlier: 3.525A pdb=" N ALA A 297 " --> pdb=" O GLY A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 310 Processing helix chain 'A' and resid 316 through 321 Processing helix chain 'A' and resid 323 through 335 Processing helix chain 'A' and resid 337 through 353 removed outlier: 4.280A pdb=" N ASP A 350 " --> pdb=" O ASP A 346 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ASN A 351 " --> pdb=" O GLU A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 378 removed outlier: 3.554A pdb=" N PHE A 378 " --> pdb=" O LEU A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 393 Processing helix chain 'A' and resid 396 through 411 removed outlier: 3.780A pdb=" N GLU A 410 " --> pdb=" O GLN A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 463 removed outlier: 3.651A pdb=" N THR A 434 " --> pdb=" O ASP A 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 16 Processing helix chain 'C' and resid 20 through 30 Processing helix chain 'C' and resid 38 through 44 removed outlier: 4.404A pdb=" N LEU C 42 " --> pdb=" O ASN C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 64 Processing helix chain 'C' and resid 70 through 72 No H-bonds generated for 'chain 'C' and resid 70 through 72' Processing helix chain 'C' and resid 73 through 88 Processing helix chain 'C' and resid 92 through 97 removed outlier: 3.611A pdb=" N THR C 97 " --> pdb=" O ARG C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 115 Processing helix chain 'C' and resid 122 through 130 removed outlier: 3.768A pdb=" N GLN C 126 " --> pdb=" O GLY C 122 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ILE C 128 " --> pdb=" O LEU C 124 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ASP C 129 " --> pdb=" O LYS C 125 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LYS C 130 " --> pdb=" O GLN C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 152 removed outlier: 4.350A pdb=" N ALA C 143 " --> pdb=" O THR C 139 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASP C 144 " --> pdb=" O SER C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 163 Processing helix chain 'C' and resid 177 through 195 removed outlier: 4.094A pdb=" N PHE C 181 " --> pdb=" O ASP C 177 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLY C 189 " --> pdb=" O TYR C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 210 removed outlier: 3.893A pdb=" N TYR C 203 " --> pdb=" O GLU C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 235 removed outlier: 3.569A pdb=" N GLU C 222 " --> pdb=" O HIS C 218 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N LYS C 226 " --> pdb=" O GLU C 222 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU C 229 " --> pdb=" O LYS C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 257 Processing helix chain 'C' and resid 258 through 267 Processing helix chain 'C' and resid 271 through 282 Processing helix chain 'C' and resid 282 through 289 Processing helix chain 'C' and resid 294 through 310 removed outlier: 3.978A pdb=" N TYR C 303 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS C 304 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 323 Processing helix chain 'C' and resid 330 through 344 Processing helix chain 'C' and resid 369 through 399 removed outlier: 3.619A pdb=" N GLU C 396 " --> pdb=" O ALA C 392 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE C 397 " --> pdb=" O MET C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 406 removed outlier: 4.018A pdb=" N GLN C 405 " --> pdb=" O PRO C 401 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LYS C 406 " --> pdb=" O GLN C 402 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 401 through 406' Processing helix chain 'D' and resid 142 through 158 Processing helix chain 'D' and resid 160 through 173 removed outlier: 3.819A pdb=" N ALA D 164 " --> pdb=" O ASP D 160 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LEU D 173 " --> pdb=" O ASN D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 198 removed outlier: 3.791A pdb=" N TYR D 187 " --> pdb=" O LEU D 183 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LYS D 188 " --> pdb=" O GLN D 184 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N VAL D 189 " --> pdb=" O ILE D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 212 Processing helix chain 'D' and resid 218 through 236 Processing helix chain 'D' and resid 239 through 252 Processing helix chain 'D' and resid 253 through 258 removed outlier: 3.598A pdb=" N GLN D 257 " --> pdb=" O ARG D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 270 Processing helix chain 'D' and resid 274 through 285 Processing helix chain 'D' and resid 298 through 313 Processing helix chain 'D' and resid 321 through 329 Processing helix chain 'D' and resid 331 through 345 Processing helix chain 'D' and resid 365 through 390 Processing helix chain 'D' and resid 392 through 406 removed outlier: 3.736A pdb=" N MET D 404 " --> pdb=" O MET D 400 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA D 405 " --> pdb=" O GLU D 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 30 removed outlier: 3.710A pdb=" N ILE E 28 " --> pdb=" O ILE E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 42 Processing helix chain 'E' and resid 59 through 73 removed outlier: 3.880A pdb=" N GLY E 73 " --> pdb=" O ALA E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 126 removed outlier: 4.133A pdb=" N ALA E 118 " --> pdb=" O TYR E 114 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN E 126 " --> pdb=" O GLU E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 162 removed outlier: 3.574A pdb=" N PHE E 161 " --> pdb=" O LEU E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 179 removed outlier: 3.584A pdb=" N ILE E 176 " --> pdb=" O PRO E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 209 No H-bonds generated for 'chain 'E' and resid 207 through 209' Processing helix chain 'E' and resid 210 through 217 removed outlier: 3.888A pdb=" N PHE E 214 " --> pdb=" O LYS E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 231 through 251 removed outlier: 4.356A pdb=" N ASN E 243 " --> pdb=" O GLU E 239 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LYS E 244 " --> pdb=" O LEU E 240 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N VAL E 247 " --> pdb=" O ASN E 243 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N ASN E 248 " --> pdb=" O LYS E 244 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N THR E 249 " --> pdb=" O TYR E 245 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU E 250 " --> pdb=" O TRP E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 258 removed outlier: 4.046A pdb=" N THR E 257 " --> pdb=" O SER E 253 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASN E 258 " --> pdb=" O SER E 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 253 through 258' Processing helix chain 'E' and resid 259 through 282 Processing helix chain 'E' and resid 298 through 329 removed outlier: 3.806A pdb=" N LYS E 302 " --> pdb=" O ASP E 298 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN E 321 " --> pdb=" O GLY E 317 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 63 removed outlier: 3.707A pdb=" N ILE F 48 " --> pdb=" O HIS F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 116 removed outlier: 3.570A pdb=" N VAL F 115 " --> pdb=" O GLN F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 143 Processing helix chain 'F' and resid 193 through 206 Processing helix chain 'F' and resid 216 through 248 Processing helix chain 'F' and resid 253 through 265 removed outlier: 3.618A pdb=" N LEU F 257 " --> pdb=" O ASN F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 272 through 313 Processing helix chain 'G' and resid 11 through 18 Processing helix chain 'G' and resid 24 through 37 Processing helix chain 'G' and resid 44 through 49 Processing helix chain 'G' and resid 49 through 55 Processing helix chain 'G' and resid 60 through 72 removed outlier: 3.810A pdb=" N LEU G 64 " --> pdb=" O ASN G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 81 Processing helix chain 'G' and resid 89 through 108 removed outlier: 3.761A pdb=" N ARG G 107 " --> pdb=" O SER G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 121 Processing helix chain 'G' and resid 124 through 138 removed outlier: 3.601A pdb=" N LEU G 128 " --> pdb=" O ASN G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 222 removed outlier: 3.676A pdb=" N ILE G 170 " --> pdb=" O ASP G 166 " (cutoff:3.500A) Processing helix chain 'I' and resid 22 through 34 Processing sheet with id=AA1, first strand: chain 'B' and resid 368 through 370 removed outlier: 7.262A pdb=" N VAL A 382 " --> pdb=" O GLY B 400 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N ILE B 402 " --> pdb=" O VAL A 382 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ALA A 384 " --> pdb=" O ILE B 402 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N VAL A 382 " --> pdb=" O ALA A 426 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N LEU C 315 " --> pdb=" O ALA A 415 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N VAL A 417 " --> pdb=" O LEU C 315 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU C 317 " --> pdb=" O VAL A 417 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N LEU C 315 " --> pdb=" O PHE C 360 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 128 through 129 Processing sheet with id=AA3, first strand: chain 'C' and resid 137 through 138 Processing sheet with id=AA4, first strand: chain 'D' and resid 351 through 353 removed outlier: 6.650A pdb=" N GLN G 142 " --> pdb=" O ASP G 155 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 221 through 223 removed outlier: 3.765A pdb=" N ASN E 132 " --> pdb=" O GLY E 83 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N MET E 81 " --> pdb=" O ILE E 134 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N TRP E 136 " --> pdb=" O GLY E 79 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N GLY E 79 " --> pdb=" O TRP E 136 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LYS E 84 " --> pdb=" O ILE E 92 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ILE E 92 " --> pdb=" O LYS E 84 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ASP E 86 " --> pdb=" O MET E 90 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N MET E 90 " --> pdb=" O ASP E 86 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ASP E 94 " --> pdb=" O SER E 58 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 178 through 186 removed outlier: 4.703A pdb=" N VAL F 167 " --> pdb=" O LEU F 186 " (cutoff:3.500A) removed outlier: 9.907A pdb=" N LEU F 150 " --> pdb=" O GLU F 120 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N LEU F 122 " --> pdb=" O LEU F 150 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N LEU F 152 " --> pdb=" O LEU F 122 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N TRP F 124 " --> pdb=" O LEU F 152 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N LEU F 154 " --> pdb=" O TRP F 124 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N THR F 126 " --> pdb=" O LEU F 154 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU F 122 " --> pdb=" O LEU F 72 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU F 72 " --> pdb=" O LEU F 122 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N TRP F 124 " --> pdb=" O GLY F 70 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N GLY F 70 " --> pdb=" O TRP F 124 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N ILE F 69 " --> pdb=" O GLU F 88 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N GLU F 88 " --> pdb=" O ILE F 69 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA F 71 " --> pdb=" O SER F 86 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N SER F 86 " --> pdb=" O ALA F 71 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ILE F 73 " --> pdb=" O MET F 84 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N SER F 40 " --> pdb=" O ILE F 81 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N VAL F 83 " --> pdb=" O SER F 40 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ALA F 42 " --> pdb=" O VAL F 83 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N ASN F 85 " --> pdb=" O ALA F 42 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 91 through 94 Processing sheet with id=AA8, first strand: chain 'I' and resid 12 through 13 removed outlier: 6.975A pdb=" N LYS I 6 " --> pdb=" O LEU I 69 " (cutoff:3.500A) 1165 hydrogen bonds defined for protein. 3417 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.64 Time building geometry restraints manager: 2.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3229 1.32 - 1.44: 4728 1.44 - 1.57: 10841 1.57 - 1.69: 0 1.69 - 1.81: 173 Bond restraints: 18971 Sorted by residual: bond pdb=" C ALA F 223 " pdb=" O ALA F 223 " ideal model delta sigma weight residual 1.236 1.318 -0.081 1.15e-02 7.56e+03 5.02e+01 bond pdb=" N LYS I 60 " pdb=" CA LYS I 60 " ideal model delta sigma weight residual 1.457 1.535 -0.077 1.29e-02 6.01e+03 3.58e+01 bond pdb=" C THR F 216 " pdb=" O THR F 216 " ideal model delta sigma weight residual 1.234 1.317 -0.084 1.46e-02 4.69e+03 3.29e+01 bond pdb=" C HIS F 220 " pdb=" O HIS F 220 " ideal model delta sigma weight residual 1.236 1.299 -0.063 1.15e-02 7.56e+03 2.98e+01 bond pdb=" C SER F 226 " pdb=" O SER F 226 " ideal model delta sigma weight residual 1.236 1.292 -0.056 1.15e-02 7.56e+03 2.38e+01 ... (remaining 18966 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.01: 25421 3.01 - 6.03: 185 6.03 - 9.04: 24 9.04 - 12.06: 3 12.06 - 15.07: 1 Bond angle restraints: 25634 Sorted by residual: angle pdb=" N VAL F 217 " pdb=" CA VAL F 217 " pdb=" C VAL F 217 " ideal model delta sigma weight residual 110.62 102.45 8.17 1.02e+00 9.61e-01 6.41e+01 angle pdb=" N GLN E 110 " pdb=" CA GLN E 110 " pdb=" C GLN E 110 " ideal model delta sigma weight residual 113.20 102.62 10.58 1.36e+00 5.41e-01 6.05e+01 angle pdb=" N ALA E 109 " pdb=" CA ALA E 109 " pdb=" C ALA E 109 " ideal model delta sigma weight residual 109.07 120.15 -11.08 1.52e+00 4.33e-01 5.31e+01 angle pdb=" N LEU C 56 " pdb=" CA LEU C 56 " pdb=" C LEU C 56 " ideal model delta sigma weight residual 111.28 104.78 6.50 1.09e+00 8.42e-01 3.56e+01 angle pdb=" C SER F 226 " pdb=" N ALA F 227 " pdb=" CA ALA F 227 " ideal model delta sigma weight residual 120.28 112.60 7.68 1.34e+00 5.57e-01 3.29e+01 ... (remaining 25629 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 9654 17.93 - 35.85: 1433 35.85 - 53.78: 391 53.78 - 71.70: 81 71.70 - 89.63: 46 Dihedral angle restraints: 11605 sinusoidal: 4747 harmonic: 6858 Sorted by residual: dihedral pdb=" CA ASP D 159 " pdb=" C ASP D 159 " pdb=" N ASP D 160 " pdb=" CA ASP D 160 " ideal model delta harmonic sigma weight residual 180.00 156.45 23.55 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA LEU E 98 " pdb=" C LEU E 98 " pdb=" N PRO E 99 " pdb=" CA PRO E 99 " ideal model delta harmonic sigma weight residual -180.00 -159.63 -20.37 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA GLU C 222 " pdb=" C GLU C 222 " pdb=" N SER C 223 " pdb=" CA SER C 223 " ideal model delta harmonic sigma weight residual 180.00 160.34 19.66 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 11602 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 2822 0.100 - 0.200: 76 0.200 - 0.300: 2 0.300 - 0.400: 0 0.400 - 0.499: 1 Chirality restraints: 2901 Sorted by residual: chirality pdb=" CB VAL C 71 " pdb=" CA VAL C 71 " pdb=" CG1 VAL C 71 " pdb=" CG2 VAL C 71 " both_signs ideal model delta sigma weight residual False -2.63 -2.13 -0.50 2.00e-01 2.50e+01 6.23e+00 chirality pdb=" CA MET B 244 " pdb=" N MET B 244 " pdb=" C MET B 244 " pdb=" CB MET B 244 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CB VAL C 64 " pdb=" CA VAL C 64 " pdb=" CG1 VAL C 64 " pdb=" CG2 VAL C 64 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 2898 not shown) Planarity restraints: 3286 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS I 60 " -0.023 2.00e-02 2.50e+03 4.61e-02 2.12e+01 pdb=" C LYS I 60 " 0.080 2.00e-02 2.50e+03 pdb=" O LYS I 60 " -0.029 2.00e-02 2.50e+03 pdb=" N ILE I 61 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER F 215 " 0.022 2.00e-02 2.50e+03 4.25e-02 1.81e+01 pdb=" C SER F 215 " -0.074 2.00e-02 2.50e+03 pdb=" O SER F 215 " 0.027 2.00e-02 2.50e+03 pdb=" N THR F 216 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL C 71 " -0.065 5.00e-02 4.00e+02 9.82e-02 1.54e+01 pdb=" N PRO C 72 " 0.170 5.00e-02 4.00e+02 pdb=" CA PRO C 72 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO C 72 " -0.054 5.00e-02 4.00e+02 ... (remaining 3283 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 22 2.51 - 3.11: 13594 3.11 - 3.71: 28262 3.71 - 4.30: 37564 4.30 - 4.90: 65829 Nonbonded interactions: 145271 Sorted by model distance: nonbonded pdb=" OD2 ASP E 151 " pdb="ZN ZN E 402 " model vdw 1.918 2.230 nonbonded pdb=" N4 6LT E 401 " pdb="ZN ZN E 402 " model vdw 1.962 2.310 nonbonded pdb=" ND2 ASN H 209 " pdb=" NZ LYS F 297 " model vdw 2.234 3.200 nonbonded pdb=" O ASP I 52 " pdb=" N LYS I 54 " model vdw 2.321 3.120 nonbonded pdb=" O ILE I 3 " pdb=" C LYS I 4 " model vdw 2.325 3.270 ... (remaining 145266 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.050 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 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 : 0.004 0.084 18973 Z= 0.238 Angle : 0.658 15.075 25634 Z= 0.376 Chirality : 0.042 0.499 2901 Planarity : 0.004 0.098 3286 Dihedral : 18.904 89.628 7159 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.83 % Allowed : 5.04 % Favored : 94.14 % Rotamer: Outliers : 2.55 % Allowed : 26.13 % Favored : 71.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.18), residues: 2302 helix: 2.04 (0.14), residues: 1515 sheet: -0.02 (0.43), residues: 148 loop : -1.75 (0.23), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 148 TYR 0.017 0.001 TYR C 267 PHE 0.021 0.001 PHE C 74 TRP 0.007 0.001 TRP H 153 HIS 0.009 0.001 HIS F 225 Details of bonding type rmsd covalent geometry : bond 0.00404 (18971) covalent geometry : angle 0.65798 (25634) hydrogen bonds : bond 0.06231 ( 1165) hydrogen bonds : angle 4.22538 ( 3417) metal coordination : bond 0.00533 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 213 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 441 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.7661 (ttmm) REVERT: C 13 ARG cc_start: 0.8077 (tpp80) cc_final: 0.7861 (mtt90) REVERT: C 63 PHE cc_start: 0.7954 (OUTLIER) cc_final: 0.6611 (t80) REVERT: D 184 GLN cc_start: 0.8198 (mp10) cc_final: 0.7354 (mm110) REVERT: E 106 ARG cc_start: 0.5049 (OUTLIER) cc_final: 0.4014 (ptm160) REVERT: F 188 TYR cc_start: 0.8920 (p90) cc_final: 0.8581 (p90) outliers start: 52 outliers final: 34 residues processed: 251 average time/residue: 0.1308 time to fit residues: 50.7604 Evaluate side-chains 233 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 196 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 412 ASP Chi-restraints excluded: chain B residue 435 ASN Chi-restraints excluded: chain B residue 441 LYS Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain H residue 196 GLN Chi-restraints excluded: chain A residue 217 HIS Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 54 HIS Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 288 HIS Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 106 ARG Chi-restraints excluded: chain E residue 307 SER Chi-restraints excluded: chain F residue 112 PHE Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 72 TYR Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain I residue 50 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 6.9990 chunk 227 optimal weight: 0.6980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 435 ASN H 209 ASN C 282 HIS ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 303 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.146459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.096229 restraints weight = 25713.698| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 2.49 r_work: 0.2992 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.0646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 18973 Z= 0.187 Angle : 0.565 8.636 25634 Z= 0.292 Chirality : 0.041 0.301 2901 Planarity : 0.004 0.088 3286 Dihedral : 6.690 86.774 2621 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.60 % Favored : 94.09 % Rotamer: Outliers : 3.59 % Allowed : 25.34 % Favored : 71.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.18), residues: 2302 helix: 2.01 (0.14), residues: 1526 sheet: 0.01 (0.44), residues: 146 loop : -1.73 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 106 TYR 0.024 0.002 TYR C 267 PHE 0.028 0.001 PHE B 259 TRP 0.008 0.001 TRP H 153 HIS 0.006 0.001 HIS E 138 Details of bonding type rmsd covalent geometry : bond 0.00454 (18971) covalent geometry : angle 0.56495 (25634) hydrogen bonds : bond 0.04704 ( 1165) hydrogen bonds : angle 3.91698 ( 3417) metal coordination : bond 0.00798 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 210 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 244 MET cc_start: -0.1239 (mpp) cc_final: -0.1500 (mpp) REVERT: B 338 MET cc_start: 0.5592 (mpp) cc_final: 0.5204 (mpp) REVERT: H 142 GLU cc_start: 0.7988 (mp0) cc_final: 0.7784 (mp0) REVERT: A 343 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.8011 (ttpp) REVERT: A 410 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.6303 (pp20) REVERT: C 10 ASN cc_start: 0.8340 (m-40) cc_final: 0.7966 (m110) REVERT: C 63 PHE cc_start: 0.7320 (OUTLIER) cc_final: 0.5535 (t80) REVERT: D 355 ILE cc_start: 0.8719 (OUTLIER) cc_final: 0.8279 (mp) REVERT: E 67 MET cc_start: 0.9034 (mmm) cc_final: 0.8819 (mmm) REVERT: E 92 ILE cc_start: 0.8596 (OUTLIER) cc_final: 0.8363 (mp) REVERT: I 32 GLU cc_start: 0.8833 (mt-10) cc_final: 0.8250 (mp0) outliers start: 73 outliers final: 38 residues processed: 266 average time/residue: 0.1429 time to fit residues: 58.7284 Evaluate side-chains 239 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 196 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 412 ASP Chi-restraints excluded: chain B residue 435 ASN Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 157 SER Chi-restraints excluded: chain H residue 208 GLU Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 54 HIS Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 88 CYS Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 385 GLU Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain F residue 112 PHE Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 72 TYR Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 108 MET Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain I residue 44 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 217 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 112 optimal weight: 0.9980 chunk 131 optimal weight: 0.8980 chunk 6 optimal weight: 30.0000 chunk 87 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 170 optimal weight: 0.8980 chunk 151 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 33 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.147994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.103823 restraints weight = 25699.384| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.88 r_work: 0.2990 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.0761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18973 Z= 0.127 Angle : 0.515 7.952 25634 Z= 0.267 Chirality : 0.039 0.394 2901 Planarity : 0.004 0.092 3286 Dihedral : 5.487 70.850 2581 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.34 % Favored : 94.40 % Rotamer: Outliers : 3.83 % Allowed : 25.10 % Favored : 71.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.18), residues: 2302 helix: 2.16 (0.14), residues: 1524 sheet: 0.14 (0.43), residues: 148 loop : -1.72 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 344 TYR 0.017 0.001 TYR I 45 PHE 0.018 0.001 PHE B 259 TRP 0.007 0.001 TRP H 57 HIS 0.004 0.001 HIS F 225 Details of bonding type rmsd covalent geometry : bond 0.00290 (18971) covalent geometry : angle 0.51486 (25634) hydrogen bonds : bond 0.04104 ( 1165) hydrogen bonds : angle 3.76643 ( 3417) metal coordination : bond 0.00498 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 209 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 282 LEU cc_start: 0.5563 (tt) cc_final: 0.5237 (tt) REVERT: H 142 GLU cc_start: 0.7926 (mp0) cc_final: 0.7696 (mp0) REVERT: A 343 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7805 (ttpp) REVERT: C 10 ASN cc_start: 0.8341 (m-40) cc_final: 0.7937 (m110) REVERT: C 63 PHE cc_start: 0.7238 (OUTLIER) cc_final: 0.5345 (t80) REVERT: E 67 MET cc_start: 0.8782 (mmm) cc_final: 0.8564 (mmm) REVERT: I 29 ARG cc_start: 0.8295 (tpp-160) cc_final: 0.7818 (tpp-160) REVERT: I 32 GLU cc_start: 0.8846 (mt-10) cc_final: 0.8240 (mp0) REVERT: I 41 GLN cc_start: 0.9061 (mt0) cc_final: 0.8811 (mt0) REVERT: I 46 SER cc_start: 0.8504 (m) cc_final: 0.8202 (p) REVERT: I 48 LYS cc_start: 0.8504 (mmmt) cc_final: 0.8145 (mmmt) outliers start: 78 outliers final: 49 residues processed: 268 average time/residue: 0.1395 time to fit residues: 57.3803 Evaluate side-chains 252 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 201 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 412 ASP Chi-restraints excluded: chain B residue 435 ASN Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 196 GLN Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 54 HIS Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 88 CYS Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 149 CYS Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain D residue 288 HIS Chi-restraints excluded: chain D residue 311 SER Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 260 ASP Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain F residue 112 PHE Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 72 TYR Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 108 MET Chi-restraints excluded: chain G residue 114 SER Chi-restraints excluded: chain G residue 155 ASP Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain G residue 163 ARG Chi-restraints excluded: chain I residue 44 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 79 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 217 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 165 optimal weight: 0.3980 chunk 15 optimal weight: 1.9990 chunk 200 optimal weight: 0.6980 chunk 221 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 202 optimal weight: 10.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 320 ASN ** E 108 ASN ** 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 = 0.3831 r_free = 0.3831 target = 0.148834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.105084 restraints weight = 25670.879| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.70 r_work: 0.3002 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.0869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18973 Z= 0.117 Angle : 0.498 8.156 25634 Z= 0.259 Chirality : 0.038 0.250 2901 Planarity : 0.004 0.087 3286 Dihedral : 5.266 71.949 2574 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.73 % Favored : 94.05 % Rotamer: Outliers : 3.83 % Allowed : 25.64 % Favored : 70.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.18), residues: 2302 helix: 2.21 (0.14), residues: 1525 sheet: 0.19 (0.44), residues: 148 loop : -1.71 (0.23), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 344 TYR 0.016 0.001 TYR C 267 PHE 0.014 0.001 PHE B 259 TRP 0.006 0.001 TRP H 57 HIS 0.004 0.001 HIS F 225 Details of bonding type rmsd covalent geometry : bond 0.00264 (18971) covalent geometry : angle 0.49825 (25634) hydrogen bonds : bond 0.03896 ( 1165) hydrogen bonds : angle 3.68317 ( 3417) metal coordination : bond 0.00433 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 207 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 343 LYS cc_start: 0.8104 (OUTLIER) cc_final: 0.7748 (ttpp) REVERT: C 10 ASN cc_start: 0.8342 (m-40) cc_final: 0.7968 (m110) REVERT: C 13 ARG cc_start: 0.7857 (tpp80) cc_final: 0.7428 (mtt90) REVERT: C 63 PHE cc_start: 0.7125 (OUTLIER) cc_final: 0.5258 (t80) REVERT: C 68 MET cc_start: 0.7026 (OUTLIER) cc_final: 0.6320 (mtt) REVERT: D 267 MET cc_start: 0.8831 (mmt) cc_final: 0.8273 (mmt) REVERT: D 355 ILE cc_start: 0.8545 (OUTLIER) cc_final: 0.8121 (mp) REVERT: E 92 ILE cc_start: 0.8363 (OUTLIER) cc_final: 0.8136 (mp) REVERT: F 188 TYR cc_start: 0.9068 (p90) cc_final: 0.8384 (p90) REVERT: F 222 ILE cc_start: 0.6538 (OUTLIER) cc_final: 0.6193 (mt) REVERT: F 285 ASP cc_start: 0.8421 (OUTLIER) cc_final: 0.8176 (m-30) REVERT: I 29 ARG cc_start: 0.8267 (tpp-160) cc_final: 0.7761 (tpp-160) REVERT: I 32 GLU cc_start: 0.8820 (mt-10) cc_final: 0.8178 (mp0) REVERT: I 41 GLN cc_start: 0.9066 (mt0) cc_final: 0.8802 (mt0) REVERT: I 60 LYS cc_start: 0.8103 (tptp) cc_final: 0.7686 (tppt) outliers start: 78 outliers final: 47 residues processed: 266 average time/residue: 0.1402 time to fit residues: 57.7904 Evaluate side-chains 256 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 202 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 412 ASP Chi-restraints excluded: chain B residue 435 ASN Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 54 HIS Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 68 MET Chi-restraints excluded: chain C residue 88 CYS Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 389 SER Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 260 ASP Chi-restraints excluded: chain F residue 112 PHE Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 222 ILE Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 285 ASP Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 72 TYR Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 108 MET Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain G residue 163 ARG Chi-restraints excluded: chain I residue 44 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 193 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 145 optimal weight: 0.9990 chunk 135 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 208 optimal weight: 6.9990 chunk 121 optimal weight: 9.9990 chunk 133 optimal weight: 0.0970 chunk 153 optimal weight: 0.0570 chunk 199 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 overall best weight: 0.8300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 209 ASN C 290 ASN G 33 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.148753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.104839 restraints weight = 25416.126| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.70 r_work: 0.3004 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.0970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18973 Z= 0.120 Angle : 0.504 8.631 25634 Z= 0.261 Chirality : 0.039 0.420 2901 Planarity : 0.004 0.095 3286 Dihedral : 5.163 72.016 2572 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.52 % Favored : 94.27 % Rotamer: Outliers : 3.73 % Allowed : 25.83 % Favored : 70.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.18), residues: 2302 helix: 2.23 (0.14), residues: 1526 sheet: 0.21 (0.44), residues: 148 loop : -1.69 (0.23), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 205 TYR 0.016 0.001 TYR C 267 PHE 0.012 0.001 PHE F 112 TRP 0.006 0.001 TRP H 57 HIS 0.004 0.001 HIS F 225 Details of bonding type rmsd covalent geometry : bond 0.00273 (18971) covalent geometry : angle 0.50414 (25634) hydrogen bonds : bond 0.03876 ( 1165) hydrogen bonds : angle 3.67352 ( 3417) metal coordination : bond 0.00430 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 206 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 244 MET cc_start: -0.2158 (mpp) cc_final: -0.2793 (mtt) REVERT: A 90 MET cc_start: 0.8012 (mmm) cc_final: 0.7089 (mmt) REVERT: A 343 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7796 (ttpp) REVERT: C 10 ASN cc_start: 0.8367 (m-40) cc_final: 0.7988 (m110) REVERT: C 13 ARG cc_start: 0.7897 (tpp80) cc_final: 0.7454 (mtt90) REVERT: C 63 PHE cc_start: 0.7096 (OUTLIER) cc_final: 0.5155 (t80) REVERT: C 68 MET cc_start: 0.7035 (OUTLIER) cc_final: 0.6354 (mtt) REVERT: D 267 MET cc_start: 0.8870 (mmt) cc_final: 0.8311 (mmt) REVERT: D 355 ILE cc_start: 0.8567 (OUTLIER) cc_final: 0.8148 (mp) REVERT: F 188 TYR cc_start: 0.9080 (p90) cc_final: 0.8391 (p90) REVERT: F 222 ILE cc_start: 0.6606 (OUTLIER) cc_final: 0.6246 (mt) REVERT: F 285 ASP cc_start: 0.8440 (OUTLIER) cc_final: 0.8176 (m-30) REVERT: I 60 LYS cc_start: 0.8144 (tptp) cc_final: 0.7781 (tppt) outliers start: 76 outliers final: 57 residues processed: 262 average time/residue: 0.1373 time to fit residues: 56.1867 Evaluate side-chains 261 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 198 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain B residue 412 ASP Chi-restraints excluded: chain B residue 435 ASN Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 196 GLN Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 54 HIS Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 68 MET Chi-restraints excluded: chain C residue 88 CYS Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 149 CYS Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 389 SER Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 260 ASP Chi-restraints excluded: chain E residue 270 SER Chi-restraints excluded: chain F residue 112 PHE Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 222 ILE Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 285 ASP Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 72 TYR Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 108 MET Chi-restraints excluded: chain G residue 119 ASP Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain I residue 44 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 135 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 162 optimal weight: 9.9990 chunk 56 optimal weight: 7.9990 chunk 187 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 111 optimal weight: 0.2980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.146691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.102471 restraints weight = 25547.387| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.81 r_work: 0.2966 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18973 Z= 0.165 Angle : 0.537 8.094 25634 Z= 0.278 Chirality : 0.040 0.325 2901 Planarity : 0.004 0.092 3286 Dihedral : 5.266 71.904 2572 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.73 % Favored : 94.05 % Rotamer: Outliers : 4.17 % Allowed : 25.83 % Favored : 69.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.18), residues: 2302 helix: 2.12 (0.14), residues: 1526 sheet: 0.18 (0.43), residues: 148 loop : -1.70 (0.23), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 165 TYR 0.021 0.001 TYR C 267 PHE 0.014 0.001 PHE F 112 TRP 0.006 0.001 TRP H 153 HIS 0.006 0.001 HIS E 138 Details of bonding type rmsd covalent geometry : bond 0.00399 (18971) covalent geometry : angle 0.53713 (25634) hydrogen bonds : bond 0.04360 ( 1165) hydrogen bonds : angle 3.75915 ( 3417) metal coordination : bond 0.00672 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 199 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 244 MET cc_start: -0.2109 (mpp) cc_final: -0.2719 (mtt) REVERT: H 142 GLU cc_start: 0.8038 (mp0) cc_final: 0.7780 (mp0) REVERT: A 343 LYS cc_start: 0.8187 (OUTLIER) cc_final: 0.7813 (ttpp) REVERT: A 410 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.6097 (pp20) REVERT: C 10 ASN cc_start: 0.8356 (m-40) cc_final: 0.7901 (m110) REVERT: C 13 ARG cc_start: 0.7922 (tpp80) cc_final: 0.7406 (mtt90) REVERT: C 63 PHE cc_start: 0.7127 (OUTLIER) cc_final: 0.5191 (t80) REVERT: C 68 MET cc_start: 0.7153 (OUTLIER) cc_final: 0.6448 (mtt) REVERT: D 267 MET cc_start: 0.8892 (mmt) cc_final: 0.8321 (mmt) REVERT: D 355 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.8186 (mp) REVERT: E 92 ILE cc_start: 0.8430 (OUTLIER) cc_final: 0.8176 (mp) REVERT: F 222 ILE cc_start: 0.6664 (OUTLIER) cc_final: 0.6255 (mt) REVERT: F 285 ASP cc_start: 0.8468 (OUTLIER) cc_final: 0.8248 (m-30) REVERT: I 60 LYS cc_start: 0.8156 (tptp) cc_final: 0.7786 (tppt) outliers start: 85 outliers final: 60 residues processed: 266 average time/residue: 0.1414 time to fit residues: 58.7481 Evaluate side-chains 262 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 194 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 412 ASP Chi-restraints excluded: chain B residue 435 ASN Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 196 GLN Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 54 HIS Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 68 MET Chi-restraints excluded: chain C residue 88 CYS Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 149 CYS Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 288 HIS Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 389 SER Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 260 ASP Chi-restraints excluded: chain E residue 270 SER Chi-restraints excluded: chain F residue 112 PHE Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 222 ILE Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 285 ASP Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 72 TYR Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 108 MET Chi-restraints excluded: chain G residue 114 SER Chi-restraints excluded: chain G residue 119 ASP Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain I residue 44 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 185 optimal weight: 0.4980 chunk 58 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 chunk 136 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 chunk 123 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 150 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 290 ASN E 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.148180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.104232 restraints weight = 25582.121| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.75 r_work: 0.2995 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18973 Z= 0.121 Angle : 0.509 9.028 25634 Z= 0.265 Chirality : 0.039 0.509 2901 Planarity : 0.004 0.104 3286 Dihedral : 5.186 72.353 2572 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.52 % Favored : 94.27 % Rotamer: Outliers : 4.03 % Allowed : 25.88 % Favored : 70.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.18), residues: 2302 helix: 2.21 (0.14), residues: 1525 sheet: 0.18 (0.44), residues: 150 loop : -1.67 (0.23), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 344 TYR 0.016 0.001 TYR C 267 PHE 0.013 0.001 PHE E 96 TRP 0.006 0.001 TRP H 57 HIS 0.004 0.001 HIS F 225 Details of bonding type rmsd covalent geometry : bond 0.00278 (18971) covalent geometry : angle 0.50941 (25634) hydrogen bonds : bond 0.03951 ( 1165) hydrogen bonds : angle 3.68874 ( 3417) metal coordination : bond 0.00438 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 200 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 244 MET cc_start: -0.2100 (mpp) cc_final: -0.2491 (mtt) REVERT: A 343 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7775 (ttpp) REVERT: A 410 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.6056 (pp20) REVERT: C 10 ASN cc_start: 0.8273 (m-40) cc_final: 0.7855 (m110) REVERT: C 63 PHE cc_start: 0.7080 (OUTLIER) cc_final: 0.5156 (t80) REVERT: D 267 MET cc_start: 0.8851 (mmt) cc_final: 0.8311 (mmt) REVERT: D 355 ILE cc_start: 0.8587 (OUTLIER) cc_final: 0.8171 (mp) REVERT: E 92 ILE cc_start: 0.8396 (OUTLIER) cc_final: 0.8140 (mp) REVERT: F 188 TYR cc_start: 0.9078 (p90) cc_final: 0.8407 (p90) REVERT: F 222 ILE cc_start: 0.6630 (OUTLIER) cc_final: 0.6244 (mt) REVERT: F 285 ASP cc_start: 0.8434 (OUTLIER) cc_final: 0.8207 (m-30) REVERT: G 160 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.8166 (mtp180) outliers start: 82 outliers final: 64 residues processed: 264 average time/residue: 0.1445 time to fit residues: 58.9719 Evaluate side-chains 265 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 193 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 255 HIS Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 412 ASP Chi-restraints excluded: chain B residue 435 ASN Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 196 GLN Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 54 HIS Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 88 CYS Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 149 CYS Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 186 HIS Chi-restraints excluded: chain D residue 288 HIS Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 389 SER Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 260 ASP Chi-restraints excluded: chain E residue 270 SER Chi-restraints excluded: chain F residue 112 PHE Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 222 ILE Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 285 ASP Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 72 TYR Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 108 MET Chi-restraints excluded: chain G residue 114 SER Chi-restraints excluded: chain G residue 119 ASP Chi-restraints excluded: chain G residue 155 ASP Chi-restraints excluded: chain G residue 160 ARG Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain I residue 44 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 73 optimal weight: 0.8980 chunk 4 optimal weight: 20.0000 chunk 127 optimal weight: 1.9990 chunk 209 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 97 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 170 optimal weight: 0.8980 chunk 62 optimal weight: 0.2980 chunk 15 optimal weight: 0.0170 chunk 49 optimal weight: 5.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN D 349 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.149597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.100010 restraints weight = 25383.707| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.45 r_work: 0.3057 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 18973 Z= 0.107 Angle : 0.505 9.253 25634 Z= 0.261 Chirality : 0.039 0.488 2901 Planarity : 0.004 0.102 3286 Dihedral : 5.067 72.666 2572 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.26 % Favored : 94.53 % Rotamer: Outliers : 3.54 % Allowed : 26.72 % Favored : 69.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.18), residues: 2302 helix: 2.33 (0.14), residues: 1515 sheet: 0.37 (0.44), residues: 151 loop : -1.71 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 205 TYR 0.013 0.001 TYR C 267 PHE 0.013 0.001 PHE E 96 TRP 0.007 0.001 TRP D 395 HIS 0.004 0.001 HIS F 225 Details of bonding type rmsd covalent geometry : bond 0.00234 (18971) covalent geometry : angle 0.50523 (25634) hydrogen bonds : bond 0.03614 ( 1165) hydrogen bonds : angle 3.60903 ( 3417) metal coordination : bond 0.00292 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 200 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 244 MET cc_start: -0.2051 (mpp) cc_final: -0.2421 (mtt) REVERT: B 338 MET cc_start: 0.5261 (mpp) cc_final: 0.3966 (ptt) REVERT: B 441 LYS cc_start: 0.7970 (OUTLIER) cc_final: 0.6586 (mtmt) REVERT: A 343 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7791 (ttpp) REVERT: C 10 ASN cc_start: 0.8276 (m-40) cc_final: 0.7864 (m110) REVERT: C 63 PHE cc_start: 0.7147 (OUTLIER) cc_final: 0.5158 (t80) REVERT: D 240 GLN cc_start: 0.7401 (tm-30) cc_final: 0.7135 (tm-30) REVERT: D 267 MET cc_start: 0.8884 (mmt) cc_final: 0.8371 (mmt) REVERT: D 355 ILE cc_start: 0.8641 (OUTLIER) cc_final: 0.8222 (mp) REVERT: E 92 ILE cc_start: 0.8467 (OUTLIER) cc_final: 0.8211 (mp) REVERT: F 188 TYR cc_start: 0.9103 (p90) cc_final: 0.8479 (p90) REVERT: F 206 MET cc_start: 0.8180 (mtp) cc_final: 0.7763 (mtt) REVERT: F 222 ILE cc_start: 0.6622 (OUTLIER) cc_final: 0.6256 (mt) REVERT: F 285 ASP cc_start: 0.8574 (OUTLIER) cc_final: 0.8355 (m-30) REVERT: G 160 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.8250 (mtp180) outliers start: 72 outliers final: 55 residues processed: 254 average time/residue: 0.1423 time to fit residues: 55.9419 Evaluate side-chains 257 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 194 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 255 HIS Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain B residue 412 ASP Chi-restraints excluded: chain B residue 435 ASN Chi-restraints excluded: chain B residue 441 LYS Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 196 GLN Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 54 HIS Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 88 CYS Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain D residue 186 HIS Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 389 SER Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 260 ASP Chi-restraints excluded: chain E residue 270 SER Chi-restraints excluded: chain F residue 112 PHE Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 222 ILE Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 285 ASP Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 72 TYR Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 155 ASP Chi-restraints excluded: chain G residue 160 ARG Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain I residue 44 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 174 optimal weight: 0.8980 chunk 133 optimal weight: 0.0270 chunk 202 optimal weight: 0.8980 chunk 125 optimal weight: 0.9980 chunk 90 optimal weight: 0.0870 chunk 155 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 193 optimal weight: 2.9990 chunk 13 optimal weight: 0.3980 chunk 164 optimal weight: 2.9990 overall best weight: 0.4616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 290 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.150484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.100763 restraints weight = 25523.460| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.46 r_work: 0.3067 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 18973 Z= 0.103 Angle : 0.499 9.276 25634 Z= 0.257 Chirality : 0.039 0.432 2901 Planarity : 0.004 0.106 3286 Dihedral : 4.998 71.396 2572 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.17 % Favored : 94.61 % Rotamer: Outliers : 3.24 % Allowed : 26.96 % Favored : 69.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.18), residues: 2302 helix: 2.38 (0.14), residues: 1515 sheet: 0.43 (0.44), residues: 151 loop : -1.67 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 244 TYR 0.012 0.001 TYR E 143 PHE 0.012 0.001 PHE E 96 TRP 0.007 0.001 TRP D 395 HIS 0.004 0.001 HIS F 225 Details of bonding type rmsd covalent geometry : bond 0.00225 (18971) covalent geometry : angle 0.49949 (25634) hydrogen bonds : bond 0.03463 ( 1165) hydrogen bonds : angle 3.55342 ( 3417) metal coordination : bond 0.00238 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 194 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 244 MET cc_start: -0.2045 (mpp) cc_final: -0.2418 (mtt) REVERT: B 282 LEU cc_start: 0.5748 (tt) cc_final: 0.5433 (tt) REVERT: B 338 MET cc_start: 0.5337 (mpp) cc_final: 0.4096 (ptt) REVERT: B 441 LYS cc_start: 0.7877 (OUTLIER) cc_final: 0.6430 (mtmt) REVERT: A 343 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7812 (ttpp) REVERT: A 410 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.6129 (pp20) REVERT: C 10 ASN cc_start: 0.8282 (m-40) cc_final: 0.7875 (m110) REVERT: C 63 PHE cc_start: 0.7097 (OUTLIER) cc_final: 0.4953 (t80) REVERT: D 267 MET cc_start: 0.8882 (mmt) cc_final: 0.8422 (mmt) REVERT: D 355 ILE cc_start: 0.8639 (OUTLIER) cc_final: 0.8246 (mp) REVERT: F 188 TYR cc_start: 0.9114 (p90) cc_final: 0.8500 (p90) REVERT: F 222 ILE cc_start: 0.6624 (OUTLIER) cc_final: 0.6288 (mt) REVERT: F 285 ASP cc_start: 0.8549 (OUTLIER) cc_final: 0.8339 (m-30) REVERT: G 160 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.8263 (mtp180) outliers start: 66 outliers final: 50 residues processed: 242 average time/residue: 0.1415 time to fit residues: 53.1642 Evaluate side-chains 249 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 191 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 255 HIS Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain B residue 412 ASP Chi-restraints excluded: chain B residue 435 ASN Chi-restraints excluded: chain B residue 441 LYS Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 196 GLN Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 54 HIS Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 88 CYS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 389 SER Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 260 ASP Chi-restraints excluded: chain F residue 112 PHE Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 222 ILE Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 285 ASP Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 72 TYR Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 119 ASP Chi-restraints excluded: chain G residue 155 ASP Chi-restraints excluded: chain G residue 160 ARG Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain I residue 44 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 143 optimal weight: 0.9990 chunk 175 optimal weight: 1.9990 chunk 172 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 174 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 chunk 195 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 320 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.147818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.097960 restraints weight = 25729.285| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.53 r_work: 0.3026 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18973 Z= 0.120 Angle : 0.518 9.411 25634 Z= 0.265 Chirality : 0.039 0.455 2901 Planarity : 0.004 0.101 3286 Dihedral : 5.035 71.939 2572 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.52 % Favored : 94.27 % Rotamer: Outliers : 2.90 % Allowed : 27.26 % Favored : 69.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.18), residues: 2302 helix: 2.34 (0.14), residues: 1513 sheet: 0.33 (0.44), residues: 148 loop : -1.64 (0.23), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 244 TYR 0.016 0.001 TYR C 267 PHE 0.012 0.001 PHE E 96 TRP 0.005 0.001 TRP H 57 HIS 0.004 0.001 HIS E 138 Details of bonding type rmsd covalent geometry : bond 0.00276 (18971) covalent geometry : angle 0.51826 (25634) hydrogen bonds : bond 0.03722 ( 1165) hydrogen bonds : angle 3.57846 ( 3417) metal coordination : bond 0.00381 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 194 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 244 MET cc_start: -0.2021 (mpp) cc_final: -0.2407 (mtt) REVERT: B 338 MET cc_start: 0.5393 (mpp) cc_final: 0.4143 (ptt) REVERT: B 441 LYS cc_start: 0.8093 (OUTLIER) cc_final: 0.6724 (mtmt) REVERT: A 343 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.7916 (ttpp) REVERT: A 410 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.6161 (pp20) REVERT: C 10 ASN cc_start: 0.8307 (m-40) cc_final: 0.7873 (m110) REVERT: C 63 PHE cc_start: 0.7195 (OUTLIER) cc_final: 0.5067 (t80) REVERT: D 267 MET cc_start: 0.9006 (mmt) cc_final: 0.8471 (mmt) REVERT: D 355 ILE cc_start: 0.8722 (OUTLIER) cc_final: 0.8326 (mp) REVERT: F 188 TYR cc_start: 0.9133 (p90) cc_final: 0.8514 (p90) REVERT: F 222 ILE cc_start: 0.6801 (OUTLIER) cc_final: 0.6417 (mt) REVERT: F 285 ASP cc_start: 0.8643 (OUTLIER) cc_final: 0.8420 (m-30) REVERT: G 160 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.8328 (mtp180) outliers start: 59 outliers final: 50 residues processed: 238 average time/residue: 0.1451 time to fit residues: 53.2763 Evaluate side-chains 251 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 193 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 255 HIS Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain B residue 412 ASP Chi-restraints excluded: chain B residue 435 ASN Chi-restraints excluded: chain B residue 441 LYS Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 196 GLN Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 54 HIS Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 88 CYS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 389 SER Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 270 SER Chi-restraints excluded: chain F residue 112 PHE Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 222 ILE Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 285 ASP Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 72 TYR Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 119 ASP Chi-restraints excluded: chain G residue 160 ARG Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain I residue 44 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 74 optimal weight: 1.9990 chunk 194 optimal weight: 3.9990 chunk 161 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 63 optimal weight: 0.3980 chunk 15 optimal weight: 3.9990 chunk 130 optimal weight: 0.8980 chunk 109 optimal weight: 0.0970 chunk 75 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 290 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.146403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.098257 restraints weight = 25783.851| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 2.93 r_work: 0.2993 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18973 Z= 0.136 Angle : 0.535 11.175 25634 Z= 0.273 Chirality : 0.040 0.431 2901 Planarity : 0.004 0.104 3286 Dihedral : 5.106 71.495 2572 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.52 % Favored : 94.27 % Rotamer: Outliers : 3.14 % Allowed : 27.16 % Favored : 69.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.18), residues: 2302 helix: 2.27 (0.14), residues: 1520 sheet: 0.28 (0.43), residues: 150 loop : -1.63 (0.23), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 244 TYR 0.018 0.001 TYR C 267 PHE 0.012 0.001 PHE F 112 TRP 0.006 0.001 TRP H 57 HIS 0.005 0.001 HIS E 138 Details of bonding type rmsd covalent geometry : bond 0.00321 (18971) covalent geometry : angle 0.53529 (25634) hydrogen bonds : bond 0.03991 ( 1165) hydrogen bonds : angle 3.64647 ( 3417) metal coordination : bond 0.00517 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5029.09 seconds wall clock time: 86 minutes 57.57 seconds (5217.57 seconds total)