Starting phenix.real_space_refine on Tue Mar 19 19:02:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xkh_33251/03_2024/7xkh_33251_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xkh_33251/03_2024/7xkh_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xkh_33251/03_2024/7xkh_33251.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xkh_33251/03_2024/7xkh_33251.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xkh_33251/03_2024/7xkh_33251_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xkh_33251/03_2024/7xkh_33251_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Residue "E TYR 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/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: 13.11, per 1000 atoms: 0.52 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 - 3.50 Amino acid : False - 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: 9.04 Conformation dependent library (CDL) restraints added in 4.5 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... running ksdssp... Secondary structure from input PDB file: 123 helices and 25 sheets defined 41.3% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.92 Creating SS restraints... Processing helix chain 'A' and resid 101 through 103 No H-bonds generated for 'chain 'A' and resid 101 through 103' Processing helix chain 'A' and resid 136 through 138 No H-bonds generated for 'chain 'A' and resid 136 through 138' Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'A' and resid 175 through 186 removed outlier: 3.604A pdb=" N ALA A 179 " --> pdb=" O LYS A 175 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLN A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 215 Processing helix chain 'A' and resid 217 through 219 No H-bonds generated for 'chain 'A' and resid 217 through 219' Processing helix chain 'A' and resid 232 through 252 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) removed outlier: 3.714A pdb=" N LYS A 252 " --> pdb=" O TYR A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 276 Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 290 through 300 removed outlier: 3.544A pdb=" N LEU A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ARG A 300 " --> pdb=" O ARG A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 335 Processing helix chain 'A' and resid 346 through 351 Processing helix chain 'A' and resid 373 through 392 removed outlier: 4.289A pdb=" N GLY A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N THR A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N LEU A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) 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 404 through 420 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) Processing helix chain 'A' and resid 430 through 441 Processing helix chain 'A' and resid 450 through 467 removed outlier: 4.923A pdb=" N ARG A 454 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG A 455 " --> pdb=" O ASP A 452 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR A 461 " --> pdb=" O LYS A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 478 Processing helix chain 'A' and resid 484 through 497 Processing helix chain 'B' and resid 101 through 103 No H-bonds generated for 'chain 'B' and resid 101 through 103' Processing helix chain 'B' and resid 136 through 138 No H-bonds generated for 'chain 'B' and resid 136 through 138' Processing helix chain 'B' and resid 151 through 156 Processing helix chain 'B' and resid 175 through 188 removed outlier: 3.623A pdb=" N ALA B 179 " --> pdb=" O LYS B 175 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLN B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LYS B 187 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N ASP B 188 " --> pdb=" O ILE B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 214 Processing helix chain 'B' and resid 218 through 220 No H-bonds generated for 'chain 'B' and resid 218 through 220' Processing helix chain 'B' and resid 232 through 236 Processing helix chain 'B' and resid 238 through 252 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) removed outlier: 3.748A pdb=" N LYS B 252 " --> pdb=" O TYR B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 276 Processing helix chain 'B' and resid 283 through 285 No H-bonds generated for 'chain 'B' and resid 283 through 285' Processing helix chain 'B' and resid 290 through 300 removed outlier: 3.732A pdb=" N LEU B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ARG B 300 " --> pdb=" O ARG B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 329 through 335 Processing helix chain 'B' and resid 346 through 351 removed outlier: 3.818A pdb=" N SER B 351 " --> pdb=" O ASP B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 395 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) removed outlier: 4.457A pdb=" N ALA B 394 " --> pdb=" O ARG B 390 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N PHE B 395 " --> pdb=" O GLU B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 420 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) Processing helix chain 'B' and resid 430 through 441 Processing helix chain 'B' and resid 450 through 467 removed outlier: 5.100A pdb=" N ARG B 454 " --> pdb=" O GLU B 451 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG B 455 " --> pdb=" O ASP B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 478 Processing helix chain 'B' and resid 484 through 497 removed outlier: 3.926A pdb=" N THR B 497 " --> pdb=" O ALA B 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 103 No H-bonds generated for 'chain 'C' and resid 101 through 103' Processing helix chain 'C' and resid 136 through 138 No H-bonds generated for 'chain 'C' and resid 136 through 138' Processing helix chain 'C' and resid 151 through 156 Processing helix chain 'C' and resid 175 through 187 removed outlier: 3.730A pdb=" N GLN C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N LYS C 187 " --> pdb=" O ILE C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 215 Processing helix chain 'C' and resid 218 through 220 No H-bonds generated for 'chain 'C' and resid 218 through 220' Processing helix chain 'C' and resid 232 through 236 Processing helix chain 'C' and resid 238 through 252 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) removed outlier: 3.843A pdb=" N LYS C 252 " --> pdb=" O TYR C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 276 Processing helix chain 'C' and resid 283 through 285 No H-bonds generated for 'chain 'C' and resid 283 through 285' Processing helix chain 'C' and resid 290 through 300 removed outlier: 3.592A pdb=" N LEU C 297 " --> pdb=" O LEU C 293 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ARG C 300 " --> pdb=" O ARG C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 335 Processing helix chain 'C' and resid 346 through 350 Processing helix chain 'C' and resid 373 through 396 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) removed outlier: 4.330A pdb=" N ALA C 394 " --> pdb=" O ARG C 390 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N PHE C 395 " --> pdb=" O GLU C 391 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ALA C 396 " --> pdb=" O LEU C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 419 removed outlier: 3.642A pdb=" N LYS C 409 " --> pdb=" O ALA C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 441 removed outlier: 3.933A pdb=" N LEU C 435 " --> pdb=" O GLU C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 466 removed outlier: 4.974A pdb=" N ARG C 454 " --> pdb=" O GLU C 451 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG C 455 " --> pdb=" O ASP C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 478 Processing helix chain 'C' and resid 484 through 497 Processing helix chain 'D' and resid 89 through 91 No H-bonds generated for 'chain 'D' and resid 89 through 91' Processing helix chain 'D' and resid 140 through 145 Processing helix chain 'D' and resid 164 through 179 Processing helix chain 'D' and resid 192 through 205 Processing helix chain 'D' and resid 207 through 210 Processing helix chain 'D' and resid 222 through 226 Processing helix chain 'D' and resid 228 through 242 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 255 through 266 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 281 through 291 removed outlier: 3.549A pdb=" N LEU D 288 " --> pdb=" O GLU D 284 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ARG D 291 " --> pdb=" O GLN D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 311 No H-bonds generated for 'chain 'D' and resid 309 through 311' Processing helix chain 'D' and resid 316 through 324 removed outlier: 3.842A pdb=" N SER D 323 " --> pdb=" O ALA D 319 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N HIS D 324 " --> pdb=" O THR D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 338 Processing helix chain 'D' and resid 361 through 387 removed outlier: 3.616A pdb=" N GLU D 379 " --> pdb=" O GLN D 375 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LEU D 380 " --> pdb=" O ARG D 376 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLN D 381 " --> pdb=" O TYR D 377 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N ASP D 382 " --> pdb=" O LYS D 378 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ILE D 383 " --> pdb=" O GLU D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 409 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 418 through 421 No H-bonds generated for 'chain 'D' and resid 418 through 421' Processing helix chain 'D' and resid 430 through 442 Processing helix chain 'D' and resid 450 through 453 Processing helix chain 'D' and resid 459 through 468 removed outlier: 3.575A pdb=" N VAL D 463 " --> pdb=" O GLU D 460 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 91 No H-bonds generated for 'chain 'E' and resid 89 through 91' Processing helix chain 'E' and resid 125 through 127 No H-bonds generated for 'chain 'E' and resid 125 through 127' Processing helix chain 'E' and resid 140 through 145 Processing helix chain 'E' and resid 164 through 178 Processing helix chain 'E' and resid 192 through 205 removed outlier: 3.637A pdb=" N SER E 205 " --> pdb=" O GLU E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 210 No H-bonds generated for 'chain 'E' and resid 208 through 210' Processing helix chain 'E' and resid 222 through 225 No H-bonds generated for 'chain 'E' and resid 222 through 225' Processing helix chain 'E' and resid 228 through 242 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 255 through 268 Processing helix chain 'E' and resid 281 through 291 removed outlier: 3.592A pdb=" N LEU E 288 " --> pdb=" O GLU E 284 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ARG E 291 " --> pdb=" O GLN E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 311 No H-bonds generated for 'chain 'E' and resid 309 through 311' Processing helix chain 'E' and resid 316 through 323 removed outlier: 3.669A pdb=" N SER E 323 " --> pdb=" O ALA E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 338 Processing helix chain 'E' and resid 361 through 385 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) removed outlier: 3.896A pdb=" N ALA E 385 " --> pdb=" O GLN E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 391 No H-bonds generated for 'chain 'E' and resid 389 through 391' Processing helix chain 'E' and resid 394 through 409 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 416 through 421 removed outlier: 3.561A pdb=" N GLN E 419 " --> pdb=" O VAL E 416 " (cutoff:3.500A) Processing helix chain 'E' and resid 430 through 442 Processing helix chain 'E' and resid 450 through 453 Processing helix chain 'E' and resid 459 through 469 removed outlier: 4.221A pdb=" N VAL E 463 " --> pdb=" O GLU E 460 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 91 No H-bonds generated for 'chain 'F' and resid 89 through 91' Processing helix chain 'F' and resid 125 through 127 No H-bonds generated for 'chain 'F' and resid 125 through 127' Processing helix chain 'F' and resid 140 through 145 Processing helix chain 'F' and resid 164 through 178 removed outlier: 4.362A pdb=" N GLN F 177 " --> pdb=" O HIS F 173 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N GLU F 178 " --> pdb=" O ASN F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 192 through 205 Processing helix chain 'F' and resid 207 through 210 Processing helix chain 'F' and resid 222 through 225 No H-bonds generated for 'chain 'F' and resid 222 through 225' Processing helix chain 'F' and resid 228 through 242 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 255 through 268 removed outlier: 3.795A pdb=" N ALA F 266 " --> pdb=" O SER F 262 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N LEU F 267 " --> pdb=" O GLU F 263 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU F 268 " --> pdb=" O VAL F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 291 removed outlier: 3.597A pdb=" N LEU F 288 " --> pdb=" O GLU F 284 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG F 291 " --> pdb=" O GLN F 287 " (cutoff:3.500A) Processing helix chain 'F' and resid 309 through 311 No H-bonds generated for 'chain 'F' and resid 309 through 311' Processing helix chain 'F' and resid 316 through 320 Processing helix chain 'F' and resid 322 through 324 No H-bonds generated for 'chain 'F' and resid 322 through 324' Processing helix chain 'F' and resid 333 through 337 Processing helix chain 'F' and resid 361 through 387 removed outlier: 3.808A pdb=" N LEU F 380 " --> pdb=" O ARG F 376 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLN F 381 " --> pdb=" O TYR F 377 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N ASP F 382 " --> pdb=" O LYS F 378 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N ILE F 383 " --> pdb=" O GLU F 379 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE F 386 " --> pdb=" O ASP F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 through 409 removed outlier: 3.564A pdb=" N ARG F 405 " --> pdb=" O HIS F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 421 removed outlier: 3.627A pdb=" N GLN F 419 " --> pdb=" O VAL F 416 " (cutoff:3.500A) Processing helix chain 'F' and resid 430 through 441 Processing helix chain 'F' and resid 450 through 453 Processing helix chain 'F' and resid 460 through 469 removed outlier: 3.740A pdb=" N GLU F 464 " --> pdb=" O GLU F 460 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 57 removed outlier: 3.808A pdb=" N GLN G 37 " --> pdb=" O ASN G 33 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N PHE G 42 " --> pdb=" O ASN G 38 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N VAL G 43 " --> pdb=" O ALA G 39 " (cutoff:3.500A) Proline residue: G 44 - end of helix removed outlier: 3.748A pdb=" N GLU G 51 " --> pdb=" O GLU G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 66 through 68 No H-bonds generated for 'chain 'G' and resid 66 through 68' Processing helix chain 'G' and resid 91 through 106 removed outlier: 4.079A pdb=" N VAL G 95 " --> pdb=" O TYR G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 112 No H-bonds generated for 'chain 'G' and resid 110 through 112' Processing helix chain 'G' and resid 120 through 128 Processing helix chain 'G' and resid 146 through 161 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 209 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 88 through 129 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= A, first strand: chain 'A' and resid 87 through 89 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: 3.567A pdb=" N ASN A 65 " --> pdb=" O GLY A 72 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL A 74 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N ALA A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing sheet with id= B, 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= C, first strand: chain 'A' and resid 107 through 109 removed outlier: 8.853A pdb=" N VAL A 108 " --> pdb=" O THR A 221 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL A 223 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N SER A 193 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N VAL A 224 " --> pdb=" O SER A 193 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TYR A 195 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N ALA A 226 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ALA A 197 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N SER A 312 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N VAL A 258 " --> pdb=" O SER A 312 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N THR A 314 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N TYR A 260 " --> pdb=" O THR A 314 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU A 316 " --> pdb=" O TYR A 260 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 341 through 343 removed outlier: 7.405A pdb=" N LEU A 166 " --> pdb=" O ILE A 342 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 28 through 30 removed outlier: 3.632A pdb=" N GLN B 33 " --> pdb=" O ARG B 40 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N HIS B 42 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N VAL B 31 " --> pdb=" O HIS B 42 " (cutoff:3.500A) Processing sheet with id= F, 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= G, first strand: chain 'B' and resid 341 through 344 removed outlier: 6.903A pdb=" N LEU B 166 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N LEU B 344 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ILE B 168 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 312 through 316 removed outlier: 3.657A pdb=" N TYR B 260 " --> pdb=" O LEU B 316 " (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) Processing sheet with id= I, first strand: chain 'C' and resid 28 through 30 removed outlier: 6.632A pdb=" N GLY C 72 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLN C 33 " --> pdb=" O ARG C 40 " (cutoff:3.500A) Processing sheet with id= J, 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= K, first strand: chain 'C' and resid 107 through 109 removed outlier: 8.829A pdb=" N VAL C 108 " --> pdb=" O THR C 221 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL C 223 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N SER C 193 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N VAL C 224 " --> pdb=" O SER C 193 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N TYR C 195 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N ALA C 226 " --> pdb=" O TYR C 195 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ALA C 197 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N SER C 312 " --> pdb=" O VAL C 256 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N VAL C 258 " --> pdb=" O SER C 312 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N THR C 314 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N TYR C 260 " --> pdb=" O THR C 314 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU C 316 " --> pdb=" O TYR C 260 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 341 through 344 removed outlier: 6.932A pdb=" N LEU C 166 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N LEU C 344 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N ILE C 168 " --> pdb=" O LEU C 344 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 5 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: 6.379A pdb=" N ILE D 62 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N VAL D 50 " --> 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) Processing sheet with id= N, first strand: chain 'D' and resid 84 through 86 Processing sheet with id= O, first strand: chain 'D' and resid 327 through 330 removed outlier: 3.694A pdb=" N ALA D 327 " --> pdb=" O LYS D 153 " (cutoff:3.500A) removed outlier: 8.969A pdb=" N ILE D 154 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N SER D 302 " --> pdb=" O ILE D 154 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N LEU D 156 " --> pdb=" O SER D 302 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLN D 304 " --> pdb=" O LEU D 156 " (cutoff:3.500A) 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) Processing sheet with id= P, first strand: chain 'E' and resid 75 through 77 removed outlier: 6.962A pdb=" N ASP E 15 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N VAL E 9 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N VAL E 13 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ILE E 62 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N VAL E 50 " --> pdb=" O ILE E 62 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 84 through 86 Processing sheet with id= R, first strand: chain 'E' and resid 327 through 330 removed outlier: 3.517A pdb=" N ALA E 327 " --> pdb=" O LYS E 153 " (cutoff:3.500A) removed outlier: 8.800A pdb=" N ILE E 154 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N SER E 302 " --> pdb=" O ILE E 154 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N LEU E 156 " --> pdb=" O SER E 302 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N GLN E 304 " --> pdb=" O LEU E 156 " (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: 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) Processing sheet with id= S, first strand: chain 'F' and resid 75 through 77 removed outlier: 6.564A pdb=" N ASP F 15 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N VAL F 9 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N VAL F 13 " --> pdb=" O VAL F 9 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL F 14 " --> pdb=" O THR F 61 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ILE F 62 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N VAL F 50 " --> pdb=" O ILE F 62 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 84 through 86 Processing sheet with id= U, first strand: chain 'F' and resid 327 through 330 removed outlier: 8.249A pdb=" N ILE F 154 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N SER F 302 " --> pdb=" O ILE F 154 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N LEU F 156 " --> pdb=" O SER F 302 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N GLN F 304 " --> pdb=" O LEU F 156 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N GLY F 158 " --> pdb=" O GLN F 304 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ILE F 306 " --> pdb=" O GLY F 158 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL F 247 " --> pdb=" O THR F 301 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N ILE F 303 " --> pdb=" O VAL F 247 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU F 249 " --> pdb=" O ILE F 303 " (cutoff:3.500A) removed outlier: 8.597A pdb=" N ALA F 305 " --> pdb=" O LEU F 249 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N ILE F 251 " --> pdb=" O ALA F 305 " (cutoff:3.500A) removed outlier: 9.076A pdb=" N TYR F 307 " --> pdb=" O ILE F 251 " (cutoff:3.500A) 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) Processing sheet with id= V, first strand: chain 'G' and resid 181 through 189 removed outlier: 3.522A pdb=" N TYR G 172 " --> pdb=" O THR G 184 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU G 188 " --> pdb=" O LEU G 168 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LEU G 168 " --> pdb=" O LEU G 188 " (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: 7.812A pdb=" N VAL G 117 " --> pdb=" O ILE G 134 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ASP G 136 " --> pdb=" O VAL G 117 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'H' and resid 41 through 44 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: 6.667A pdb=" N HIS H 5 " --> pdb=" O VAL H 75 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N ILE H 77 " --> pdb=" O HIS H 5 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N SER H 7 " --> pdb=" O ILE H 77 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N ALA H 79 " --> pdb=" O SER H 7 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N VAL H 9 " --> pdb=" O ALA H 79 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TYR H 16 " --> pdb=" O VAL H 8 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N THR H 10 " --> pdb=" O PRO H 14 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'H' and resid 22 through 25 Processing sheet with id= Y, first strand: chain 'H' and resid 48 through 52 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) 944 hydrogen bonds defined for protein. 2613 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: 7.79 Time building geometry restraints manager: 9.88 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: 100.63 - 107.10: 769 107.10 - 113.57: 14042 113.57 - 120.04: 8525 120.04 - 126.51: 10957 126.51 - 132.98: 215 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: 6279 2.81 - 3.33: 22614 3.33 - 3.85: 37378 3.85 - 4.38: 42498 4.38 - 4.90: 78241 Nonbonded interactions: 187010 Sorted by model distance: nonbonded pdb=" O GLN A 163 " pdb=" OG1 THR A 314 " model vdw 2.283 2.440 nonbonded pdb=" OE1 GLN G 50 " pdb=" OH TYR G 220 " model vdw 2.283 2.440 nonbonded pdb=" OD1 ASP B 170 " pdb=" OG1 THR B 321 " model vdw 2.287 2.440 nonbonded pdb=" NE2 HIS G 65 " pdb=" OD1 ASP G 214 " model vdw 2.308 2.520 nonbonded pdb=" O GLN C 163 " pdb=" OG1 THR C 314 " model vdw 2.309 2.440 ... (remaining 187005 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 2.770 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: 11.350 Check model and map are aligned: 0.380 Set scattering table: 0.230 Process input model: 64.540 Find NCS groups from input model: 2.030 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.230 ------------------------------------------------------------------------------- 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= 0.116 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.002 0.000 HIS C 42 PHE 0.009 0.001 PHE C 494 TYR 0.008 0.001 TYR G 91 ARG 0.003 0.000 ARG A 164 *********************** 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 fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 3.131 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: 0.7947 (mttm) 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: 0.7975 (m-30) REVERT: H 112 ASP cc_start: 0.8161 (m-30) cc_final: 0.7852 (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: 0.4379 time to fit residues: 125.4145 Evaluate side-chains 129 residues out of total 2671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 2.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 271 optimal weight: 6.9990 chunk 244 optimal weight: 0.9990 chunk 135 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 164 optimal weight: 7.9990 chunk 130 optimal weight: 4.9990 chunk 252 optimal weight: 8.9990 chunk 97 optimal weight: 5.9990 chunk 153 optimal weight: 0.9990 chunk 187 optimal weight: 0.6980 chunk 292 optimal weight: 0.4980 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 425 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.0958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 25480 Z= 0.151 Angle : 0.449 9.758 34508 Z= 0.238 Chirality : 0.043 0.153 3988 Planarity : 0.004 0.051 4532 Dihedral : 3.571 19.616 3538 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.37 % Allowed : 3.67 % Favored : 95.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.15), residues: 3241 helix: 1.99 (0.15), residues: 1318 sheet: 1.56 (0.22), residues: 543 loop : -0.36 (0.15), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 42 PHE 0.011 0.001 PHE C 463 TYR 0.017 0.001 TYR H 16 ARG 0.007 0.000 ARG H 84 *********************** 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 135 residues out of total 2671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 125 time to evaluate : 3.073 Fit side-chains REVERT: D 226 MET cc_start: 0.7894 (mtt) cc_final: 0.7682 (mtt) REVERT: G 191 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8210 (pp) REVERT: H 18 ASP cc_start: 0.6430 (m-30) cc_final: 0.6174 (m-30) REVERT: H 47 ILE cc_start: 0.9403 (mt) cc_final: 0.9194 (mm) REVERT: H 53 LYS cc_start: 0.8692 (mttt) cc_final: 0.8465 (mmtp) REVERT: H 105 GLN cc_start: 0.7638 (tp40) cc_final: 0.7373 (tp40) REVERT: H 108 GLN cc_start: 0.7837 (tp40) cc_final: 0.7102 (tp-100) REVERT: H 112 ASP cc_start: 0.8365 (m-30) cc_final: 0.8029 (m-30) REVERT: H 124 MET cc_start: 0.8867 (tpp) cc_final: 0.8617 (tpt) outliers start: 10 outliers final: 6 residues processed: 132 average time/residue: 0.4201 time to fit residues: 85.6204 Evaluate side-chains 122 residues out of total 2671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 115 time to evaluate : 3.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 73 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 162 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 243 optimal weight: 0.0770 chunk 199 optimal weight: 8.9990 chunk 80 optimal weight: 8.9990 chunk 292 optimal weight: 10.0000 chunk 316 optimal weight: 6.9990 chunk 260 optimal weight: 5.9990 chunk 290 optimal weight: 3.9990 chunk 99 optimal weight: 0.6980 chunk 235 optimal weight: 7.9990 overall best weight: 1.5342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 38 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25480 Z= 0.190 Angle : 0.463 8.804 34508 Z= 0.248 Chirality : 0.044 0.149 3988 Planarity : 0.004 0.043 4532 Dihedral : 3.774 19.897 3538 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.60 % Allowed : 5.43 % Favored : 93.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.15), residues: 3241 helix: 1.94 (0.15), residues: 1283 sheet: 1.38 (0.22), residues: 549 loop : -0.52 (0.15), residues: 1409 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 363 PHE 0.012 0.001 PHE F 257 TYR 0.019 0.001 TYR H 16 ARG 0.008 0.000 ARG H 126 *********************** 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 133 residues out of total 2671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 117 time to evaluate : 3.070 Fit side-chains REVERT: D 226 MET cc_start: 0.8512 (mtt) cc_final: 0.8298 (mtt) REVERT: H 18 ASP cc_start: 0.7006 (m-30) cc_final: 0.6745 (m-30) REVERT: H 47 ILE cc_start: 0.9378 (mt) cc_final: 0.9133 (mm) REVERT: H 53 LYS cc_start: 0.8473 (mttt) cc_final: 0.8223 (mmtp) REVERT: H 102 ARG cc_start: 0.7925 (mtm-85) cc_final: 0.7458 (mmm160) REVERT: H 108 GLN cc_start: 0.7841 (tp40) cc_final: 0.7085 (tp-100) REVERT: H 112 ASP cc_start: 0.8430 (m-30) cc_final: 0.8073 (m-30) outliers start: 16 outliers final: 9 residues processed: 125 average time/residue: 0.4532 time to fit residues: 89.2648 Evaluate side-chains 121 residues out of total 2671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 112 time to evaluate : 3.067 ------------------------------------------------------------------------------- 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 254 ILE Chi-restraints excluded: chain F residue 467 LYS Chi-restraints excluded: chain H residue 19 ASP Chi-restraints excluded: chain H residue 22 MET Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain H residue 110 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 289 optimal weight: 9.9990 chunk 220 optimal weight: 0.3980 chunk 152 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 139 optimal weight: 0.1980 chunk 196 optimal weight: 7.9990 chunk 293 optimal weight: 0.9990 chunk 311 optimal weight: 8.9990 chunk 153 optimal weight: 0.8980 chunk 278 optimal weight: 0.4980 chunk 83 optimal weight: 2.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 25480 Z= 0.115 Angle : 0.419 10.844 34508 Z= 0.221 Chirality : 0.042 0.145 3988 Planarity : 0.004 0.045 4532 Dihedral : 3.570 18.989 3538 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.75 % Allowed : 5.95 % Favored : 93.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.15), residues: 3241 helix: 1.93 (0.15), residues: 1285 sheet: 1.58 (0.22), residues: 544 loop : -0.42 (0.15), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS C 42 PHE 0.008 0.001 PHE F 125 TYR 0.016 0.001 TYR H 16 ARG 0.006 0.000 ARG H 126 *********************** 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 135 residues out of total 2671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 115 time to evaluate : 2.999 Fit side-chains REVERT: H 18 ASP cc_start: 0.6951 (m-30) cc_final: 0.6704 (m-30) REVERT: H 47 ILE cc_start: 0.9376 (mt) cc_final: 0.9133 (mm) REVERT: H 53 LYS cc_start: 0.8474 (mttt) cc_final: 0.8237 (mmtp) REVERT: H 102 ARG cc_start: 0.7946 (mtm-85) cc_final: 0.7509 (mmm160) REVERT: H 103 ARG cc_start: 0.7946 (ttm-80) cc_final: 0.7699 (mtm-85) REVERT: H 108 GLN cc_start: 0.7808 (tp40) cc_final: 0.7347 (mm-40) REVERT: H 112 ASP cc_start: 0.8412 (m-30) cc_final: 0.8178 (m-30) outliers start: 20 outliers final: 8 residues processed: 127 average time/residue: 0.3845 time to fit residues: 78.0193 Evaluate side-chains 123 residues out of total 2671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 115 time to evaluate : 2.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 H residue 19 ASP Chi-restraints excluded: chain H residue 22 MET Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain H residue 88 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 259 optimal weight: 5.9990 chunk 176 optimal weight: 4.9990 chunk 4 optimal weight: 7.9990 chunk 231 optimal weight: 1.9990 chunk 128 optimal weight: 9.9990 chunk 265 optimal weight: 0.9980 chunk 215 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 158 optimal weight: 3.9990 chunk 279 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 59 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25480 Z= 0.220 Angle : 0.480 9.561 34508 Z= 0.256 Chirality : 0.044 0.150 3988 Planarity : 0.004 0.043 4532 Dihedral : 3.851 19.633 3538 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.45 % Allowed : 6.89 % Favored : 92.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.15), residues: 3241 helix: 1.90 (0.15), residues: 1265 sheet: 1.25 (0.22), residues: 568 loop : -0.59 (0.15), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 363 PHE 0.013 0.001 PHE F 257 TYR 0.017 0.001 TYR H 16 ARG 0.006 0.000 ARG H 126 *********************** 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 129 residues out of total 2671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 117 time to evaluate : 2.833 Fit side-chains revert: symmetry clash REVERT: H 47 ILE cc_start: 0.9391 (mt) cc_final: 0.9154 (mm) REVERT: H 51 ARG cc_start: 0.8258 (mtm-85) cc_final: 0.7633 (mtm-85) REVERT: H 102 ARG cc_start: 0.8023 (mtm-85) cc_final: 0.7615 (mmm160) REVERT: H 103 ARG cc_start: 0.8020 (ttm-80) cc_final: 0.7792 (ttp80) REVERT: H 108 GLN cc_start: 0.7866 (tp40) cc_final: 0.7372 (mm-40) REVERT: H 112 ASP cc_start: 0.8467 (m-30) cc_final: 0.8224 (m-30) outliers start: 12 outliers final: 10 residues processed: 124 average time/residue: 0.4048 time to fit residues: 78.9303 Evaluate side-chains 124 residues out of total 2671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 114 time to evaluate : 2.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 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 456 VAL Chi-restraints excluded: chain F residue 467 LYS Chi-restraints excluded: chain H residue 19 ASP Chi-restraints excluded: chain H residue 22 MET Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain H residue 110 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 104 optimal weight: 1.9990 chunk 280 optimal weight: 7.9990 chunk 61 optimal weight: 1.9990 chunk 182 optimal weight: 0.0040 chunk 76 optimal weight: 0.9980 chunk 311 optimal weight: 9.9990 chunk 258 optimal weight: 5.9990 chunk 144 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 163 optimal weight: 5.9990 overall best weight: 1.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25480 Z= 0.174 Angle : 0.449 9.721 34508 Z= 0.239 Chirality : 0.043 0.144 3988 Planarity : 0.004 0.045 4532 Dihedral : 3.796 19.489 3538 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.60 % Allowed : 7.34 % Favored : 92.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.15), residues: 3241 helix: 1.86 (0.15), residues: 1266 sheet: 1.23 (0.22), residues: 568 loop : -0.60 (0.15), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 363 PHE 0.010 0.001 PHE F 257 TYR 0.016 0.001 TYR H 16 ARG 0.007 0.000 ARG H 126 *********************** 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 131 residues out of total 2671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 115 time to evaluate : 3.013 Fit side-chains REVERT: B 289 ASP cc_start: 0.8420 (OUTLIER) cc_final: 0.8066 (m-30) REVERT: H 47 ILE cc_start: 0.9391 (mt) cc_final: 0.9152 (mm) REVERT: H 51 ARG cc_start: 0.8322 (mtm-85) cc_final: 0.7690 (mtm-85) REVERT: H 102 ARG cc_start: 0.7987 (mtm-85) cc_final: 0.7634 (mmm160) REVERT: H 103 ARG cc_start: 0.8024 (ttm-80) cc_final: 0.7751 (mtm-85) REVERT: H 108 GLN cc_start: 0.7863 (tp40) cc_final: 0.7435 (mm-40) REVERT: H 112 ASP cc_start: 0.8435 (m-30) cc_final: 0.8204 (m-30) outliers start: 16 outliers final: 12 residues processed: 124 average time/residue: 0.3958 time to fit residues: 77.8716 Evaluate side-chains 125 residues out of total 2671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 112 time to evaluate : 2.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain F residue 218 MET Chi-restraints excluded: chain F 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 22 MET Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain H residue 88 ILE Chi-restraints excluded: chain H residue 110 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 300 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 177 optimal weight: 7.9990 chunk 227 optimal weight: 8.9990 chunk 176 optimal weight: 2.9990 chunk 262 optimal weight: 4.9990 chunk 173 optimal weight: 7.9990 chunk 310 optimal weight: 0.0020 chunk 194 optimal weight: 6.9990 chunk 189 optimal weight: 2.9990 chunk 143 optimal weight: 6.9990 overall best weight: 2.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 25480 Z= 0.267 Angle : 0.510 10.886 34508 Z= 0.273 Chirality : 0.045 0.153 3988 Planarity : 0.004 0.045 4532 Dihedral : 4.053 19.417 3538 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.67 % Allowed : 7.64 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.14), residues: 3241 helix: 1.73 (0.15), residues: 1255 sheet: 1.05 (0.22), residues: 560 loop : -0.78 (0.15), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 363 PHE 0.014 0.001 PHE F 257 TYR 0.019 0.001 TYR H 60 ARG 0.007 0.000 ARG H 126 *********************** 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 129 residues out of total 2671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 111 time to evaluate : 2.877 Fit side-chains REVERT: B 289 ASP cc_start: 0.8494 (OUTLIER) cc_final: 0.8117 (m-30) REVERT: H 47 ILE cc_start: 0.9406 (mt) cc_final: 0.9167 (mm) REVERT: H 51 ARG cc_start: 0.8343 (mtm-85) cc_final: 0.7700 (mtm-85) REVERT: H 102 ARG cc_start: 0.8118 (mtm-85) cc_final: 0.7763 (mmm160) REVERT: H 103 ARG cc_start: 0.8043 (ttm-80) cc_final: 0.7824 (ttp80) REVERT: H 108 GLN cc_start: 0.7919 (tp40) cc_final: 0.7453 (mm-40) REVERT: H 112 ASP cc_start: 0.8439 (m-30) cc_final: 0.8209 (m-30) outliers start: 18 outliers final: 13 residues processed: 122 average time/residue: 0.3854 time to fit residues: 74.7341 Evaluate side-chains 125 residues out of total 2671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 111 time to evaluate : 2.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 289 ASP 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 218 MET Chi-restraints excluded: chain F residue 456 VAL Chi-restraints excluded: chain F residue 467 LYS Chi-restraints excluded: chain H residue 22 MET Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 73 ASP 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 192 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 185 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 197 optimal weight: 0.3980 chunk 211 optimal weight: 0.6980 chunk 153 optimal weight: 0.8980 chunk 28 optimal weight: 8.9990 chunk 243 optimal weight: 0.9980 chunk 282 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1916 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= 0.146 Angle : 0.442 12.810 34508 Z= 0.233 Chirality : 0.043 0.141 3988 Planarity : 0.004 0.045 4532 Dihedral : 3.794 19.185 3538 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.60 % Allowed : 7.71 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.15), residues: 3241 helix: 1.83 (0.15), residues: 1256 sheet: 1.21 (0.22), residues: 561 loop : -0.68 (0.15), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 363 PHE 0.009 0.001 PHE F 257 TYR 0.015 0.001 TYR H 60 ARG 0.007 0.000 ARG H 99 *********************** 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 129 residues out of total 2671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 113 time to evaluate : 3.143 Fit side-chains REVERT: B 289 ASP cc_start: 0.8401 (OUTLIER) cc_final: 0.8040 (m-30) REVERT: H 47 ILE cc_start: 0.9399 (mt) cc_final: 0.9162 (mm) REVERT: H 51 ARG cc_start: 0.8400 (mtm-85) cc_final: 0.7763 (mtm-85) REVERT: H 102 ARG cc_start: 0.7941 (mtm-85) cc_final: 0.7641 (mmm160) REVERT: H 103 ARG cc_start: 0.8028 (ttm-80) cc_final: 0.7794 (mtm-85) REVERT: H 108 GLN cc_start: 0.7843 (tp40) cc_final: 0.7437 (mm-40) REVERT: H 112 ASP cc_start: 0.8445 (m-30) cc_final: 0.8215 (m-30) outliers start: 16 outliers final: 9 residues processed: 124 average time/residue: 0.4231 time to fit residues: 83.9916 Evaluate side-chains 122 residues out of total 2671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 112 time to evaluate : 2.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain F residue 218 MET Chi-restraints excluded: chain F residue 456 VAL Chi-restraints excluded: chain H residue 22 MET Chi-restraints excluded: chain H residue 23 VAL 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 297 optimal weight: 0.8980 chunk 271 optimal weight: 7.9990 chunk 289 optimal weight: 7.9990 chunk 174 optimal weight: 3.9990 chunk 125 optimal weight: 6.9990 chunk 227 optimal weight: 8.9990 chunk 88 optimal weight: 8.9990 chunk 261 optimal weight: 7.9990 chunk 273 optimal weight: 0.9990 chunk 288 optimal weight: 5.9990 chunk 189 optimal weight: 2.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 25480 Z= 0.333 Angle : 0.533 10.465 34508 Z= 0.284 Chirality : 0.046 0.163 3988 Planarity : 0.004 0.045 4532 Dihedral : 4.083 19.218 3538 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.52 % Allowed : 8.09 % Favored : 91.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.14), residues: 3241 helix: 1.69 (0.15), residues: 1250 sheet: 1.00 (0.22), residues: 569 loop : -0.87 (0.15), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 363 PHE 0.014 0.001 PHE F 257 TYR 0.022 0.001 TYR H 16 ARG 0.008 0.000 ARG H 99 *********************** 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 126 residues out of total 2671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 112 time to evaluate : 3.195 Fit side-chains REVERT: B 289 ASP cc_start: 0.8536 (OUTLIER) cc_final: 0.8171 (m-30) REVERT: H 47 ILE cc_start: 0.9439 (mt) cc_final: 0.9205 (mm) REVERT: H 51 ARG cc_start: 0.8347 (mtm-85) cc_final: 0.7747 (mtm-85) REVERT: H 102 ARG cc_start: 0.8065 (mtm-85) cc_final: 0.7768 (mmm160) REVERT: H 103 ARG cc_start: 0.8087 (ttm-80) cc_final: 0.7869 (ttp80) REVERT: H 108 GLN cc_start: 0.7919 (tp40) cc_final: 0.7468 (mm-40) REVERT: H 112 ASP cc_start: 0.8450 (m-30) cc_final: 0.8216 (m-30) outliers start: 14 outliers final: 13 residues processed: 120 average time/residue: 0.3837 time to fit residues: 72.5287 Evaluate side-chains 126 residues out of total 2671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 112 time to evaluate : 2.597 ------------------------------------------------------------------------------- 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 B residue 289 ASP Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain F residue 218 MET Chi-restraints excluded: chain F residue 456 VAL Chi-restraints excluded: chain H residue 22 MET Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain H residue 110 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 305 optimal weight: 6.9990 chunk 186 optimal weight: 8.9990 chunk 145 optimal weight: 2.9990 chunk 212 optimal weight: 0.0670 chunk 320 optimal weight: 5.9990 chunk 295 optimal weight: 9.9990 chunk 255 optimal weight: 6.9990 chunk 26 optimal weight: 0.5980 chunk 197 optimal weight: 0.9990 chunk 156 optimal weight: 4.9990 chunk 202 optimal weight: 0.8980 overall best weight: 1.1122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 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 : 0.002 0.043 25480 Z= 0.159 Angle : 0.456 13.022 34508 Z= 0.240 Chirality : 0.043 0.141 3988 Planarity : 0.004 0.045 4532 Dihedral : 3.859 18.975 3538 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.56 % Allowed : 8.01 % Favored : 91.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.15), residues: 3241 helix: 1.78 (0.15), residues: 1247 sheet: 1.14 (0.22), residues: 561 loop : -0.77 (0.15), residues: 1433 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 363 PHE 0.011 0.001 PHE G 160 TYR 0.022 0.001 TYR H 16 ARG 0.009 0.000 ARG H 99 ********************** 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 127 residues out of total 2671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 112 time to evaluate : 2.475 Fit side-chains REVERT: B 289 ASP cc_start: 0.8426 (OUTLIER) cc_final: 0.8058 (m-30) REVERT: H 47 ILE cc_start: 0.9430 (mt) cc_final: 0.9195 (mm) REVERT: H 51 ARG cc_start: 0.8368 (mtm-85) cc_final: 0.7711 (mtm-85) REVERT: H 102 ARG cc_start: 0.7940 (mtm-85) cc_final: 0.7675 (mmm160) REVERT: H 108 GLN cc_start: 0.7850 (tp40) cc_final: 0.7435 (mm-40) REVERT: H 112 ASP cc_start: 0.8452 (m-30) cc_final: 0.8215 (m-30) outliers start: 15 outliers final: 12 residues processed: 121 average time/residue: 0.3906 time to fit residues: 75.4779 Evaluate side-chains 125 residues out of total 2671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 112 time to evaluate : 2.809 ------------------------------------------------------------------------------- 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 B residue 289 ASP Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain F residue 218 MET Chi-restraints excluded: chain F residue 456 VAL Chi-restraints excluded: chain H residue 22 MET Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 88 ILE Chi-restraints excluded: chain H residue 110 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 272 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 235 optimal weight: 6.9990 chunk 37 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 chunk 255 optimal weight: 7.9990 chunk 107 optimal weight: 0.9990 chunk 262 optimal weight: 0.3980 chunk 32 optimal weight: 4.9990 chunk 47 optimal weight: 8.9990 chunk 224 optimal weight: 7.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- 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 = 0.2996 r_free = 0.2996 target = 0.059986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2612 r_free = 0.2612 target = 0.044201 restraints weight = 70125.797| |-----------------------------------------------------------------------------| r_work (start): 0.2602 rms_B_bonded: 2.91 r_work: 0.2469 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 moved from start: 0.2101 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= 0.219 Angle : 0.486 15.111 34508 Z= 0.255 Chirality : 0.044 0.143 3988 Planarity : 0.004 0.045 4532 Dihedral : 3.912 18.916 3538 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.49 % Allowed : 8.31 % Favored : 91.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.15), residues: 3241 helix: 1.78 (0.15), residues: 1245 sheet: 1.07 (0.22), residues: 564 loop : -0.79 (0.15), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 363 PHE 0.012 0.001 PHE F 257 TYR 0.010 0.001 TYR F 427 ARG 0.008 0.000 ARG H 99 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3923.48 seconds wall clock time: 72 minutes 7.05 seconds (4327.05 seconds total)