Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 27 11:16:12 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xkr_33265/04_2023/7xkr_33265_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xkr_33265/04_2023/7xkr_33265.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xkr_33265/04_2023/7xkr_33265.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xkr_33265/04_2023/7xkr_33265.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xkr_33265/04_2023/7xkr_33265_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xkr_33265/04_2023/7xkr_33265_updated.pdb" } resolution = 2.6 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 ------------------------------------------------------------------------------- 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 16 5.49 5 Mg 5 5.21 5 S 79 5.16 5 C 15900 2.51 5 N 4397 2.21 5 O 4849 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 299": "OE1" <-> "OE2" Residue "D PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 396": "OD1" <-> "OD2" Residue "E TYR 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 252": "OD1" <-> "OD2" Residue "F TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 19": "OD1" <-> "OD2" Residue "H ASP 109": "OD1" <-> "OD2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 25246 Number of models: 1 Model: "" Number of chains: 14 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: {'PCIS': 1, 'PTRANS': 22, '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': 1, 'PTRANS': 9, '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: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 13.15, per 1000 atoms: 0.52 Number of scatterers: 25246 At special positions: 0 Unit cell: (130.24, 123.2, 157.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 79 16.00 P 16 15.00 Mg 5 11.99 O 4849 8.00 N 4397 7.00 C 15900 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: 11.39 Conformation dependent library (CDL) restraints added in 4.0 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 42.1% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.03 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 188 removed outlier: 3.852A pdb=" N GLN A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N LYS A 187 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N ASP A 188 " --> pdb=" O ILE A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 214 Processing helix chain 'A' and resid 217 through 220 Processing helix chain 'A' and resid 232 through 250 Proline residue: A 239 - end of helix removed outlier: 3.621A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 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: 3.504A pdb=" N HIS A 294 " --> pdb=" O ILE A 290 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ARG A 300 " --> pdb=" O ARG A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 308 No H-bonds generated for 'chain 'A' and resid 306 through 308' Processing helix chain 'A' and resid 329 through 337 Processing helix chain 'A' and resid 346 through 350 Processing helix chain 'A' and resid 373 through 398 removed outlier: 4.177A pdb=" N GLY A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N THR A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A 392 " --> pdb=" O ALA A 388 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ALA A 394 " --> pdb=" O ARG A 390 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N PHE A 395 " --> pdb=" O GLU A 391 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA A 396 " --> pdb=" O LEU A 392 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N GLN A 397 " --> pdb=" O GLU A 393 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N PHE A 398 " --> pdb=" O ALA A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 420 Processing helix chain 'A' and resid 430 through 441 Processing helix chain 'A' and resid 450 through 467 removed outlier: 4.974A pdb=" N ARG A 454 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR A 461 " --> pdb=" O LYS A 458 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASN A 467 " --> pdb=" O LEU A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 478 Processing helix chain 'A' and resid 484 through 497 removed outlier: 3.587A pdb=" N THR A 497 " --> pdb=" O ALA A 493 " (cutoff:3.500A) 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: 3.580A pdb=" N GLN B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N LYS B 187 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 5.811A 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 217 through 219 No H-bonds generated for 'chain 'B' and resid 217 through 219' Processing helix chain 'B' and resid 232 through 252 Proline residue: B 239 - end of helix removed outlier: 3.665A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS B 252 " --> pdb=" O TYR B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 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 288 through 300 removed outlier: 4.258A pdb=" N PHE B 291 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU B 293 " --> pdb=" O ILE B 290 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG B 296 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU B 299 " --> pdb=" O ARG B 296 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG B 300 " --> pdb=" O LEU B 297 " (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 350 Processing helix chain 'B' and resid 373 through 379 removed outlier: 3.705A pdb=" N VAL B 378 " --> pdb=" O ALA B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 397 removed outlier: 4.013A pdb=" N ALA B 394 " --> pdb=" O ARG B 390 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE B 395 " --> pdb=" O GLU B 391 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLN B 397 " --> pdb=" O GLU B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 407 Processing helix chain 'B' and resid 410 through 420 Processing helix chain 'B' and resid 430 through 441 Processing helix chain 'B' and resid 450 through 464 removed outlier: 3.518A pdb=" N VAL B 453 " --> pdb=" O VAL B 450 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N ARG B 454 " --> pdb=" O GLU B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 478 Processing helix chain 'B' and resid 484 through 497 removed outlier: 3.688A 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: 3.535A pdb=" N GLN C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N LYS C 187 " --> pdb=" O ILE C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 214 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 232 through 252 Proline residue: C 239 - end of helix removed outlier: 3.861A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS C 252 " --> pdb=" O TYR C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 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 288 through 300 removed outlier: 4.648A pdb=" N PHE C 291 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU C 293 " --> pdb=" O ILE C 290 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU C 298 " --> pdb=" O SER C 295 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLU C 299 " --> pdb=" O ARG C 296 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG C 300 " --> pdb=" O LEU C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 335 Processing helix chain 'C' and resid 346 through 351 Processing helix chain 'C' and resid 373 through 395 removed outlier: 3.783A pdb=" N VAL C 378 " --> pdb=" O ALA C 374 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLY C 380 " --> pdb=" O LYS C 376 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N THR C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ALA C 394 " --> pdb=" O ARG C 390 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N PHE C 395 " --> pdb=" O GLU C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 420 Processing helix chain 'C' and resid 430 through 441 removed outlier: 3.631A pdb=" N LEU C 435 " --> pdb=" O GLU C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 467 removed outlier: 4.876A pdb=" N ARG C 454 " --> pdb=" O GLU C 451 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASN C 467 " --> pdb=" O LEU C 464 " (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 125 through 127 No H-bonds generated for 'chain 'D' and resid 125 through 127' 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 243 removed outlier: 3.600A pdb=" N ARG D 227 " --> pdb=" O GLY D 223 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ALA D 229 " --> pdb=" O ARG D 225 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N LEU D 230 " --> pdb=" O MET D 226 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR D 238 " --> pdb=" O THR D 234 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N PHE D 239 " --> pdb=" O MET D 235 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN D 243 " --> pdb=" O PHE D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 265 removed outlier: 3.935A pdb=" N THR D 258 " --> pdb=" O ILE D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 291 removed outlier: 4.387A 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: 3.686A pdb=" N SER D 323 " --> pdb=" O ALA D 319 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N HIS D 324 " --> pdb=" O THR D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 337 Processing helix chain 'D' and resid 356 through 359 No H-bonds generated for 'chain 'D' and resid 356 through 359' Processing helix chain 'D' and resid 361 through 386 removed outlier: 3.880A pdb=" N LEU D 380 " --> pdb=" O ARG D 376 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLN D 381 " --> pdb=" O TYR D 377 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N ASP D 382 " --> pdb=" O LYS D 378 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ILE D 383 " --> pdb=" O GLU D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 409 removed outlier: 3.633A 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 441 Processing helix chain 'D' and resid 450 through 453 removed outlier: 3.679A pdb=" N PHE D 453 " --> pdb=" O GLU D 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 450 through 453' Processing helix chain 'D' and resid 459 through 469 removed outlier: 3.574A pdb=" N VAL D 463 " --> pdb=" O ILE D 459 " (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 204 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 243 removed outlier: 3.589A pdb=" N ARG E 227 " --> pdb=" O GLY E 223 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL E 228 " --> pdb=" O ALA E 224 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ALA E 229 " --> pdb=" O ARG E 225 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N LEU E 230 " --> pdb=" O MET E 226 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE E 239 " --> pdb=" O MET E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 268 Processing helix chain 'E' and resid 281 through 291 removed outlier: 4.268A 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 324 removed outlier: 4.267A pdb=" N HIS E 324 " --> pdb=" O THR E 320 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 338 Processing helix chain 'E' and resid 356 through 359 No H-bonds generated for 'chain 'E' and resid 356 through 359' Processing helix chain 'E' and resid 361 through 386 removed outlier: 4.785A pdb=" N ASP E 382 " --> pdb=" O LYS E 378 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ILE E 383 " --> pdb=" O GLU E 379 " (cutoff:3.500A) Processing helix chain 'E' and resid 394 through 409 removed outlier: 3.754A pdb=" N ARG E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 421 removed outlier: 3.898A pdb=" N GLN E 419 " --> pdb=" O VAL E 416 " (cutoff:3.500A) Processing helix chain 'E' and resid 430 through 441 Processing helix chain 'E' and resid 450 through 453 Processing helix chain 'E' and resid 459 through 469 removed outlier: 3.773A pdb=" N VAL E 463 " --> pdb=" O ILE E 459 " (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: 4.453A pdb=" N GLN F 177 " --> pdb=" O HIS F 173 " (cutoff:3.500A) removed outlier: 5.347A 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 226 Processing helix chain 'F' and resid 228 through 242 removed outlier: 3.599A pdb=" N PHE F 239 " --> pdb=" O MET F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 268 removed outlier: 3.962A pdb=" N ALA F 266 " --> pdb=" O SER F 262 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LEU F 267 " --> pdb=" O GLU F 263 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 291 removed outlier: 4.244A 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 324 removed outlier: 3.660A pdb=" N PHE F 322 " --> pdb=" O PRO F 318 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N SER F 323 " --> pdb=" O ALA F 319 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N HIS F 324 " --> pdb=" O THR F 320 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 337 Processing helix chain 'F' and resid 356 through 359 No H-bonds generated for 'chain 'F' and resid 356 through 359' Processing helix chain 'F' and resid 361 through 387 removed outlier: 3.588A pdb=" N GLN F 381 " --> pdb=" O TYR F 377 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ASP F 382 " --> pdb=" O LYS F 378 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N ILE F 383 " --> pdb=" O GLU F 379 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 through 409 removed outlier: 3.631A pdb=" N ARG F 405 " --> pdb=" O HIS F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 421 removed outlier: 3.537A pdb=" N GLN F 419 " --> pdb=" O VAL F 416 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR F 421 " --> pdb=" O GLU F 418 " (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 459 through 468 Processing helix chain 'G' and resid 4 through 57 removed outlier: 3.762A pdb=" N PHE G 42 " --> pdb=" O ASN G 38 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N VAL G 43 " --> pdb=" O ALA G 39 " (cutoff:3.500A) Proline residue: G 44 - end of helix Processing helix chain 'G' and resid 91 through 106 removed outlier: 3.968A 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 147 through 161 removed outlier: 4.362A pdb=" N GLU G 151 " --> pdb=" O ALA G 147 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ILE G 152 " --> pdb=" O ASP G 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 283 removed outlier: 4.605A pdb=" N VAL G 215 " --> pdb=" O GLU G 211 " (cutoff:3.500A) Proline residue: G 218 - end of helix removed outlier: 3.693A pdb=" N LEU G 260 " --> pdb=" O ARG G 256 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 129 removed outlier: 3.656A pdb=" N ARG H 99 " --> pdb=" O ALA H 95 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA H 100 " --> pdb=" O ALA H 96 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU H 101 " --> pdb=" O LYS H 97 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 87 through 89 removed outlier: 6.432A pdb=" N ARG A 40 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N VAL A 34 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ILE A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL A 74 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ALA A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU A 51 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N ARG A 93 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N GLU A 54 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N THR A 91 " --> pdb=" O GLU A 54 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 96 through 99 removed outlier: 4.210A pdb=" N GLU A 125 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 341 through 344 removed outlier: 6.862A pdb=" N LEU A 166 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N LEU A 344 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ILE A 168 " --> pdb=" O LEU A 344 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 221 through 226 removed outlier: 6.742A pdb=" N SER A 193 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N VAL A 224 " --> pdb=" O SER A 193 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N TYR A 195 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N ALA A 226 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ALA A 197 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N SER A 312 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N VAL A 258 " --> pdb=" O SER A 312 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N THR A 314 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N TYR A 260 " --> pdb=" O THR A 314 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU A 316 " --> pdb=" O TYR A 260 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 28 through 30 removed outlier: 6.477A pdb=" N GLY B 72 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N LEU B 66 " --> pdb=" O ASN B 70 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ASN B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N HIS B 42 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 5.496A 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: 3.851A 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: 6.660A pdb=" N LEU B 166 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N LEU B 344 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ILE B 168 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 221 through 226 removed outlier: 6.766A pdb=" N SER B 193 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N VAL B 224 " --> pdb=" O SER B 193 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N TYR B 195 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N ALA B 226 " --> pdb=" O TYR B 195 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ALA B 197 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N SER B 312 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N VAL B 258 " --> pdb=" O SER B 312 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N THR B 314 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N TYR B 260 " --> pdb=" O THR B 314 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU B 316 " --> pdb=" O TYR B 260 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 28 through 30 removed outlier: 6.521A pdb=" N GLY C 72 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N HIS C 42 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N VAL C 31 " --> pdb=" O HIS C 42 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 96 through 99 removed outlier: 4.143A 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: 8.455A pdb=" N VAL C 108 " --> pdb=" O THR C 221 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VAL C 223 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 8.714A pdb=" N ILE C 222 " --> pdb=" O MET C 191 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N SER C 193 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N VAL C 224 " --> pdb=" O SER C 193 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N TYR C 195 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N ALA C 226 " --> pdb=" O TYR C 195 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ALA C 197 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N HIS C 255 " --> pdb=" O ILE C 192 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N ILE C 194 " --> pdb=" O HIS C 255 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU C 257 " --> pdb=" O ILE C 194 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N VAL C 196 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N VAL C 259 " --> pdb=" O VAL C 196 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N ILE C 198 " --> pdb=" O VAL C 259 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N SER C 312 " --> pdb=" O VAL C 256 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N VAL C 258 " --> pdb=" O SER C 312 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N THR C 314 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N TYR C 260 " --> pdb=" O THR C 314 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU C 316 " --> pdb=" O TYR C 260 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'C' and resid 341 through 344 removed outlier: 6.971A pdb=" N LEU C 166 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N LEU C 344 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE C 168 " --> pdb=" O LEU C 344 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 75 through 77 removed outlier: 6.542A pdb=" N ASP D 15 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N VAL D 9 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N VAL D 13 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ILE D 62 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N VAL D 50 " --> pdb=" O ILE D 62 " (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: 8.568A pdb=" N ILE D 154 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N SER D 302 " --> pdb=" O ILE D 154 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N LEU D 156 " --> pdb=" O SER D 302 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLN D 304 " --> pdb=" O LEU D 156 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 75 through 77 removed outlier: 6.654A pdb=" N ASP E 15 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N VAL E 9 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL E 13 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ILE E 62 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 5.806A 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 331 removed outlier: 8.571A pdb=" N ILE E 154 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N SER E 302 " --> pdb=" O ILE E 154 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N LEU E 156 " --> pdb=" O SER E 302 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N GLN E 304 " --> pdb=" O LEU E 156 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N GLY E 158 " --> pdb=" O GLN E 304 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 75 through 77 removed outlier: 6.516A pdb=" N ASP F 15 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N VAL F 9 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N VAL F 13 " --> pdb=" O VAL F 9 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ILE F 62 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 5.709A 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: 7.859A pdb=" N ILE F 154 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N SER F 302 " --> pdb=" O ILE F 154 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N LEU F 156 " --> pdb=" O SER F 302 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLN F 304 " --> pdb=" O LEU F 156 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N GLY F 158 " --> pdb=" O GLN F 304 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ILE F 306 " --> pdb=" O GLY F 158 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL F 247 " --> pdb=" O THR F 301 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N ILE F 303 " --> pdb=" O VAL F 247 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU F 249 " --> pdb=" O ILE F 303 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ALA F 305 " --> pdb=" O LEU F 249 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ILE F 251 " --> pdb=" O ALA F 305 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N TYR F 307 " --> pdb=" O ILE F 251 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE F 182 " --> pdb=" O LEU F 248 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N PHE F 250 " --> pdb=" O ILE F 182 " (cutoff:3.500A) removed outlier: 6.559A 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: 7.489A pdb=" N LEU G 168 " --> pdb=" O LEU G 188 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N ASN G 173 " --> pdb=" O ILE G 81 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N VAL G 117 " --> pdb=" O ILE G 134 " (cutoff:3.500A) removed outlier: 4.187A 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 45 removed outlier: 3.566A pdb=" N LEU H 41 " --> pdb=" O VAL H 70 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR H 16 " --> pdb=" O VAL H 8 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'H' and resid 22 through 27 Processing sheet with id= Y, first strand: chain 'H' and resid 62 through 64 1010 hydrogen bonds defined for protein. 2820 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: 8.36 Time building geometry restraints manager: 12.05 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: 8576 1.34 - 1.46: 5068 1.46 - 1.58: 11842 1.58 - 1.70: 22 1.70 - 1.82: 158 Bond restraints: 25666 Sorted by residual: bond pdb=" CA LEU A 402 " pdb=" CB LEU A 402 " ideal model delta sigma weight residual 1.523 1.544 -0.021 1.35e-02 5.49e+03 2.44e+00 bond pdb=" CG PRO F 342 " pdb=" CD PRO F 342 " ideal model delta sigma weight residual 1.512 1.478 0.034 2.70e-02 1.37e+03 1.63e+00 bond pdb=" N PRO G 132 " pdb=" CA PRO G 132 " ideal model delta sigma weight residual 1.469 1.484 -0.015 1.28e-02 6.10e+03 1.45e+00 bond pdb=" C4 ADP F 602 " pdb=" C5 ADP F 602 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 1.04e+00 bond pdb=" N ILE F 292 " pdb=" CA ILE F 292 " ideal model delta sigma weight residual 1.474 1.459 0.016 1.57e-02 4.06e+03 1.02e+00 ... (remaining 25661 not shown) Histogram of bond angle deviations from ideal: 99.82 - 107.83: 997 107.83 - 115.85: 16107 115.85 - 123.87: 17207 123.87 - 131.89: 473 131.89 - 139.90: 16 Bond angle restraints: 34800 Sorted by residual: angle pdb=" N VAL C 366 " pdb=" CA VAL C 366 " pdb=" C VAL C 366 " ideal model delta sigma weight residual 111.77 107.35 4.42 1.04e+00 9.25e-01 1.81e+01 angle pdb=" N ASP A 401 " pdb=" CA ASP A 401 " pdb=" C ASP A 401 " ideal model delta sigma weight residual 112.13 106.95 5.18 1.37e+00 5.33e-01 1.43e+01 angle pdb=" N VAL E 275 " pdb=" CA VAL E 275 " pdb=" C VAL E 275 " ideal model delta sigma weight residual 111.91 108.66 3.25 8.90e-01 1.26e+00 1.34e+01 angle pdb=" CA ARG C 164 " pdb=" CB ARG C 164 " pdb=" CG ARG C 164 " ideal model delta sigma weight residual 114.10 120.97 -6.87 2.00e+00 2.50e-01 1.18e+01 angle pdb=" C TYR A 329 " pdb=" N ILE A 330 " pdb=" CA ILE A 330 " ideal model delta sigma weight residual 120.33 122.96 -2.63 8.00e-01 1.56e+00 1.08e+01 ... (remaining 34795 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.02: 14870 22.02 - 44.03: 587 44.03 - 66.05: 75 66.05 - 88.07: 37 88.07 - 110.08: 3 Dihedral angle restraints: 15572 sinusoidal: 6278 harmonic: 9294 Sorted by residual: dihedral pdb=" O1B ADP D 501 " pdb=" O3A ADP D 501 " pdb=" PB ADP D 501 " pdb=" PA ADP D 501 " ideal model delta sinusoidal sigma weight residual -60.00 -170.08 110.08 1 2.00e+01 2.50e-03 3.22e+01 dihedral pdb=" O1B ADP F 602 " pdb=" O3A ADP F 602 " pdb=" PB ADP F 602 " pdb=" PA ADP F 602 " ideal model delta sinusoidal sigma weight residual -60.00 -154.72 94.72 1 2.00e+01 2.50e-03 2.60e+01 dihedral pdb=" C5' ADP F 602 " pdb=" O5' ADP F 602 " pdb=" PA ADP F 602 " pdb=" O2A ADP F 602 " ideal model delta sinusoidal sigma weight residual -60.00 -139.62 79.63 1 2.00e+01 2.50e-03 1.97e+01 ... (remaining 15569 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 2550 0.032 - 0.065: 968 0.065 - 0.097: 290 0.097 - 0.129: 190 0.129 - 0.162: 14 Chirality restraints: 4012 Sorted by residual: chirality pdb=" CA ARG H 71 " pdb=" N ARG H 71 " pdb=" C ARG H 71 " pdb=" CB ARG H 71 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.54e-01 chirality pdb=" CB VAL C 366 " pdb=" CA VAL C 366 " pdb=" CG1 VAL C 366 " pdb=" CG2 VAL C 366 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.39e-01 chirality pdb=" CA ILE E 109 " pdb=" N ILE E 109 " pdb=" C ILE E 109 " pdb=" CB ILE E 109 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.91e-01 ... (remaining 4009 not shown) Planarity restraints: 4538 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU G 206 " -0.036 5.00e-02 4.00e+02 5.53e-02 4.90e+00 pdb=" N PRO G 207 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO G 207 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO G 207 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 109 " -0.024 5.00e-02 4.00e+02 3.69e-02 2.17e+00 pdb=" N PRO C 110 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO C 110 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 110 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 315 " 0.024 5.00e-02 4.00e+02 3.66e-02 2.14e+00 pdb=" N PRO E 316 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO E 316 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO E 316 " 0.020 5.00e-02 4.00e+02 ... (remaining 4535 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 129 2.59 - 3.16: 20912 3.16 - 3.74: 37992 3.74 - 4.32: 54885 4.32 - 4.90: 92444 Nonbonded interactions: 206362 Sorted by model distance: nonbonded pdb=" O2G ATP A 600 " pdb="MG MG A 601 " model vdw 2.006 2.170 nonbonded pdb=" OG1 THR A 176 " pdb="MG MG A 601 " model vdw 2.012 2.170 nonbonded pdb=" OG1 THR B 176 " pdb="MG MG B 601 " model vdw 2.052 2.170 nonbonded pdb=" OG1 THR C 176 " pdb="MG MG C 601 " model vdw 2.064 2.170 nonbonded pdb="MG MG E 501 " pdb=" O2B ATP E 502 " model vdw 2.070 2.170 ... (remaining 206357 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' and resid 24 through 501) selection = (chain 'B' and resid 24 through 501) selection = (chain 'C' and resid 24 through 501) } 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: 3.820 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: 14.360 Check model and map are aligned: 0.390 Set scattering table: 0.270 Process input model: 65.830 Find NCS groups from input model: 1.870 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:12.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 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 : 0.003 0.034 25666 Z= 0.171 Angle : 0.535 8.221 34800 Z= 0.301 Chirality : 0.042 0.162 4012 Planarity : 0.003 0.055 4538 Dihedral : 12.535 110.082 9620 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer Outliers : 0.00 % 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: 1.93 (0.15), residues: 3241 helix: 2.20 (0.15), residues: 1272 sheet: 1.23 (0.22), residues: 571 loop : 0.55 (0.17), residues: 1398 *********************** 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 164 residues out of total 2671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 3.398 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 1.5861 time to fit residues: 298.3200 Evaluate side-chains 127 residues out of total 2671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 3.129 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.0194 ------------------------------------------------------------------------------- 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: 7.9990 chunk 244 optimal weight: 7.9990 chunk 135 optimal weight: 6.9990 chunk 83 optimal weight: 4.9990 chunk 164 optimal weight: 6.9990 chunk 130 optimal weight: 9.9990 chunk 252 optimal weight: 0.0770 chunk 97 optimal weight: 3.9990 chunk 153 optimal weight: 0.0570 chunk 187 optimal weight: 6.9990 chunk 292 optimal weight: 9.9990 overall best weight: 3.2262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 20 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.062 25666 Z= 0.366 Angle : 0.583 8.004 34800 Z= 0.301 Chirality : 0.047 0.172 4012 Planarity : 0.004 0.047 4538 Dihedral : 5.535 79.957 3572 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer Outliers : 0.41 % 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: 1.53 (0.15), residues: 3241 helix: 1.83 (0.15), residues: 1290 sheet: 0.94 (0.21), residues: 588 loop : 0.37 (0.16), residues: 1363 *********************** 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 138 residues out of total 2671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 127 time to evaluate : 3.494 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 131 average time/residue: 1.6204 time to fit residues: 244.7285 Evaluate side-chains 127 residues out of total 2671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 122 time to evaluate : 3.123 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 3 residues processed: 2 average time/residue: 0.2228 time to fit residues: 4.9769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 162 optimal weight: 6.9990 chunk 90 optimal weight: 0.9990 chunk 243 optimal weight: 0.5980 chunk 199 optimal weight: 0.5980 chunk 80 optimal weight: 0.9990 chunk 292 optimal weight: 9.9990 chunk 316 optimal weight: 5.9990 chunk 260 optimal weight: 3.9990 chunk 290 optimal weight: 10.0000 chunk 99 optimal weight: 0.9990 chunk 235 optimal weight: 5.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- 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: 0.8835 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 25666 Z= 0.141 Angle : 0.471 9.486 34800 Z= 0.238 Chirality : 0.042 0.147 4012 Planarity : 0.003 0.048 4538 Dihedral : 5.004 62.445 3572 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer Outliers : 0.86 % 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: 1.70 (0.15), residues: 3241 helix: 1.96 (0.15), residues: 1297 sheet: 1.09 (0.21), residues: 583 loop : 0.43 (0.17), residues: 1361 *********************** 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 149 residues out of total 2671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 126 time to evaluate : 3.343 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 11 residues processed: 142 average time/residue: 1.5944 time to fit residues: 261.2220 Evaluate side-chains 135 residues out of total 2671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 124 time to evaluate : 3.139 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 10 residues processed: 1 average time/residue: 0.2377 time to fit residues: 4.6444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 289 optimal weight: 4.9990 chunk 220 optimal weight: 0.9990 chunk 152 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 139 optimal weight: 3.9990 chunk 196 optimal weight: 6.9990 chunk 293 optimal weight: 4.9990 chunk 311 optimal weight: 20.0000 chunk 153 optimal weight: 0.0970 chunk 278 optimal weight: 7.9990 chunk 83 optimal weight: 9.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- 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: 0.8893 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.056 25666 Z= 0.333 Angle : 0.544 8.685 34800 Z= 0.278 Chirality : 0.046 0.213 4012 Planarity : 0.004 0.057 4538 Dihedral : 5.227 60.138 3572 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer Outliers : 1.24 % 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: 1.50 (0.15), residues: 3241 helix: 1.86 (0.15), residues: 1292 sheet: 0.89 (0.21), residues: 586 loop : 0.30 (0.16), residues: 1363 *********************** 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 157 residues out of total 2671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 124 time to evaluate : 3.136 Fit side-chains outliers start: 33 outliers final: 15 residues processed: 144 average time/residue: 1.5617 time to fit residues: 261.4496 Evaluate side-chains 136 residues out of total 2671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 121 time to evaluate : 3.371 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 13 residues processed: 2 average time/residue: 0.2358 time to fit residues: 5.3496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 259 optimal weight: 7.9990 chunk 176 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 231 optimal weight: 5.9990 chunk 128 optimal weight: 8.9990 chunk 265 optimal weight: 2.9990 chunk 215 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 158 optimal weight: 3.9990 chunk 279 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 381 GLN F 423 GLN H 59 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.062 25666 Z= 0.387 Angle : 0.558 9.010 34800 Z= 0.287 Chirality : 0.046 0.193 4012 Planarity : 0.004 0.060 4538 Dihedral : 5.379 64.806 3572 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer Outliers : 1.27 % 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: 1.32 (0.15), residues: 3241 helix: 1.73 (0.15), residues: 1290 sheet: 0.79 (0.21), residues: 577 loop : 0.20 (0.16), residues: 1374 *********************** 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 157 residues out of total 2671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 123 time to evaluate : 3.370 Fit side-chains revert: symmetry clash outliers start: 34 outliers final: 19 residues processed: 145 average time/residue: 1.5101 time to fit residues: 253.5844 Evaluate side-chains 139 residues out of total 2671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 120 time to evaluate : 3.229 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 16 residues processed: 3 average time/residue: 0.5348 time to fit residues: 6.3148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 104 optimal weight: 0.9990 chunk 280 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 182 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 311 optimal weight: 0.7980 chunk 258 optimal weight: 1.9990 chunk 144 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 103 optimal weight: 0.4980 chunk 163 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 197 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.039 25666 Z= 0.138 Angle : 0.477 9.920 34800 Z= 0.240 Chirality : 0.042 0.154 4012 Planarity : 0.003 0.060 4538 Dihedral : 4.949 61.984 3572 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer Outliers : 1.27 % 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: 1.54 (0.15), residues: 3241 helix: 1.93 (0.15), residues: 1300 sheet: 0.92 (0.21), residues: 580 loop : 0.28 (0.16), residues: 1361 *********************** 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 161 residues out of total 2671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 127 time to evaluate : 3.267 Fit side-chains outliers start: 34 outliers final: 18 residues processed: 153 average time/residue: 1.5704 time to fit residues: 279.8757 Evaluate side-chains 138 residues out of total 2671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 120 time to evaluate : 2.934 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 16 residues processed: 2 average time/residue: 0.2190 time to fit residues: 4.8287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 300 optimal weight: 10.0000 chunk 35 optimal weight: 0.9980 chunk 177 optimal weight: 3.9990 chunk 227 optimal weight: 7.9990 chunk 176 optimal weight: 2.9990 chunk 262 optimal weight: 0.0870 chunk 173 optimal weight: 5.9990 chunk 310 optimal weight: 0.7980 chunk 194 optimal weight: 3.9990 chunk 189 optimal weight: 0.7980 chunk 143 optimal weight: 8.9990 overall best weight: 1.1360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 488 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 25666 Z= 0.165 Angle : 0.479 11.528 34800 Z= 0.240 Chirality : 0.042 0.154 4012 Planarity : 0.003 0.062 4538 Dihedral : 4.798 60.305 3572 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer Outliers : 1.12 % 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: 1.62 (0.15), residues: 3241 helix: 2.01 (0.15), residues: 1299 sheet: 0.94 (0.21), residues: 576 loop : 0.32 (0.16), residues: 1366 *********************** 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 152 residues out of total 2671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 122 time to evaluate : 3.476 Fit side-chains outliers start: 30 outliers final: 19 residues processed: 147 average time/residue: 1.5590 time to fit residues: 265.3882 Evaluate side-chains 140 residues out of total 2671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 121 time to evaluate : 3.077 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 17 residues processed: 2 average time/residue: 0.8577 time to fit residues: 6.3748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 192 optimal weight: 0.8980 chunk 123 optimal weight: 5.9990 chunk 185 optimal weight: 4.9990 chunk 93 optimal weight: 0.6980 chunk 60 optimal weight: 5.9990 chunk 197 optimal weight: 5.9990 chunk 211 optimal weight: 4.9990 chunk 153 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 243 optimal weight: 0.5980 chunk 282 optimal weight: 4.9990 overall best weight: 2.2384 ------------------------------------------------------------------------------- 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: 0.8881 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 25666 Z= 0.256 Angle : 0.511 11.509 34800 Z= 0.257 Chirality : 0.044 0.157 4012 Planarity : 0.004 0.066 4538 Dihedral : 4.938 59.442 3572 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer Outliers : 0.94 % 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: 1.52 (0.15), residues: 3241 helix: 1.93 (0.15), residues: 1301 sheet: 0.91 (0.21), residues: 580 loop : 0.25 (0.16), residues: 1360 *********************** 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 145 residues out of total 2671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 120 time to evaluate : 3.285 Fit side-chains outliers start: 25 outliers final: 19 residues processed: 142 average time/residue: 1.6740 time to fit residues: 275.5151 Evaluate side-chains 138 residues out of total 2671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 119 time to evaluate : 3.254 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 17 residues processed: 2 average time/residue: 0.2648 time to fit residues: 5.2420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 297 optimal weight: 1.9990 chunk 271 optimal weight: 3.9990 chunk 289 optimal weight: 3.9990 chunk 174 optimal weight: 9.9990 chunk 125 optimal weight: 4.9990 chunk 227 optimal weight: 6.9990 chunk 88 optimal weight: 8.9990 chunk 261 optimal weight: 7.9990 chunk 273 optimal weight: 0.8980 chunk 288 optimal weight: 9.9990 chunk 189 optimal weight: 3.9990 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: 0.8900 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.055 25666 Z= 0.329 Angle : 0.540 8.581 34800 Z= 0.275 Chirality : 0.045 0.176 4012 Planarity : 0.004 0.069 4538 Dihedral : 5.182 60.988 3572 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer Outliers : 1.05 % 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: 1.42 (0.15), residues: 3241 helix: 1.84 (0.15), residues: 1296 sheet: 0.86 (0.21), residues: 577 loop : 0.20 (0.16), residues: 1368 *********************** 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 146 residues out of total 2671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 118 time to evaluate : 3.216 Fit side-chains outliers start: 28 outliers final: 20 residues processed: 139 average time/residue: 1.5728 time to fit residues: 251.8434 Evaluate side-chains 138 residues out of total 2671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 118 time to evaluate : 3.105 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 17 residues processed: 3 average time/residue: 0.5798 time to fit residues: 6.4730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 305 optimal weight: 10.0000 chunk 186 optimal weight: 6.9990 chunk 145 optimal weight: 0.7980 chunk 212 optimal weight: 3.9990 chunk 320 optimal weight: 0.9990 chunk 295 optimal weight: 4.9990 chunk 255 optimal weight: 3.9990 chunk 26 optimal weight: 0.3980 chunk 197 optimal weight: 4.9990 chunk 156 optimal weight: 8.9990 chunk 202 optimal weight: 0.0470 overall best weight: 1.2482 ------------------------------------------------------------------------------- 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: 0.8864 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 25666 Z= 0.171 Angle : 0.489 12.957 34800 Z= 0.244 Chirality : 0.043 0.156 4012 Planarity : 0.003 0.067 4538 Dihedral : 4.894 61.637 3572 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer Outliers : 0.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.51 (0.15), residues: 3241 helix: 1.93 (0.15), residues: 1302 sheet: 0.91 (0.21), residues: 576 loop : 0.23 (0.16), residues: 1363 ********************** 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 137 residues out of total 2671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 120 time to evaluate : 3.146 Fit side-chains outliers start: 17 outliers final: 18 residues processed: 137 average time/residue: 1.7401 time to fit residues: 275.5409 Evaluate side-chains 137 residues out of total 2671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 119 time to evaluate : 2.940 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 18 residues processed: 1 average time/residue: 1.2610 time to fit residues: 5.3338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 272 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 235 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 70 optimal weight: 6.9990 chunk 255 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 262 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 47 optimal weight: 10.0000 chunk 224 optimal weight: 10.0000 overall best weight: 2.5786 ------------------------------------------------------------------------------- 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 = 0.2972 r_free = 0.2972 target = 0.057049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2562 r_free = 0.2562 target = 0.040684 restraints weight = 65228.169| |-----------------------------------------------------------------------------| r_work (start): 0.2560 rms_B_bonded: 2.68 r_work: 0.2422 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2295 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9072 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 25666 Z= 0.290 Angle : 0.526 10.649 34800 Z= 0.266 Chirality : 0.044 0.165 4012 Planarity : 0.004 0.065 4538 Dihedral : 5.040 60.143 3572 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer Outliers : 0.79 % 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: 1.44 (0.15), residues: 3241 helix: 1.85 (0.15), residues: 1298 sheet: 0.89 (0.21), residues: 577 loop : 0.20 (0.16), residues: 1366 =============================================================================== Job complete usr+sys time: 6192.56 seconds wall clock time: 112 minutes 9.23 seconds (6729.23 seconds total)