Starting phenix.real_space_refine on Thu Mar 5 20:14:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xkh_33251/03_2026/7xkh_33251.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xkh_33251/03_2026/7xkh_33251.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xkh_33251/03_2026/7xkh_33251.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xkh_33251/03_2026/7xkh_33251.map" model { file = "/net/cci-nas-00/data/ceres_data/7xkh_33251/03_2026/7xkh_33251.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xkh_33251/03_2026/7xkh_33251.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 79 5.16 5 C 15840 2.51 5 N 4367 2.21 5 O 4781 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25068 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3661 Classifications: {'peptide': 478} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 454} Chain: "B" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3661 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 23, 'TRANS': 454} Chain: "C" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3661 Classifications: {'peptide': 478} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 454} Chain: "D" Number of atoms: 3622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3622 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 446} Chain: "E" Number of atoms: 3623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3623 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 446} Chain: "F" Number of atoms: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3630 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 447} Chain: "G" Number of atoms: 2218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2218 Classifications: {'peptide': 283} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 272} Chain: "H" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 987 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain: "F" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {' PI': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.91, per 1000 atoms: 0.24 Number of scatterers: 25068 At special positions: 0 Unit cell: (135.34, 125.24, 159.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 79 16.00 P 1 15.00 O 4781 8.00 N 4367 7.00 C 15840 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: 1.83 Conformation dependent library (CDL) restraints added in 1.1 seconds 6482 Ramachandran restraints generated. 3241 Oldfield, 0 Emsley, 3241 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5952 Finding SS restraints... Secondary structure from input PDB file: 135 helices and 27 sheets defined 47.0% alpha, 17.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 100 through 104 removed outlier: 3.782A pdb=" N LEU A 103 " --> pdb=" O GLY A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 139 removed outlier: 4.034A pdb=" N ARG A 139 " --> pdb=" O VAL A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 157 Processing helix chain 'A' and resid 174 through 185 removed outlier: 4.027A pdb=" N VAL A 178 " --> pdb=" O GLY A 174 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA A 179 " --> pdb=" O LYS A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 215 Processing helix chain 'A' and resid 216 through 219 removed outlier: 4.252A pdb=" N ASP A 219 " --> pdb=" O GLY A 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 216 through 219' Processing helix chain 'A' and resid 231 through 251 removed outlier: 3.632A pdb=" N LEU A 235 " --> pdb=" O PRO A 231 " (cutoff:3.500A) Proline residue: A 239 - end of helix removed outlier: 3.751A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 277 Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 289 through 299 removed outlier: 3.544A pdb=" N LEU A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 336 Processing helix chain 'A' and resid 345 through 352 Processing helix chain 'A' and resid 372 through 379 Processing helix chain 'A' and resid 379 through 393 removed outlier: 4.442A pdb=" N ARG A 383 " --> pdb=" O ALA A 379 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N LEU A 384 " --> pdb=" O GLY A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 421 removed outlier: 3.723A pdb=" N GLN A 407 " --> pdb=" O ASP A 403 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA A 408 " --> pdb=" O LYS A 404 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA A 414 " --> pdb=" O LEU A 410 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG A 415 " --> pdb=" O ALA A 411 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS A 421 " --> pdb=" O VAL A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 442 Processing helix chain 'A' and resid 449 through 451 No H-bonds generated for 'chain 'A' and resid 449 through 451' Processing helix chain 'A' and resid 452 through 468 removed outlier: 3.541A pdb=" N LEU A 462 " --> pdb=" O LYS A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 479 Processing helix chain 'A' and resid 483 through 498 Processing helix chain 'B' and resid 100 through 104 removed outlier: 3.510A pdb=" N LEU B 103 " --> pdb=" O GLY B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 139 removed outlier: 3.538A pdb=" N ASP B 138 " --> pdb=" O GLY B 135 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG B 139 " --> pdb=" O VAL B 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 135 through 139' Processing helix chain 'B' and resid 150 through 157 Processing helix chain 'B' and resid 174 through 185 removed outlier: 3.931A pdb=" N VAL B 178 " --> pdb=" O GLY B 174 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA B 179 " --> pdb=" O LYS B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 189 removed outlier: 3.578A pdb=" N GLN B 189 " --> pdb=" O GLN B 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 186 through 189' Processing helix chain 'B' and resid 201 through 215 Processing helix chain 'B' and resid 217 through 219 No H-bonds generated for 'chain 'B' and resid 217 through 219' Processing helix chain 'B' and resid 231 through 237 removed outlier: 3.706A pdb=" N LEU B 237 " --> pdb=" O PRO B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 251 removed outlier: 3.883A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 277 Processing helix chain 'B' and resid 282 through 286 Processing helix chain 'B' and resid 289 through 299 removed outlier: 3.732A pdb=" N LEU B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 309 removed outlier: 3.577A pdb=" N GLY B 309 " --> pdb=" O ASP B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 336 Processing helix chain 'B' and resid 345 through 350 Processing helix chain 'B' and resid 372 through 393 removed outlier: 3.549A pdb=" N LYS B 376 " --> pdb=" O ILE B 372 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS B 377 " --> pdb=" O LYS B 373 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL B 378 " --> pdb=" O ALA B 374 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N GLY B 380 " --> pdb=" O LYS B 376 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N THR B 381 " --> pdb=" O LYS B 377 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU B 382 " --> pdb=" O VAL B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 396 No H-bonds generated for 'chain 'B' and resid 394 through 396' Processing helix chain 'B' and resid 403 through 421 removed outlier: 3.820A pdb=" N LYS B 409 " --> pdb=" O ALA B 405 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU B 410 " --> pdb=" O THR B 406 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA B 411 " --> pdb=" O GLN B 407 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS B 421 " --> pdb=" O VAL B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 442 Processing helix chain 'B' and resid 449 through 451 No H-bonds generated for 'chain 'B' and resid 449 through 451' Processing helix chain 'B' and resid 452 through 468 Processing helix chain 'B' and resid 468 through 479 Processing helix chain 'B' and resid 483 through 498 removed outlier: 3.926A pdb=" N THR B 497 " --> pdb=" O ALA B 493 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE B 498 " --> pdb=" O PHE B 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 104 removed outlier: 3.809A pdb=" N LEU C 103 " --> pdb=" O GLY C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 139 removed outlier: 3.520A pdb=" N ASP C 138 " --> pdb=" O GLY C 135 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG C 139 " --> pdb=" O VAL C 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 135 through 139' Processing helix chain 'C' and resid 150 through 157 Processing helix chain 'C' and resid 174 through 186 removed outlier: 3.730A pdb=" N GLN C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 215 Processing helix chain 'C' and resid 217 through 219 No H-bonds generated for 'chain 'C' and resid 217 through 219' Processing helix chain 'C' and resid 231 through 237 removed outlier: 3.515A pdb=" N LEU C 237 " --> pdb=" O PRO C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 251 removed outlier: 3.642A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 277 Processing helix chain 'C' and resid 282 through 286 Processing helix chain 'C' and resid 289 through 299 removed outlier: 3.592A pdb=" N LEU C 297 " --> pdb=" O LEU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 309 Processing helix chain 'C' and resid 328 through 336 removed outlier: 3.505A pdb=" N SER C 336 " --> pdb=" O THR C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 351 Processing helix chain 'C' and resid 372 through 393 removed outlier: 3.716A pdb=" N VAL C 378 " --> pdb=" O ALA C 374 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N GLY C 380 " --> pdb=" O LYS C 376 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N THR C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU C 382 " --> pdb=" O VAL C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 397 removed outlier: 3.961A pdb=" N GLN C 397 " --> pdb=" O ALA C 394 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 394 through 397' Processing helix chain 'C' and resid 403 through 420 removed outlier: 3.642A pdb=" N LYS C 409 " --> pdb=" O ALA C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 442 removed outlier: 3.933A pdb=" N LEU C 435 " --> pdb=" O GLU C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 451 No H-bonds generated for 'chain 'C' and resid 449 through 451' Processing helix chain 'C' and resid 452 through 467 removed outlier: 3.759A pdb=" N GLN C 466 " --> pdb=" O LEU C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 479 removed outlier: 3.548A pdb=" N LEU C 472 " --> pdb=" O GLY C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 498 removed outlier: 3.869A pdb=" N LEU C 487 " --> pdb=" O ASN C 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 92 removed outlier: 3.580A pdb=" N THR D 91 " --> pdb=" O GLY D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 146 Processing helix chain 'D' and resid 163 through 180 Processing helix chain 'D' and resid 191 through 206 Processing helix chain 'D' and resid 207 through 209 No H-bonds generated for 'chain 'D' and resid 207 through 209' Processing helix chain 'D' and resid 221 through 227 removed outlier: 3.996A pdb=" N ARG D 227 " --> pdb=" O GLY D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 243 removed outlier: 4.099A pdb=" N TYR D 238 " --> pdb=" O THR D 234 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N PHE D 239 " --> pdb=" O MET D 235 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG D 240 " --> pdb=" O ALA D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 266 removed outlier: 3.597A pdb=" N THR D 258 " --> pdb=" O ILE D 254 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY D 261 " --> pdb=" O PHE D 257 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA D 266 " --> pdb=" O SER D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 290 removed outlier: 3.549A pdb=" N LEU D 288 " --> pdb=" O GLU D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 312 removed outlier: 3.543A pdb=" N ASP D 311 " --> pdb=" O VAL D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 323 removed outlier: 3.842A pdb=" N SER D 323 " --> pdb=" O ALA D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 339 removed outlier: 3.655A pdb=" N GLY D 339 " --> pdb=" O LEU D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 360 through 379 removed outlier: 3.616A pdb=" N GLU D 379 " --> pdb=" O GLN D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 388 Processing helix chain 'D' and resid 393 through 410 removed outlier: 3.765A pdb=" N LEU D 398 " --> pdb=" O ASP D 394 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG D 404 " --> pdb=" O VAL D 400 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 422 removed outlier: 3.552A pdb=" N THR D 421 " --> pdb=" O ALA D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 443 Processing helix chain 'D' and resid 449 through 454 removed outlier: 3.550A pdb=" N ARG D 454 " --> pdb=" O ASP D 451 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 469 removed outlier: 4.155A pdb=" N VAL D 463 " --> pdb=" O ILE D 459 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU D 464 " --> pdb=" O GLU D 460 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 92 removed outlier: 3.557A pdb=" N THR E 91 " --> pdb=" O GLY E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 146 Processing helix chain 'E' and resid 163 through 179 Processing helix chain 'E' and resid 191 through 204 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 221 through 226 Processing helix chain 'E' and resid 227 through 243 removed outlier: 3.988A pdb=" N TYR E 238 " --> pdb=" O THR E 234 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N PHE E 239 " --> pdb=" O MET E 235 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ARG E 240 " --> pdb=" O ALA E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 269 removed outlier: 3.558A pdb=" N THR E 258 " --> pdb=" O ILE E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 290 removed outlier: 3.592A pdb=" N LEU E 288 " --> pdb=" O GLU E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 312 Processing helix chain 'E' and resid 315 through 322 Processing helix chain 'E' and resid 332 through 339 Processing helix chain 'E' and resid 360 through 384 removed outlier: 3.975A pdb=" N ASP E 382 " --> pdb=" O LYS E 378 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE E 383 " --> pdb=" O GLU E 379 " (cutoff:3.500A) Processing helix chain 'E' and resid 388 through 392 Processing helix chain 'E' and resid 393 through 410 removed outlier: 3.612A pdb=" N ARG E 404 " --> pdb=" O VAL E 400 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ARG E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 422 Processing helix chain 'E' and resid 429 through 442 Processing helix chain 'E' and resid 449 through 454 removed outlier: 3.747A pdb=" N ARG E 454 " --> pdb=" O ASP E 451 " (cutoff:3.500A) Processing helix chain 'E' and resid 459 through 470 removed outlier: 4.292A pdb=" N VAL E 463 " --> pdb=" O ILE E 459 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLU E 464 " --> pdb=" O GLU E 460 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 92 Processing helix chain 'F' and resid 124 through 128 removed outlier: 3.626A pdb=" N GLU F 127 " --> pdb=" O LYS F 124 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU F 128 " --> pdb=" O PHE F 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 124 through 128' Processing helix chain 'F' and resid 139 through 146 Processing helix chain 'F' and resid 163 through 176 removed outlier: 3.510A pdb=" N LEU F 167 " --> pdb=" O GLY F 163 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 179 No H-bonds generated for 'chain 'F' and resid 177 through 179' Processing helix chain 'F' and resid 191 through 206 removed outlier: 3.556A pdb=" N GLY F 195 " --> pdb=" O ARG F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 207 through 209 No H-bonds generated for 'chain 'F' and resid 207 through 209' Processing helix chain 'F' and resid 221 through 226 Processing helix chain 'F' and resid 227 through 243 removed outlier: 4.116A pdb=" N TYR F 238 " --> pdb=" O THR F 234 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N PHE F 239 " --> pdb=" O MET F 235 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ARG F 240 " --> pdb=" O ALA F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 266 removed outlier: 3.936A pdb=" N THR F 258 " --> pdb=" O ILE F 254 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA F 266 " --> pdb=" O SER F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 269 No H-bonds generated for 'chain 'F' and resid 267 through 269' Processing helix chain 'F' and resid 280 through 290 removed outlier: 3.597A pdb=" N LEU F 288 " --> pdb=" O GLU F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 309 through 312 Processing helix chain 'F' and resid 315 through 321 removed outlier: 3.701A pdb=" N THR F 321 " --> pdb=" O ALA F 317 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 325 removed outlier: 3.761A pdb=" N LEU F 325 " --> pdb=" O PHE F 322 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 322 through 325' Processing helix chain 'F' and resid 332 through 338 removed outlier: 3.578A pdb=" N MET F 338 " --> pdb=" O LYS F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 360 through 379 Processing helix chain 'F' and resid 380 through 388 removed outlier: 3.693A pdb=" N ILE F 386 " --> pdb=" O ASP F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 410 removed outlier: 3.564A pdb=" N ARG F 405 " --> pdb=" O HIS F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 417 through 422 Processing helix chain 'F' and resid 429 through 442 Processing helix chain 'F' and resid 449 through 454 removed outlier: 3.828A pdb=" N ARG F 454 " --> pdb=" O ASP F 451 " (cutoff:3.500A) Processing helix chain 'F' and resid 459 through 470 removed outlier: 4.089A pdb=" N VAL F 463 " --> pdb=" O ILE F 459 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU F 464 " --> pdb=" O GLU F 460 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 41 removed outlier: 3.808A pdb=" N GLN G 37 " --> pdb=" O ASN G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 58 removed outlier: 3.868A pdb=" N MET G 46 " --> pdb=" O PHE G 42 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU G 51 " --> pdb=" O GLU G 47 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU G 58 " --> pdb=" O ALA G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 69 Processing helix chain 'G' and resid 90 through 107 removed outlier: 4.079A pdb=" N VAL G 95 " --> pdb=" O TYR G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 111 No H-bonds generated for 'chain 'G' and resid 109 through 111' Processing helix chain 'G' and resid 119 through 129 removed outlier: 3.770A pdb=" N ARG G 129 " --> pdb=" O PHE G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 162 removed outlier: 4.272A pdb=" N ILE G 149 " --> pdb=" O SER G 145 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS G 150 " --> pdb=" O PHE G 146 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N GLU G 151 " --> pdb=" O ALA G 147 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N ILE G 152 " --> pdb=" O ASP G 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 283 removed outlier: 3.587A pdb=" N LEU G 213 " --> pdb=" O GLN G 209 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ASP G 214 " --> pdb=" O GLU G 210 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL G 215 " --> pdb=" O GLU G 211 " (cutoff:3.500A) Proline residue: G 218 - end of helix removed outlier: 4.271A pdb=" N ARG G 256 " --> pdb=" O ASN G 252 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N THR G 257 " --> pdb=" O GLU G 253 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER G 261 " --> pdb=" O THR G 257 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE G 270 " --> pdb=" O ARG G 266 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THR G 275 " --> pdb=" O THR G 271 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA G 283 " --> pdb=" O ALA G 279 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 130 removed outlier: 3.823A pdb=" N ALA H 100 " --> pdb=" O ALA H 96 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU H 101 " --> pdb=" O LYS H 97 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA H 116 " --> pdb=" O ASP H 112 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG H 126 " --> pdb=" O ARG H 122 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LEU H 127 " --> pdb=" O ALA H 123 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER H 128 " --> pdb=" O MET H 124 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 35 removed outlier: 6.525A pdb=" N ARG A 40 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL A 34 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLY A 72 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLU A 51 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N LEU A 52 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N THR A 91 " --> pdb=" O LEU A 52 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 99 removed outlier: 3.530A pdb=" N VAL A 97 " --> pdb=" O ARG A 127 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG A 127 " --> pdb=" O VAL A 97 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU A 125 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 107 through 108 removed outlier: 6.401A pdb=" N ILE A 192 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N VAL A 259 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ILE A 194 " --> pdb=" O VAL A 259 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR A 260 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU A 344 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 10.416A pdb=" N GLN A 341 " --> pdb=" O GLY A 360 " (cutoff:3.500A) removed outlier: 8.731A pdb=" N GLY A 360 " --> pdb=" O GLN A 341 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N PHE A 343 " --> pdb=" O ASN A 358 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 145 through 146 removed outlier: 4.825A pdb=" N ILE A 159 " --> pdb=" O LEU A 146 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 28 through 35 removed outlier: 6.628A pdb=" N ARG B 40 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N VAL B 34 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N GLY B 72 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLU B 51 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N LEU B 52 " --> pdb=" O THR B 91 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 96 through 99 removed outlier: 3.875A pdb=" N GLU B 125 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 107 through 108 removed outlier: 6.919A pdb=" N SER B 193 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N VAL B 224 " --> pdb=" O SER B 193 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N TYR B 195 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N ALA B 226 " --> pdb=" O TYR B 195 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ALA B 197 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ILE B 192 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N VAL B 259 " --> pdb=" O ILE B 192 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE B 194 " --> pdb=" O VAL B 259 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR B 260 " --> pdb=" O LEU B 316 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 318 through 320 removed outlier: 6.626A pdb=" N ILE B 167 " --> pdb=" O VAL B 319 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN B 341 " --> pdb=" O VAL B 363 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL B 363 " --> pdb=" O GLN B 341 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 28 through 35 removed outlier: 6.486A pdb=" N ARG C 40 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N VAL C 34 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLY C 72 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLU C 51 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ARG C 93 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 8.568A pdb=" N GLU C 54 " --> pdb=" O THR C 91 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N THR C 91 " --> pdb=" O GLU C 54 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 96 through 99 removed outlier: 4.093A pdb=" N GLU C 125 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 107 through 108 removed outlier: 3.600A pdb=" N THR C 225 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ILE C 192 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N VAL C 259 " --> pdb=" O ILE C 192 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE C 194 " --> pdb=" O VAL C 259 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL C 256 " --> pdb=" O SER C 312 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR C 260 " --> pdb=" O LEU C 316 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ILE C 167 " --> pdb=" O VAL C 319 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 4 through 9 removed outlier: 6.775A pdb=" N ASP D 15 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N VAL D 9 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N VAL D 13 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N THR D 58 " --> pdb=" O HIS D 53 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N HIS D 53 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ARG D 60 " --> pdb=" O ALA D 51 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU D 49 " --> pdb=" O ILE D 62 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE D 44 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N GLN D 33 " --> pdb=" O GLU D 75 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N GLU D 75 " --> pdb=" O GLN D 33 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 84 through 86 Processing sheet with id=AB5, first strand: chain 'D' and resid 95 through 96 removed outlier: 6.537A pdb=" N ILE D 182 " --> pdb=" O LEU D 248 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N PHE D 250 " --> pdb=" O ILE D 182 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL D 184 " --> pdb=" O PHE D 250 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N VAL D 247 " --> pdb=" O THR D 301 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N ILE D 303 " --> pdb=" O VAL D 247 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LEU D 249 " --> pdb=" O ILE D 303 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N ALA D 305 " --> pdb=" O LEU D 249 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ILE D 251 " --> pdb=" O ALA D 305 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ILE D 154 " --> pdb=" O GLN D 304 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA D 327 " --> pdb=" O LYS D 153 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR D 350 " --> pdb=" O THR D 328 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 134 through 135 removed outlier: 4.503A pdb=" N TYR D 148 " --> pdb=" O LEU D 135 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 3 through 10 removed outlier: 5.848A pdb=" N VAL E 6 " --> pdb=" O LYS E 17 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N LYS E 17 " --> pdb=" O VAL E 6 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN E 8 " --> pdb=" O ASP E 15 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N THR E 58 " --> pdb=" O HIS E 53 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N HIS E 53 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ARG E 60 " --> pdb=" O ALA E 51 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N GLN E 33 " --> pdb=" O GLU E 75 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N GLU E 75 " --> pdb=" O GLN E 33 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 84 through 86 Processing sheet with id=AB9, first strand: chain 'E' and resid 95 through 96 removed outlier: 6.585A pdb=" N ILE E 182 " --> pdb=" O LEU E 248 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N PHE E 250 " --> pdb=" O ILE E 182 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL E 184 " --> pdb=" O PHE E 250 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL E 247 " --> pdb=" O THR E 301 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N ILE E 303 " --> pdb=" O VAL E 247 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU E 249 " --> pdb=" O ILE E 303 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N ALA E 305 " --> pdb=" O LEU E 249 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N ILE E 251 " --> pdb=" O ALA E 305 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY E 298 " --> pdb=" O THR E 295 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 95 through 96 removed outlier: 6.585A pdb=" N ILE E 182 " --> pdb=" O LEU E 248 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N PHE E 250 " --> pdb=" O ILE E 182 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL E 184 " --> pdb=" O PHE E 250 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL E 247 " --> pdb=" O THR E 301 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N ILE E 303 " --> pdb=" O VAL E 247 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU E 249 " --> pdb=" O ILE E 303 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N ALA E 305 " --> pdb=" O LEU E 249 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N ILE E 251 " --> pdb=" O ALA E 305 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA E 327 " --> pdb=" O LYS E 153 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 134 through 135 removed outlier: 4.426A pdb=" N TYR E 148 " --> pdb=" O LEU E 135 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 3 through 9 removed outlier: 5.885A pdb=" N VAL F 6 " --> pdb=" O LYS F 17 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LYS F 17 " --> pdb=" O VAL F 6 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLN F 8 " --> pdb=" O ASP F 15 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL F 14 " --> pdb=" O THR F 61 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N THR F 58 " --> pdb=" O HIS F 53 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N HIS F 53 " --> pdb=" O THR F 58 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ARG F 60 " --> pdb=" O ALA F 51 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N GLN F 33 " --> pdb=" O GLU F 75 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N GLU F 75 " --> pdb=" O GLN F 33 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 84 through 86 Processing sheet with id=AC5, first strand: chain 'F' and resid 95 through 96 removed outlier: 6.280A pdb=" N ILE F 182 " --> pdb=" O LEU F 248 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N PHE F 250 " --> pdb=" O ILE F 182 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL F 184 " --> pdb=" O PHE F 250 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA F 305 " --> pdb=" O ILE F 251 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE F 154 " --> pdb=" O GLN F 304 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ILE F 306 " --> pdb=" O ILE F 154 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU F 156 " --> pdb=" O ILE F 306 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR F 350 " --> pdb=" O THR F 328 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 134 through 135 removed outlier: 4.199A pdb=" N TYR F 148 " --> pdb=" O LEU F 135 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 133 through 137 removed outlier: 8.201A pdb=" N ILE G 134 " --> pdb=" O TYR G 113 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N ILE G 115 " --> pdb=" O ILE G 134 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ASP G 136 " --> pdb=" O ILE G 115 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N VAL G 117 " --> pdb=" O ASP G 136 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N THR G 76 " --> pdb=" O ALA G 114 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N ILE G 116 " --> pdb=" O THR G 76 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N TYR G 78 " --> pdb=" O ILE G 116 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ILE G 118 " --> pdb=" O TYR G 78 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL G 80 " --> pdb=" O ILE G 118 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR G 169 " --> pdb=" O GLY G 77 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N ASN G 173 " --> pdb=" O ILE G 81 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LEU G 168 " --> pdb=" O LEU G 188 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU G 188 " --> pdb=" O LEU G 168 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR G 172 " --> pdb=" O THR G 184 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 204 through 205 removed outlier: 6.286A pdb=" N GLU G 204 " --> pdb=" O VAL H 42 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU H 41 " --> pdb=" O VAL H 70 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL H 70 " --> pdb=" O LEU H 41 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA H 43 " --> pdb=" O LEU H 68 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N VAL H 6 " --> pdb=" O GLU H 17 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N GLU H 17 " --> pdb=" O VAL H 6 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N VAL H 8 " --> pdb=" O VAL H 15 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 32 through 34 removed outlier: 3.907A pdb=" N SER H 48 " --> pdb=" O VAL H 63 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA H 81 " --> pdb=" O SER H 64 " (cutoff:3.500A) 1137 hydrogen bonds defined for protein. 3264 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: 4.98 Time building geometry restraints manager: 2.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 8548 1.34 - 1.46: 3465 1.46 - 1.57: 13309 1.57 - 1.69: 0 1.69 - 1.80: 158 Bond restraints: 25480 Sorted by residual: bond pdb=" O3 PI F 501 " pdb=" P PI F 501 " ideal model delta sigma weight residual 1.562 1.523 0.039 2.00e-02 2.50e+03 3.74e+00 bond pdb=" O4 PI F 501 " pdb=" P PI F 501 " ideal model delta sigma weight residual 1.562 1.524 0.038 2.00e-02 2.50e+03 3.65e+00 bond pdb=" O2 PI F 501 " pdb=" P PI F 501 " ideal model delta sigma weight residual 1.562 1.524 0.038 2.00e-02 2.50e+03 3.60e+00 bond pdb=" O1 PI F 501 " pdb=" P PI F 501 " ideal model delta sigma weight residual 1.562 1.524 0.038 2.00e-02 2.50e+03 3.53e+00 bond pdb=" CG PRO D 342 " pdb=" CD PRO D 342 " ideal model delta sigma weight residual 1.512 1.483 0.029 2.70e-02 1.37e+03 1.13e+00 ... (remaining 25475 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 33774 1.20 - 2.39: 537 2.39 - 3.59: 159 3.59 - 4.78: 32 4.78 - 5.98: 6 Bond angle restraints: 34508 Sorted by residual: angle pdb=" N VAL D 162 " pdb=" CA VAL D 162 " pdb=" C VAL D 162 " ideal model delta sigma weight residual 113.53 109.00 4.53 9.80e-01 1.04e+00 2.13e+01 angle pdb=" N VAL B 25 " pdb=" CA VAL B 25 " pdb=" C VAL B 25 " ideal model delta sigma weight residual 113.47 109.07 4.40 1.01e+00 9.80e-01 1.90e+01 angle pdb=" C LEU G 189 " pdb=" N PRO G 190 " pdb=" CA PRO G 190 " ideal model delta sigma weight residual 127.00 132.98 -5.98 2.40e+00 1.74e-01 6.20e+00 angle pdb=" CA VAL D 162 " pdb=" C VAL D 162 " pdb=" N GLY D 163 " ideal model delta sigma weight residual 119.31 116.69 2.62 1.15e+00 7.56e-01 5.18e+00 angle pdb=" CA VAL B 25 " pdb=" C VAL B 25 " pdb=" O VAL B 25 " ideal model delta sigma weight residual 118.98 120.95 -1.97 9.00e-01 1.23e+00 4.80e+00 ... (remaining 34503 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 14418 17.80 - 35.60: 894 35.60 - 53.40: 157 53.40 - 71.19: 47 71.19 - 88.99: 22 Dihedral angle restraints: 15538 sinusoidal: 6244 harmonic: 9294 Sorted by residual: dihedral pdb=" CA GLY F 216 " pdb=" C GLY F 216 " pdb=" N GLN F 217 " pdb=" CA GLN F 217 " ideal model delta harmonic sigma weight residual 180.00 -160.20 -19.80 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA GLN F 217 " pdb=" C GLN F 217 " pdb=" N MET F 218 " pdb=" CA MET F 218 " ideal model delta harmonic sigma weight residual -180.00 -161.97 -18.03 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA MET D 226 " pdb=" C MET D 226 " pdb=" N ARG D 227 " pdb=" CA ARG D 227 " ideal model delta harmonic sigma weight residual -180.00 -162.95 -17.05 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 15535 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 2390 0.028 - 0.055: 953 0.055 - 0.083: 313 0.083 - 0.111: 231 0.111 - 0.138: 101 Chirality restraints: 3988 Sorted by residual: chirality pdb=" CA ILE H 39 " pdb=" N ILE H 39 " pdb=" C ILE H 39 " pdb=" CB ILE H 39 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.79e-01 chirality pdb=" CA VAL F 214 " pdb=" N VAL F 214 " pdb=" C VAL F 214 " pdb=" CB VAL F 214 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.71e-01 chirality pdb=" CA ILE A 222 " pdb=" N ILE A 222 " pdb=" C ILE A 222 " pdb=" CB ILE A 222 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.40e-01 ... (remaining 3985 not shown) Planarity restraints: 4532 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP E 315 " 0.039 5.00e-02 4.00e+02 5.90e-02 5.58e+00 pdb=" N PRO E 316 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO E 316 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO E 316 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR H 10 " 0.030 5.00e-02 4.00e+02 4.50e-02 3.24e+00 pdb=" N PRO H 11 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO H 11 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO H 11 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL F 428 " 0.028 5.00e-02 4.00e+02 4.20e-02 2.82e+00 pdb=" N PRO F 429 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO F 429 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO F 429 " 0.023 5.00e-02 4.00e+02 ... (remaining 4529 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 6273 2.81 - 3.33: 22446 3.33 - 3.85: 37151 3.85 - 4.38: 42190 4.38 - 4.90: 78206 Nonbonded interactions: 186266 Sorted by model distance: nonbonded pdb=" O GLN A 163 " pdb=" OG1 THR A 314 " model vdw 2.283 3.040 nonbonded pdb=" OE1 GLN G 50 " pdb=" OH TYR G 220 " model vdw 2.283 3.040 nonbonded pdb=" OD1 ASP B 170 " pdb=" OG1 THR B 321 " model vdw 2.287 3.040 nonbonded pdb=" NE2 HIS G 65 " pdb=" OD1 ASP G 214 " model vdw 2.308 3.120 nonbonded pdb=" O GLN C 163 " pdb=" OG1 THR C 314 " model vdw 2.309 3.040 ... (remaining 186261 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = (chain 'D' and resid 2 through 470) selection = (chain 'E' and resid 2 through 470) selection = (chain 'F' and resid 2 through 470) } 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: 2.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 23.420 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 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 : 0.002 0.039 25480 Z= 0.096 Angle : 0.438 5.977 34508 Z= 0.240 Chirality : 0.042 0.138 3988 Planarity : 0.004 0.059 4532 Dihedral : 12.684 88.992 9586 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.15), residues: 3241 helix: 2.10 (0.15), residues: 1319 sheet: 1.54 (0.22), residues: 537 loop : -0.34 (0.16), residues: 1385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 164 TYR 0.008 0.001 TYR G 91 PHE 0.009 0.001 PHE C 494 HIS 0.002 0.000 HIS C 42 Details of bonding type rmsd covalent geometry : bond 0.00175 (25480) covalent geometry : angle 0.43833 (34508) hydrogen bonds : bond 0.16830 ( 1130) hydrogen bonds : angle 5.75825 ( 3264) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6482 Ramachandran restraints generated. 3241 Oldfield, 0 Emsley, 3241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6482 Ramachandran restraints generated. 3241 Oldfield, 0 Emsley, 3241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.981 Fit side-chains revert: symmetry clash REVERT: H 47 ILE cc_start: 0.9347 (mt) cc_final: 0.9122 (mm) REVERT: H 53 LYS cc_start: 0.8393 (mttt) cc_final: 0.8021 (mmtp) REVERT: H 105 GLN cc_start: 0.7624 (tp40) cc_final: 0.7127 (tp40) REVERT: H 108 GLN cc_start: 0.7666 (tp40) cc_final: 0.7290 (tp-100) REVERT: H 109 ASP cc_start: 0.8197 (m-30) cc_final: 0.7976 (m-30) REVERT: H 112 ASP cc_start: 0.8161 (m-30) cc_final: 0.7851 (m-30) REVERT: H 124 MET cc_start: 0.8800 (tpp) cc_final: 0.8522 (tpt) outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.2143 time to fit residues: 60.8747 Evaluate side-chains 129 residues out of total 2671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 9.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 425 HIS H 38 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.061006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.045512 restraints weight = 71048.290| |-----------------------------------------------------------------------------| r_work (start): 0.2624 rms_B_bonded: 2.73 r_work: 0.2498 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 25480 Z= 0.165 Angle : 0.523 10.001 34508 Z= 0.283 Chirality : 0.045 0.152 3988 Planarity : 0.005 0.052 4532 Dihedral : 3.975 19.785 3538 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.26 % Allowed : 4.61 % Favored : 95.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.22 (0.15), residues: 3241 helix: 2.05 (0.15), residues: 1299 sheet: 1.21 (0.22), residues: 558 loop : -0.57 (0.15), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 84 TYR 0.016 0.001 TYR H 16 PHE 0.014 0.001 PHE F 257 HIS 0.006 0.001 HIS D 363 Details of bonding type rmsd covalent geometry : bond 0.00394 (25480) covalent geometry : angle 0.52329 (34508) hydrogen bonds : bond 0.06398 ( 1130) hydrogen bonds : angle 4.66361 ( 3264) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6482 Ramachandran restraints generated. 3241 Oldfield, 0 Emsley, 3241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6482 Ramachandran restraints generated. 3241 Oldfield, 0 Emsley, 3241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 2671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 122 time to evaluate : 1.013 Fit side-chains REVERT: D 226 MET cc_start: 0.8462 (mtt) cc_final: 0.8255 (mtt) REVERT: G 191 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8606 (pp) REVERT: H 47 ILE cc_start: 0.9439 (mt) cc_final: 0.9212 (mm) REVERT: H 51 ARG cc_start: 0.7772 (mtm-85) cc_final: 0.7067 (mtm-85) REVERT: H 53 LYS cc_start: 0.8653 (mttt) cc_final: 0.8414 (mmtp) REVERT: H 105 GLN cc_start: 0.8084 (tp40) cc_final: 0.7571 (tp40) REVERT: H 108 GLN cc_start: 0.8154 (tp40) cc_final: 0.7509 (tp-100) REVERT: H 109 ASP cc_start: 0.8465 (m-30) cc_final: 0.8264 (m-30) REVERT: H 112 ASP cc_start: 0.8755 (m-30) cc_final: 0.8465 (m-30) outliers start: 7 outliers final: 5 residues processed: 127 average time/residue: 0.2017 time to fit residues: 39.2034 Evaluate side-chains 123 residues out of total 2671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 117 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain F residue 467 LYS Chi-restraints excluded: chain G residue 191 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 136 optimal weight: 0.6980 chunk 293 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 307 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 234 optimal weight: 7.9990 chunk 118 optimal weight: 6.9990 chunk 181 optimal weight: 1.9990 chunk 317 optimal weight: 0.9990 chunk 205 optimal weight: 5.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 172 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.059953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.044484 restraints weight = 71193.847| |-----------------------------------------------------------------------------| r_work (start): 0.2595 rms_B_bonded: 2.74 r_work: 0.2465 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8963 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 25480 Z= 0.155 Angle : 0.509 8.557 34508 Z= 0.277 Chirality : 0.045 0.153 3988 Planarity : 0.005 0.056 4532 Dihedral : 4.108 20.589 3538 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.64 % Allowed : 5.92 % Favored : 93.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.14), residues: 3241 helix: 1.89 (0.15), residues: 1309 sheet: 1.02 (0.21), residues: 562 loop : -0.78 (0.15), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 126 TYR 0.015 0.001 TYR H 16 PHE 0.012 0.001 PHE A 494 HIS 0.005 0.001 HIS D 363 Details of bonding type rmsd covalent geometry : bond 0.00370 (25480) covalent geometry : angle 0.50893 (34508) hydrogen bonds : bond 0.06435 ( 1130) hydrogen bonds : angle 4.52989 ( 3264) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6482 Ramachandran restraints generated. 3241 Oldfield, 0 Emsley, 3241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6482 Ramachandran restraints generated. 3241 Oldfield, 0 Emsley, 3241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 2671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 1.025 Fit side-chains revert: symmetry clash REVERT: H 47 ILE cc_start: 0.9446 (mt) cc_final: 0.9223 (mm) REVERT: H 53 LYS cc_start: 0.8558 (mttt) cc_final: 0.8259 (mmtp) REVERT: H 59 GLN cc_start: 0.7839 (tp-100) cc_final: 0.7560 (tp-100) REVERT: H 105 GLN cc_start: 0.8161 (tp40) cc_final: 0.7847 (tp40) REVERT: H 108 GLN cc_start: 0.8182 (tp40) cc_final: 0.7540 (tp-100) REVERT: H 112 ASP cc_start: 0.8797 (m-30) cc_final: 0.8503 (m-30) outliers start: 17 outliers final: 10 residues processed: 131 average time/residue: 0.1750 time to fit residues: 35.9922 Evaluate side-chains 125 residues out of total 2671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 115 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain F residue 467 LYS Chi-restraints excluded: chain G residue 107 HIS Chi-restraints excluded: chain H residue 19 ASP Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain H residue 129 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 299 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 287 optimal weight: 10.0000 chunk 43 optimal weight: 8.9990 chunk 126 optimal weight: 4.9990 chunk 165 optimal weight: 6.9990 chunk 161 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 136 optimal weight: 0.0060 chunk 223 optimal weight: 7.9990 chunk 246 optimal weight: 9.9990 overall best weight: 2.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.058097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2555 r_free = 0.2555 target = 0.042678 restraints weight = 71282.313| |-----------------------------------------------------------------------------| r_work (start): 0.2547 rms_B_bonded: 2.74 r_work: 0.2417 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8986 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 25480 Z= 0.200 Angle : 0.558 10.556 34508 Z= 0.305 Chirality : 0.047 0.163 3988 Planarity : 0.005 0.062 4532 Dihedral : 4.340 19.686 3538 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.94 % Allowed : 7.15 % Favored : 91.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.14), residues: 3241 helix: 1.72 (0.15), residues: 1311 sheet: 0.83 (0.21), residues: 560 loop : -1.02 (0.15), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 126 TYR 0.015 0.001 TYR H 60 PHE 0.015 0.002 PHE F 257 HIS 0.006 0.001 HIS D 363 Details of bonding type rmsd covalent geometry : bond 0.00494 (25480) covalent geometry : angle 0.55835 (34508) hydrogen bonds : bond 0.07453 ( 1130) hydrogen bonds : angle 4.63468 ( 3264) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6482 Ramachandran restraints generated. 3241 Oldfield, 0 Emsley, 3241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6482 Ramachandran restraints generated. 3241 Oldfield, 0 Emsley, 3241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 2671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 117 time to evaluate : 1.007 Fit side-chains revert: symmetry clash REVERT: H 47 ILE cc_start: 0.9462 (mt) cc_final: 0.9254 (mm) REVERT: H 102 ARG cc_start: 0.8066 (mtm-85) cc_final: 0.7710 (mmm160) REVERT: H 108 GLN cc_start: 0.8230 (tp40) cc_final: 0.7594 (tp-100) REVERT: H 112 ASP cc_start: 0.8828 (m-30) cc_final: 0.8541 (m-30) outliers start: 25 outliers final: 13 residues processed: 135 average time/residue: 0.1915 time to fit residues: 40.2845 Evaluate side-chains 126 residues out of total 2671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 467 LYS Chi-restraints excluded: chain H residue 19 ASP Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 88 ILE Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain H residue 129 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 15 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 159 optimal weight: 8.9990 chunk 73 optimal weight: 0.8980 chunk 321 optimal weight: 3.9990 chunk 128 optimal weight: 10.0000 chunk 266 optimal weight: 0.5980 chunk 9 optimal weight: 0.2980 chunk 124 optimal weight: 0.1980 chunk 295 optimal weight: 0.7980 chunk 206 optimal weight: 9.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.062335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.047087 restraints weight = 70422.052| |-----------------------------------------------------------------------------| r_work (start): 0.2665 rms_B_bonded: 2.71 r_work: 0.2543 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 25480 Z= 0.098 Angle : 0.449 9.096 34508 Z= 0.242 Chirality : 0.043 0.147 3988 Planarity : 0.004 0.054 4532 Dihedral : 3.896 19.176 3538 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.45 % Allowed : 7.86 % Favored : 91.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.14), residues: 3241 helix: 1.98 (0.15), residues: 1299 sheet: 0.99 (0.21), residues: 558 loop : -0.80 (0.15), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 126 TYR 0.021 0.001 TYR H 16 PHE 0.009 0.001 PHE F 125 HIS 0.003 0.000 HIS C 42 Details of bonding type rmsd covalent geometry : bond 0.00194 (25480) covalent geometry : angle 0.44908 (34508) hydrogen bonds : bond 0.04680 ( 1130) hydrogen bonds : angle 4.26865 ( 3264) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6482 Ramachandran restraints generated. 3241 Oldfield, 0 Emsley, 3241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6482 Ramachandran restraints generated. 3241 Oldfield, 0 Emsley, 3241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 2671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 118 time to evaluate : 0.914 Fit side-chains revert: symmetry clash REVERT: H 16 TYR cc_start: 0.8497 (t80) cc_final: 0.8274 (t80) REVERT: H 102 ARG cc_start: 0.7973 (mtm-85) cc_final: 0.7646 (mmm160) REVERT: H 108 GLN cc_start: 0.8147 (tp40) cc_final: 0.7472 (tp-100) REVERT: H 112 ASP cc_start: 0.8767 (m-30) cc_final: 0.8459 (m-30) outliers start: 12 outliers final: 7 residues processed: 127 average time/residue: 0.1856 time to fit residues: 36.6417 Evaluate side-chains 122 residues out of total 2671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 115 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 235 MET Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain G residue 107 HIS Chi-restraints excluded: chain H residue 88 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 274 optimal weight: 1.9990 chunk 297 optimal weight: 3.9990 chunk 242 optimal weight: 6.9990 chunk 146 optimal weight: 2.9990 chunk 128 optimal weight: 0.0030 chunk 70 optimal weight: 4.9990 chunk 205 optimal weight: 5.9990 chunk 264 optimal weight: 8.9990 chunk 80 optimal weight: 5.9990 chunk 236 optimal weight: 6.9990 chunk 144 optimal weight: 4.9990 overall best weight: 2.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 345 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.058671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2557 r_free = 0.2557 target = 0.042791 restraints weight = 71642.839| |-----------------------------------------------------------------------------| r_work (start): 0.2550 rms_B_bonded: 2.93 r_work: 0.2416 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8953 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 25480 Z= 0.191 Angle : 0.542 9.086 34508 Z= 0.295 Chirality : 0.046 0.161 3988 Planarity : 0.005 0.060 4532 Dihedral : 4.169 19.527 3538 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.86 % Allowed : 8.24 % Favored : 90.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.14), residues: 3241 helix: 1.82 (0.15), residues: 1310 sheet: 0.81 (0.21), residues: 565 loop : -1.04 (0.15), residues: 1366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 126 TYR 0.022 0.001 TYR H 16 PHE 0.015 0.001 PHE F 257 HIS 0.005 0.001 HIS F 363 Details of bonding type rmsd covalent geometry : bond 0.00470 (25480) covalent geometry : angle 0.54239 (34508) hydrogen bonds : bond 0.06969 ( 1130) hydrogen bonds : angle 4.48604 ( 3264) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6482 Ramachandran restraints generated. 3241 Oldfield, 0 Emsley, 3241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6482 Ramachandran restraints generated. 3241 Oldfield, 0 Emsley, 3241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 2671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 1.048 Fit side-chains revert: symmetry clash REVERT: E 74 MET cc_start: 0.9150 (mtm) cc_final: 0.8830 (mtp) REVERT: F 202 MET cc_start: 0.8636 (mmm) cc_final: 0.8333 (mtp) REVERT: H 16 TYR cc_start: 0.8480 (t80) cc_final: 0.8155 (t80) REVERT: H 102 ARG cc_start: 0.8003 (mtm-85) cc_final: 0.7717 (mmm160) REVERT: H 108 GLN cc_start: 0.8175 (tp40) cc_final: 0.7567 (tp-100) REVERT: H 112 ASP cc_start: 0.8827 (m-30) cc_final: 0.8529 (m-30) outliers start: 23 outliers final: 11 residues processed: 133 average time/residue: 0.1922 time to fit residues: 40.4305 Evaluate side-chains 127 residues out of total 2671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain G residue 107 HIS Chi-restraints excluded: chain H residue 88 ILE Chi-restraints excluded: chain H residue 129 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 37 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 162 optimal weight: 0.7980 chunk 305 optimal weight: 4.9990 chunk 299 optimal weight: 2.9990 chunk 238 optimal weight: 7.9990 chunk 184 optimal weight: 0.6980 chunk 259 optimal weight: 6.9990 chunk 247 optimal weight: 6.9990 chunk 318 optimal weight: 9.9990 chunk 303 optimal weight: 0.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.059232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2572 r_free = 0.2572 target = 0.043406 restraints weight = 71380.376| |-----------------------------------------------------------------------------| r_work (start): 0.2565 rms_B_bonded: 2.93 r_work: 0.2432 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 25480 Z= 0.151 Angle : 0.509 10.139 34508 Z= 0.276 Chirality : 0.045 0.146 3988 Planarity : 0.005 0.061 4532 Dihedral : 4.150 19.663 3538 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.79 % Allowed : 8.50 % Favored : 90.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.14), residues: 3241 helix: 1.78 (0.15), residues: 1317 sheet: 0.78 (0.21), residues: 561 loop : -1.06 (0.15), residues: 1363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 126 TYR 0.022 0.001 TYR H 16 PHE 0.012 0.001 PHE B 236 HIS 0.004 0.001 HIS D 363 Details of bonding type rmsd covalent geometry : bond 0.00364 (25480) covalent geometry : angle 0.50900 (34508) hydrogen bonds : bond 0.06338 ( 1130) hydrogen bonds : angle 4.41969 ( 3264) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6482 Ramachandran restraints generated. 3241 Oldfield, 0 Emsley, 3241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6482 Ramachandran restraints generated. 3241 Oldfield, 0 Emsley, 3241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 2671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 1.002 Fit side-chains revert: symmetry clash REVERT: E 74 MET cc_start: 0.9098 (mtm) cc_final: 0.8815 (mtp) REVERT: F 202 MET cc_start: 0.8655 (mmm) cc_final: 0.8348 (mtp) REVERT: H 16 TYR cc_start: 0.8469 (t80) cc_final: 0.8163 (t80) REVERT: H 53 LYS cc_start: 0.8392 (mttm) cc_final: 0.8024 (mmtp) REVERT: H 102 ARG cc_start: 0.7985 (mtm-85) cc_final: 0.7704 (mmm160) REVERT: H 103 ARG cc_start: 0.8095 (ttm-80) cc_final: 0.7873 (ttp80) REVERT: H 108 GLN cc_start: 0.8164 (tp40) cc_final: 0.7579 (tp-100) REVERT: H 112 ASP cc_start: 0.8804 (m-30) cc_final: 0.8513 (m-30) outliers start: 21 outliers final: 17 residues processed: 131 average time/residue: 0.1766 time to fit residues: 36.8084 Evaluate side-chains 133 residues out of total 2671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 456 VAL Chi-restraints excluded: chain G residue 107 HIS Chi-restraints excluded: chain H residue 88 ILE Chi-restraints excluded: chain H residue 110 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 153 optimal weight: 0.8980 chunk 85 optimal weight: 10.0000 chunk 278 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 274 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 189 optimal weight: 4.9990 chunk 110 optimal weight: 5.9990 chunk 306 optimal weight: 0.9990 chunk 310 optimal weight: 0.8980 chunk 273 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.059301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2574 r_free = 0.2574 target = 0.043470 restraints weight = 71352.674| |-----------------------------------------------------------------------------| r_work (start): 0.2568 rms_B_bonded: 2.93 r_work: 0.2433 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8939 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 25480 Z= 0.145 Angle : 0.503 9.954 34508 Z= 0.272 Chirality : 0.045 0.147 3988 Planarity : 0.004 0.059 4532 Dihedral : 4.109 19.301 3538 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.75 % Allowed : 8.61 % Favored : 90.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.14), residues: 3241 helix: 1.81 (0.15), residues: 1316 sheet: 0.78 (0.21), residues: 563 loop : -1.05 (0.15), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 126 TYR 0.022 0.001 TYR H 16 PHE 0.012 0.001 PHE F 257 HIS 0.006 0.001 HIS F 363 Details of bonding type rmsd covalent geometry : bond 0.00347 (25480) covalent geometry : angle 0.50319 (34508) hydrogen bonds : bond 0.06263 ( 1130) hydrogen bonds : angle 4.39684 ( 3264) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6482 Ramachandran restraints generated. 3241 Oldfield, 0 Emsley, 3241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6482 Ramachandran restraints generated. 3241 Oldfield, 0 Emsley, 3241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 2671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 1.016 Fit side-chains revert: symmetry clash REVERT: E 74 MET cc_start: 0.9094 (mtm) cc_final: 0.8811 (mtp) REVERT: F 202 MET cc_start: 0.8670 (mmm) cc_final: 0.8359 (mtp) REVERT: H 16 TYR cc_start: 0.8459 (t80) cc_final: 0.8233 (t80) REVERT: H 53 LYS cc_start: 0.8440 (mttm) cc_final: 0.8127 (mmtp) REVERT: H 102 ARG cc_start: 0.7975 (mtm-85) cc_final: 0.7711 (mmm160) REVERT: H 108 GLN cc_start: 0.8159 (tp40) cc_final: 0.7580 (tp-100) REVERT: H 112 ASP cc_start: 0.8804 (m-30) cc_final: 0.8514 (m-30) outliers start: 20 outliers final: 15 residues processed: 131 average time/residue: 0.1714 time to fit residues: 35.8417 Evaluate side-chains 131 residues out of total 2671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 456 VAL Chi-restraints excluded: chain G residue 107 HIS Chi-restraints excluded: chain H residue 88 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 117 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 73 optimal weight: 0.4980 chunk 264 optimal weight: 7.9990 chunk 131 optimal weight: 8.9990 chunk 143 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 chunk 113 optimal weight: 5.9990 chunk 160 optimal weight: 0.9990 chunk 280 optimal weight: 8.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.058512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2552 r_free = 0.2552 target = 0.042649 restraints weight = 71734.938| |-----------------------------------------------------------------------------| r_work (start): 0.2546 rms_B_bonded: 2.93 r_work: 0.2412 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8956 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 25480 Z= 0.173 Angle : 0.531 11.511 34508 Z= 0.288 Chirality : 0.046 0.150 3988 Planarity : 0.005 0.060 4532 Dihedral : 4.213 19.802 3538 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.64 % Allowed : 9.02 % Favored : 90.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.14), residues: 3241 helix: 1.76 (0.15), residues: 1315 sheet: 0.71 (0.21), residues: 568 loop : -1.14 (0.15), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 99 TYR 0.023 0.001 TYR H 16 PHE 0.014 0.001 PHE F 257 HIS 0.006 0.001 HIS F 363 Details of bonding type rmsd covalent geometry : bond 0.00423 (25480) covalent geometry : angle 0.53117 (34508) hydrogen bonds : bond 0.06809 ( 1130) hydrogen bonds : angle 4.47130 ( 3264) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6482 Ramachandran restraints generated. 3241 Oldfield, 0 Emsley, 3241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6482 Ramachandran restraints generated. 3241 Oldfield, 0 Emsley, 3241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 2671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 1.027 Fit side-chains REVERT: E 1 MET cc_start: 0.7697 (tpt) cc_final: 0.7434 (tpt) REVERT: F 156 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.8897 (mt) REVERT: F 202 MET cc_start: 0.8650 (mmm) cc_final: 0.8351 (mtp) REVERT: G 170 MET cc_start: 0.9206 (mtp) cc_final: 0.8909 (mtp) REVERT: H 16 TYR cc_start: 0.8484 (t80) cc_final: 0.8259 (t80) REVERT: H 51 ARG cc_start: 0.8231 (mtm-85) cc_final: 0.7349 (mtm-85) REVERT: H 53 LYS cc_start: 0.8453 (mttm) cc_final: 0.8241 (mmtp) REVERT: H 102 ARG cc_start: 0.8000 (mtm-85) cc_final: 0.7755 (mmm160) REVERT: H 108 GLN cc_start: 0.8183 (tp40) cc_final: 0.7606 (tp-100) REVERT: H 112 ASP cc_start: 0.8808 (m-30) cc_final: 0.8524 (m-30) outliers start: 17 outliers final: 13 residues processed: 130 average time/residue: 0.1976 time to fit residues: 40.5060 Evaluate side-chains 129 residues out of total 2671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 456 VAL Chi-restraints excluded: chain G residue 107 HIS Chi-restraints excluded: chain H residue 88 ILE Chi-restraints excluded: chain H residue 129 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 258 optimal weight: 4.9990 chunk 281 optimal weight: 4.9990 chunk 47 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 167 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 304 optimal weight: 4.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.059443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2579 r_free = 0.2579 target = 0.043616 restraints weight = 71034.407| |-----------------------------------------------------------------------------| r_work (start): 0.2574 rms_B_bonded: 2.92 r_work: 0.2443 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 25480 Z= 0.138 Angle : 0.501 10.640 34508 Z= 0.270 Chirality : 0.044 0.146 3988 Planarity : 0.004 0.059 4532 Dihedral : 4.105 19.367 3538 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.60 % Allowed : 9.17 % Favored : 90.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.14), residues: 3241 helix: 1.81 (0.15), residues: 1313 sheet: 0.77 (0.21), residues: 562 loop : -1.09 (0.15), residues: 1366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 99 TYR 0.022 0.001 TYR H 16 PHE 0.012 0.001 PHE F 257 HIS 0.005 0.001 HIS F 363 Details of bonding type rmsd covalent geometry : bond 0.00325 (25480) covalent geometry : angle 0.50055 (34508) hydrogen bonds : bond 0.06101 ( 1130) hydrogen bonds : angle 4.37209 ( 3264) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6482 Ramachandran restraints generated. 3241 Oldfield, 0 Emsley, 3241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6482 Ramachandran restraints generated. 3241 Oldfield, 0 Emsley, 3241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 2671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 1.017 Fit side-chains revert: symmetry clash REVERT: E 1 MET cc_start: 0.7739 (tpt) cc_final: 0.7427 (tpt) REVERT: F 202 MET cc_start: 0.8650 (mmm) cc_final: 0.8328 (mtp) REVERT: G 170 MET cc_start: 0.9176 (mtp) cc_final: 0.8886 (mtp) REVERT: H 102 ARG cc_start: 0.8076 (mtm-85) cc_final: 0.7867 (mmm160) REVERT: H 108 GLN cc_start: 0.8140 (tp40) cc_final: 0.7559 (tp-100) REVERT: H 112 ASP cc_start: 0.8787 (m-30) cc_final: 0.8499 (m-30) outliers start: 16 outliers final: 15 residues processed: 126 average time/residue: 0.1841 time to fit residues: 36.7639 Evaluate side-chains 130 residues out of total 2671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 456 VAL Chi-restraints excluded: chain G residue 107 HIS Chi-restraints excluded: chain H residue 88 ILE Chi-restraints excluded: chain H residue 129 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 97 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 196 optimal weight: 0.6980 chunk 304 optimal weight: 5.9990 chunk 219 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 chunk 207 optimal weight: 6.9990 chunk 156 optimal weight: 0.8980 chunk 175 optimal weight: 2.9990 chunk 164 optimal weight: 0.7980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.060386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2605 r_free = 0.2605 target = 0.044613 restraints weight = 70933.035| |-----------------------------------------------------------------------------| r_work (start): 0.2601 rms_B_bonded: 2.90 r_work: 0.2467 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8912 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25480 Z= 0.114 Angle : 0.477 10.773 34508 Z= 0.256 Chirality : 0.044 0.142 3988 Planarity : 0.004 0.056 4532 Dihedral : 3.975 19.264 3538 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.45 % Allowed : 9.25 % Favored : 90.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.15), residues: 3241 helix: 1.97 (0.15), residues: 1303 sheet: 0.85 (0.22), residues: 560 loop : -1.01 (0.15), residues: 1378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 99 TYR 0.034 0.001 TYR H 16 PHE 0.010 0.001 PHE F 257 HIS 0.004 0.001 HIS F 363 Details of bonding type rmsd covalent geometry : bond 0.00255 (25480) covalent geometry : angle 0.47665 (34508) hydrogen bonds : bond 0.05511 ( 1130) hydrogen bonds : angle 4.27540 ( 3264) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4437.40 seconds wall clock time: 77 minutes 1.30 seconds (4621.30 seconds total)