Starting phenix.real_space_refine on Mon Feb 19 09:25:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hhb_34758/02_2024/8hhb_34758_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hhb_34758/02_2024/8hhb_34758.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hhb_34758/02_2024/8hhb_34758.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hhb_34758/02_2024/8hhb_34758.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hhb_34758/02_2024/8hhb_34758_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hhb_34758/02_2024/8hhb_34758_updated.pdb" } resolution = 3.5 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: 6 Type Number sf(0) Gaussians P 15 5.49 5 Mg 5 5.21 5 S 77 5.16 5 C 15277 2.51 5 N 4214 2.21 5 O 4657 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 67": "OE1" <-> "OE2" Residue "A TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 401": "OD1" <-> "OD2" Residue "A GLU 451": "OE1" <-> "OE2" Residue "A GLU 484": "OE1" <-> "OE2" Residue "A ASP 485": "OD1" <-> "OD2" Residue "B ASP 45": "OD1" <-> "OD2" Residue "B GLU 84": "OE1" <-> "OE2" Residue "B GLU 101": "OE1" <-> "OE2" Residue "B GLU 122": "OE1" <-> "OE2" Residue "B TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 272": "OE1" <-> "OE2" Residue "B GLU 320": "OE1" <-> "OE2" Residue "B ASP 347": "OD1" <-> "OD2" Residue "B GLU 391": "OE1" <-> "OE2" Residue "B ASP 446": "OD1" <-> "OD2" Residue "B GLU 451": "OE1" <-> "OE2" Residue "C GLU 54": "OE1" <-> "OE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 67": "OE1" <-> "OE2" Residue "C TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 181": "OD1" <-> "OD2" Residue "C GLU 210": "OE1" <-> "OE2" Residue "C GLU 284": "OE1" <-> "OE2" Residue "C ASP 347": "OD1" <-> "OD2" Residue "C PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 459": "OE1" <-> "OE2" Residue "C ASP 485": "OD1" <-> "OD2" Residue "D PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 136": "OE1" <-> "OE2" Residue "D ASP 143": "OD1" <-> "OD2" Residue "D PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 263": "OE1" <-> "OE2" Residue "D ASP 311": "OD1" <-> "OD2" Residue "D TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 332": "OE1" <-> "OE2" Residue "E GLU 133": "OE1" <-> "OE2" Residue "E ASP 197": "OD1" <-> "OD2" Residue "E TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 201": "OE1" <-> "OE2" Residue "E ASP 204": "OD1" <-> "OD2" Residue "E GLU 237": "OE1" <-> "OE2" Residue "E TYR 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 263": "OE1" <-> "OE2" Residue "E GLU 290": "OE1" <-> "OE2" Residue "E GLU 460": "OE1" <-> "OE2" Residue "E GLU 461": "OE1" <-> "OE2" Residue "F GLU 19": "OE1" <-> "OE2" Residue "F ASP 57": "OD1" <-> "OD2" Residue "F ASP 204": "OD1" <-> "OD2" Residue "F PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 391": "OE1" <-> "OE2" Residue "F GLU 395": "OE1" <-> "OE2" Residue "F TYR 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 439": "OE1" <-> "OE2" Residue "F ASP 451": "OD1" <-> "OD2" Residue "G TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 196": "OE1" <-> "OE2" Residue "G GLU 210": "OE1" <-> "OE2" Residue "G TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 273": "OE1" <-> "OE2" Residue "G GLU 276": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 24245 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" 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: "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: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3630 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 447} 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: {'PTRANS': 10, 'TRANS': 272} 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: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" 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} Time building chain proxies: 12.43, per 1000 atoms: 0.51 Number of scatterers: 24245 At special positions: 0 Unit cell: (128.48, 120.56, 154.88, 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 77 16.00 P 15 15.00 Mg 5 11.99 O 4657 8.00 N 4214 7.00 C 15277 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: 10.41 Conformation dependent library (CDL) restraints added in 4.6 seconds 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5712 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 121 helices and 23 sheets defined 42.1% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.45 Creating SS restraints... Processing helix chain 'A' and resid 79 through 81 No H-bonds generated for 'chain 'A' and resid 79 through 81' 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 187 removed outlier: 3.650A pdb=" N GLN A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N LYS A 187 " --> pdb=" O ILE A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 215 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: 3.655A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.193A 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: 3.646A pdb=" N HIS A 294 " --> pdb=" O ILE A 290 " (cutoff:3.500A) removed outlier: 4.059A 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 392 removed outlier: 3.923A pdb=" N VAL A 378 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLY A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N THR A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU A 384 " --> pdb=" O GLY A 380 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP A 385 " --> pdb=" O THR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 396 No H-bonds generated for 'chain 'A' and resid 394 through 396' Processing helix chain 'A' and resid 402 through 404 No H-bonds generated for 'chain 'A' and resid 402 through 404' Processing helix chain 'A' and resid 411 through 420 Processing helix chain 'A' and resid 430 through 441 Processing helix chain 'A' and resid 450 through 467 removed outlier: 3.613A pdb=" N VAL A 453 " --> pdb=" O VAL A 450 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N ARG A 454 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 3.575A 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 187 removed outlier: 3.563A pdb=" N GLN B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LYS B 187 " --> pdb=" O ILE B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 214 Processing helix chain 'B' and resid 217 through 220 Processing helix chain 'B' and resid 232 through 252 Proline residue: B 239 - end of helix removed outlier: 3.817A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) removed outlier: 3.849A 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 290 through 300 removed outlier: 3.785A pdb=" N LEU B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ARG B 300 " --> pdb=" O ARG B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 335 Processing helix chain 'B' and resid 346 through 352 removed outlier: 4.704A pdb=" N SER B 351 " --> pdb=" O ASP B 347 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N GLY B 352 " --> pdb=" O LEU B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 378 Processing helix chain 'B' and resid 382 through 398 removed outlier: 3.581A pdb=" N GLU B 391 " --> pdb=" O ALA B 387 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN B 397 " --> pdb=" O GLU B 393 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N PHE B 398 " --> pdb=" O ALA B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 Processing helix chain 'B' and resid 413 through 419 Processing helix chain 'B' and resid 430 through 441 removed outlier: 3.637A pdb=" N LEU B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE B 436 " --> pdb=" O LYS B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 467 removed outlier: 3.514A pdb=" N VAL B 453 " --> pdb=" O VAL B 450 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ARG B 454 " --> pdb=" O GLU B 451 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASP B 465 " --> pdb=" O LEU B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 478 Processing helix chain 'B' and resid 484 through 495 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 188 removed outlier: 3.567A pdb=" N GLN C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LYS C 187 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ASP C 188 " --> pdb=" O ILE C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 215 Processing helix chain 'C' and resid 232 through 250 Proline residue: C 239 - end of helix removed outlier: 3.693A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (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 290 through 300 removed outlier: 4.320A pdb=" N ARG C 300 " --> pdb=" O ARG C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 308 No H-bonds generated for 'chain 'C' and resid 306 through 308' Processing helix chain 'C' and resid 329 through 337 Processing helix chain 'C' and resid 346 through 350 Processing helix chain 'C' and resid 373 through 398 removed outlier: 3.699A pdb=" N VAL C 378 " --> pdb=" O ALA C 374 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLY C 380 " --> pdb=" O LYS C 376 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N THR C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ALA C 394 " --> pdb=" O ARG C 390 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N PHE C 395 " --> pdb=" O GLU C 391 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA C 396 " --> pdb=" O LEU C 392 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLN C 397 " --> pdb=" O GLU C 393 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N PHE C 398 " --> pdb=" O ALA C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 420 removed outlier: 4.020A pdb=" N ALA C 408 " --> pdb=" O LYS C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 441 removed outlier: 3.712A pdb=" N LEU C 435 " --> pdb=" O GLU C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 466 removed outlier: 4.690A pdb=" N ARG C 454 " --> pdb=" O GLU C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 478 Processing helix chain 'C' and resid 484 through 497 removed outlier: 3.559A pdb=" N THR C 497 " --> pdb=" O ALA C 493 " (cutoff:3.500A) 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 241 removed outlier: 4.004A pdb=" N ARG D 227 " --> pdb=" O GLY D 223 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL D 228 " --> pdb=" O ALA D 224 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N ALA D 229 " --> pdb=" O ARG D 225 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N LEU D 230 " --> pdb=" O MET D 226 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TYR D 238 " --> pdb=" O THR D 234 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N PHE D 239 " --> pdb=" O MET D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 268 Processing helix chain 'D' and resid 281 through 291 removed outlier: 4.659A 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: 4.156A pdb=" N SER D 323 " --> pdb=" O ALA D 319 " (cutoff:3.500A) removed outlier: 4.844A 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 356 through 359 No H-bonds generated for 'chain 'D' and resid 356 through 359' Processing helix chain 'D' and resid 361 through 379 removed outlier: 3.694A pdb=" N GLU D 379 " --> pdb=" O GLN D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 386 Processing helix chain 'D' and resid 389 through 391 No H-bonds generated for 'chain 'D' and resid 389 through 391' Processing helix chain 'D' and resid 394 through 410 removed outlier: 3.766A pdb=" N ARG D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 421 removed outlier: 3.881A pdb=" N GLN D 419 " --> pdb=" O VAL D 416 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR D 421 " --> pdb=" O GLU D 418 " (cutoff:3.500A) 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 469 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 Processing helix chain 'E' and resid 207 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: 4.003A pdb=" N PHE E 239 " --> pdb=" O MET E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 268 removed outlier: 3.567A pdb=" N THR E 258 " --> pdb=" O ILE E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 291 removed outlier: 4.299A 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 322 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 387 removed outlier: 4.257A pdb=" N ASP E 382 " --> pdb=" O LYS E 378 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE E 383 " --> pdb=" O GLU E 379 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ILE E 384 " --> pdb=" O LEU E 380 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ALA E 385 " --> pdb=" O GLN E 381 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ILE E 386 " --> pdb=" O ASP E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 394 through 409 removed outlier: 3.901A pdb=" N ARG E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 418 through 421 No H-bonds generated for 'chain 'E' and resid 418 through 421' Processing helix chain 'E' and resid 430 through 442 Processing helix chain 'E' and resid 459 through 469 removed outlier: 3.563A 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 140 through 145 Processing helix chain 'F' and resid 164 through 178 removed outlier: 4.261A pdb=" N GLN F 177 " --> pdb=" O HIS F 173 " (cutoff:3.500A) removed outlier: 5.100A 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 242 removed outlier: 4.731A pdb=" N ALA F 229 " --> pdb=" O ARG F 225 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N LEU F 230 " --> pdb=" O MET F 226 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE F 239 " --> pdb=" O MET F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 268 removed outlier: 4.496A pdb=" N ALA F 266 " --> pdb=" O SER F 262 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N LEU F 267 " --> pdb=" O GLU F 263 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 291 removed outlier: 4.644A pdb=" N ALA F 282 " --> pdb=" O PRO F 279 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR F 283 " --> pdb=" O THR F 280 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU F 284 " --> pdb=" O LEU F 281 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN F 287 " --> pdb=" O GLU F 284 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLU F 290 " --> 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: 3.671A pdb=" N THR F 321 " --> pdb=" O ALA F 317 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE F 322 " --> pdb=" O PRO F 318 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N SER F 323 " --> pdb=" O ALA F 319 " (cutoff:3.500A) removed outlier: 4.784A 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: 3.649A pdb=" N GLN F 381 " --> pdb=" O TYR F 377 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N ASP F 382 " --> pdb=" O LYS F 378 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N ILE F 383 " --> pdb=" O GLU F 379 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 through 409 removed outlier: 3.720A pdb=" N ARG F 405 " --> pdb=" O HIS F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 418 No H-bonds generated for 'chain 'F' and resid 416 through 418' 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 469 removed outlier: 3.565A pdb=" N VAL F 463 " --> pdb=" O ILE F 459 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 56 removed outlier: 3.993A pdb=" N THR G 9 " --> pdb=" O ARG G 5 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ARG G 10 " --> pdb=" O ASP G 6 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLN G 37 " --> pdb=" O ASN G 33 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ASN G 38 " --> pdb=" O ARG G 34 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA G 39 " --> pdb=" O ALA G 35 " (cutoff:3.500A) Proline residue: G 44 - end of helix removed outlier: 3.520A pdb=" N VAL G 52 " --> pdb=" O LYS G 48 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ASN G 55 " --> pdb=" O GLU G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 106 removed outlier: 3.780A pdb=" N VAL G 95 " --> pdb=" O TYR G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 120 through 128 removed outlier: 3.712A pdb=" N LYS G 128 " --> pdb=" O SER G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 146 through 163 removed outlier: 4.630A pdb=" N GLU G 151 " --> pdb=" O ALA G 147 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N ILE G 152 " --> pdb=" O ASP G 148 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ASP G 162 " --> pdb=" O GLY G 158 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N GLY G 163 " --> pdb=" O LEU G 159 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 283 removed outlier: 3.773A pdb=" N LEU G 213 " --> pdb=" O GLN G 209 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL G 215 " --> pdb=" O GLU G 211 " (cutoff:3.500A) Proline residue: G 218 - end of helix removed outlier: 3.578A pdb=" N ALA G 268 " --> pdb=" O ARG G 264 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 87 through 89 removed outlier: 6.387A pdb=" N ARG A 40 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N VAL A 34 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL A 74 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 5.673A 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: 4.249A 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: 8.516A pdb=" N VAL A 108 " --> pdb=" O THR A 221 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL A 223 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 8.753A pdb=" N ILE A 222 " --> pdb=" O MET A 191 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N SER A 193 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N VAL A 224 " --> pdb=" O SER A 193 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N TYR A 195 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ALA A 226 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ALA A 197 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N HIS A 255 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N ILE A 194 " --> pdb=" O HIS A 255 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU A 257 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N VAL A 196 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N VAL A 259 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N ILE A 198 " --> pdb=" O VAL A 259 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N SER A 312 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N VAL A 258 " --> pdb=" O SER A 312 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N THR A 314 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N TYR A 260 " --> pdb=" O THR A 314 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LEU A 316 " --> pdb=" O TYR A 260 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 340 through 344 Processing sheet with id= E, first strand: chain 'B' and resid 87 through 89 removed outlier: 6.530A pdb=" N ARG B 40 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N VAL B 34 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN B 65 " --> pdb=" O GLY B 72 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL B 74 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N ALA B 63 " --> pdb=" O VAL B 74 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 96 through 99 removed outlier: 4.054A 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: 6.758A pdb=" N LEU B 166 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N LEU B 344 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.499A 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: 6.721A pdb=" N SER B 193 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N VAL B 224 " --> pdb=" O SER B 193 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N TYR B 195 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N ALA B 226 " --> pdb=" O TYR B 195 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ALA B 197 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N SER B 312 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N VAL B 258 " --> pdb=" O SER B 312 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N THR B 314 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N TYR B 260 " --> pdb=" O THR B 314 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 28 through 30 removed outlier: 4.560A pdb=" N MET C 60 " --> pdb=" O LEU C 76 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLY C 72 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N HIS C 42 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 5.493A 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: 3.672A 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: 8.602A pdb=" N VAL C 108 " --> pdb=" O THR C 221 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL C 223 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N SER C 193 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N VAL C 224 " --> pdb=" O SER C 193 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N TYR C 195 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N ALA C 226 " --> pdb=" O TYR C 195 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ALA C 197 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N SER C 312 " --> pdb=" O VAL C 256 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N VAL C 258 " --> pdb=" O SER C 312 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N THR C 314 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N TYR C 260 " --> pdb=" O THR C 314 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 340 through 344 Processing sheet with id= M, first strand: chain 'D' and resid 75 through 77 removed outlier: 6.486A pdb=" N ASP D 15 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N VAL D 9 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL D 13 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ILE D 62 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 5.521A 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: 3.549A pdb=" N ALA D 327 " --> pdb=" O LYS D 153 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N ILE D 154 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N SER D 302 " --> pdb=" O ILE D 154 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N LEU D 156 " --> pdb=" O SER D 302 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLN D 304 " --> pdb=" O LEU D 156 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N GLY D 158 " --> pdb=" O GLN D 304 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ILE D 306 " --> pdb=" O GLY D 158 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 4 through 10 removed outlier: 6.595A pdb=" N ASP E 15 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N VAL E 9 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL E 13 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ILE E 62 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N VAL E 50 " --> pdb=" O ILE E 62 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE E 44 " --> pdb=" O HIS E 34 " (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: 3.579A pdb=" N ALA E 327 " --> pdb=" O LYS E 153 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N ILE E 154 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N SER E 302 " --> pdb=" O ILE E 154 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N LEU E 156 " --> pdb=" O SER E 302 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N GLN E 304 " --> pdb=" O LEU E 156 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 3 through 5 removed outlier: 3.566A pdb=" N VAL F 76 " --> pdb=" O GLY F 4 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 6 through 10 removed outlier: 6.507A pdb=" N ASP F 15 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N VAL F 9 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N VAL F 13 " --> pdb=" O VAL F 9 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ILE F 62 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N VAL F 50 " --> pdb=" O ILE F 62 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 84 through 86 Processing sheet with id= V, first strand: chain 'F' and resid 94 through 96 removed outlier: 4.064A pdb=" N ARG F 94 " --> pdb=" O THR F 211 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N SER F 183 " --> pdb=" O ALA F 212 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N VAL F 214 " --> pdb=" O SER F 183 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N PHE F 185 " --> pdb=" O VAL F 214 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N GLY F 216 " --> pdb=" O PHE F 185 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N GLY F 187 " --> pdb=" O GLY F 216 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ALA F 327 " --> pdb=" O GLY F 155 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N PHE F 157 " --> pdb=" O ALA F 327 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N THR F 329 " --> pdb=" O PHE F 157 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'G' and resid 116 through 118 removed outlier: 3.551A pdb=" N ILE G 81 " --> pdb=" O TYR G 171 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N ASN G 173 " --> pdb=" O ILE G 81 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG G 186 " --> pdb=" O MET G 170 " (cutoff:3.500A) 935 hydrogen bonds defined for protein. 2634 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: 8.73 Time building geometry restraints manager: 10.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8232 1.34 - 1.46: 4728 1.46 - 1.58: 11523 1.58 - 1.70: 14 1.70 - 1.82: 154 Bond restraints: 24651 Sorted by residual: bond pdb=" O4 PO4 D 602 " pdb=" P PO4 D 602 " ideal model delta sigma weight residual 1.568 1.504 0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" O3 PO4 D 602 " pdb=" P PO4 D 602 " ideal model delta sigma weight residual 1.569 1.506 0.063 2.00e-02 2.50e+03 9.95e+00 bond pdb=" O1 PO4 D 602 " pdb=" P PO4 D 602 " ideal model delta sigma weight residual 1.565 1.505 0.060 2.00e-02 2.50e+03 8.97e+00 bond pdb=" O2 PO4 D 602 " pdb=" P PO4 D 602 " ideal model delta sigma weight residual 1.567 1.508 0.059 2.00e-02 2.50e+03 8.82e+00 bond pdb=" C HIS G 65 " pdb=" N PRO G 66 " ideal model delta sigma weight residual 1.332 1.350 -0.017 8.90e-03 1.26e+04 3.71e+00 ... (remaining 24646 not shown) Histogram of bond angle deviations from ideal: 98.60 - 106.83: 790 106.83 - 115.06: 15015 115.06 - 123.29: 16822 123.29 - 131.52: 785 131.52 - 139.75: 15 Bond angle restraints: 33427 Sorted by residual: angle pdb=" N VAL A 25 " pdb=" CA VAL A 25 " pdb=" C VAL A 25 " ideal model delta sigma weight residual 113.20 108.54 4.66 9.60e-01 1.09e+00 2.35e+01 angle pdb=" CA GLY F 298 " pdb=" C GLY F 298 " pdb=" N SER F 299 " ideal model delta sigma weight residual 114.58 117.48 -2.90 8.60e-01 1.35e+00 1.14e+01 angle pdb=" N VAL D 275 " pdb=" CA VAL D 275 " pdb=" C VAL D 275 " ideal model delta sigma weight residual 111.77 108.31 3.46 1.04e+00 9.25e-01 1.11e+01 angle pdb=" C GLY D 443 " pdb=" N LYS D 444 " pdb=" CA LYS D 444 " ideal model delta sigma weight residual 122.55 115.83 6.72 2.03e+00 2.43e-01 1.09e+01 angle pdb=" N ASP B 262 " pdb=" CA ASP B 262 " pdb=" C ASP B 262 " ideal model delta sigma weight residual 107.32 112.58 -5.26 1.65e+00 3.67e-01 1.02e+01 ... (remaining 33422 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.25: 14066 21.25 - 42.50: 811 42.50 - 63.74: 125 63.74 - 84.99: 45 84.99 - 106.24: 12 Dihedral angle restraints: 15059 sinusoidal: 6134 harmonic: 8925 Sorted by residual: dihedral pdb=" O1B ADP D 603 " pdb=" O3A ADP D 603 " pdb=" PB ADP D 603 " pdb=" PA ADP D 603 " ideal model delta sinusoidal sigma weight residual -60.00 -166.24 106.24 1 2.00e+01 2.50e-03 3.07e+01 dihedral pdb=" CA GLU G 204 " pdb=" C GLU G 204 " pdb=" N PHE G 205 " pdb=" CA PHE G 205 " ideal model delta harmonic sigma weight residual 180.00 -157.10 -22.90 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CA TYR G 203 " pdb=" C TYR G 203 " pdb=" N GLU G 204 " pdb=" CA GLU G 204 " ideal model delta harmonic sigma weight residual 180.00 158.34 21.66 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 15056 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2613 0.041 - 0.082: 873 0.082 - 0.123: 332 0.123 - 0.165: 32 0.165 - 0.206: 2 Chirality restraints: 3852 Sorted by residual: chirality pdb=" CA PRO B 482 " pdb=" N PRO B 482 " pdb=" C PRO B 482 " pdb=" CB PRO B 482 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CB VAL D 87 " pdb=" CA VAL D 87 " pdb=" CG1 VAL D 87 " pdb=" CG2 VAL D 87 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 6.81e-01 chirality pdb=" CA LEU G 189 " pdb=" N LEU G 189 " pdb=" C LEU G 189 " pdb=" CB LEU G 189 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.36e-01 ... (remaining 3849 not shown) Planarity restraints: 4362 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER G 109 " -0.063 5.00e-02 4.00e+02 9.43e-02 1.42e+01 pdb=" N PRO G 110 " 0.163 5.00e-02 4.00e+02 pdb=" CA PRO G 110 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO G 110 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 481 " -0.063 5.00e-02 4.00e+02 9.28e-02 1.38e+01 pdb=" N PRO B 482 " 0.160 5.00e-02 4.00e+02 pdb=" CA PRO B 482 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO B 482 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 409 " 0.010 2.00e-02 2.50e+03 1.94e-02 3.75e+00 pdb=" C LYS B 409 " -0.033 2.00e-02 2.50e+03 pdb=" O LYS B 409 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU B 410 " 0.011 2.00e-02 2.50e+03 ... (remaining 4359 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 104 2.51 - 3.10: 18152 3.10 - 3.70: 36443 3.70 - 4.30: 52657 4.30 - 4.90: 89730 Nonbonded interactions: 197086 Sorted by model distance: nonbonded pdb=" O2G ATP F 501 " pdb="MG MG F 502 " model vdw 1.908 2.170 nonbonded pdb=" OG1 THR F 165 " pdb="MG MG F 502 " model vdw 1.912 2.170 nonbonded pdb="MG MG D 601 " pdb=" O2 PO4 D 602 " model vdw 1.953 2.170 nonbonded pdb="MG MG C 601 " pdb=" O1G ATP C 602 " model vdw 1.962 2.170 nonbonded pdb="MG MG C 601 " pdb=" O2B ATP C 602 " model vdw 2.004 2.170 ... (remaining 197081 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 1 through 470) selection = chain 'E' selection = (chain 'F' and resid 1 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.850 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: 11.220 Check model and map are aligned: 0.350 Set scattering table: 0.250 Process input model: 66.080 Find NCS groups from input model: 2.300 Set up NCS constraints: 0.150 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 24651 Z= 0.285 Angle : 0.628 8.689 33427 Z= 0.356 Chirality : 0.046 0.206 3852 Planarity : 0.005 0.094 4362 Dihedral : 14.333 106.240 9347 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.99 (0.15), residues: 3115 helix: 1.45 (0.15), residues: 1242 sheet: 0.76 (0.22), residues: 556 loop : -0.05 (0.17), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 401 PHE 0.030 0.001 PHE G 205 TYR 0.019 0.002 TYR C 329 ARG 0.007 0.000 ARG B 140 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 2.895 Fit side-chains REVERT: B 272 GLU cc_start: 0.7994 (tt0) cc_final: 0.7705 (tp30) REVERT: D 56 ASP cc_start: 0.7183 (t0) cc_final: 0.6742 (t0) REVERT: F 74 MET cc_start: 0.8794 (mtt) cc_final: 0.8545 (mtt) REVERT: F 170 GLU cc_start: 0.8041 (tp30) cc_final: 0.7777 (tp30) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.3500 time to fit residues: 92.0114 Evaluate side-chains 131 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 2.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 261 optimal weight: 9.9990 chunk 234 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 158 optimal weight: 0.7980 chunk 125 optimal weight: 0.9980 chunk 242 optimal weight: 8.9990 chunk 94 optimal weight: 8.9990 chunk 147 optimal weight: 9.9990 chunk 180 optimal weight: 2.9990 chunk 281 optimal weight: 6.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 189 GLN C 466 GLN ** F 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.0569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 24651 Z= 0.261 Angle : 0.546 7.307 33427 Z= 0.286 Chirality : 0.045 0.171 3852 Planarity : 0.004 0.063 4362 Dihedral : 7.879 89.759 3546 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.35 % Allowed : 4.95 % Favored : 94.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.95 (0.15), residues: 3115 helix: 1.50 (0.15), residues: 1240 sheet: 0.69 (0.22), residues: 550 loop : -0.15 (0.17), residues: 1325 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 363 PHE 0.015 0.001 PHE G 205 TYR 0.014 0.001 TYR G 169 ARG 0.004 0.000 ARG B 140 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 137 time to evaluate : 2.834 Fit side-chains REVERT: D 56 ASP cc_start: 0.7252 (t0) cc_final: 0.6691 (t0) REVERT: F 170 GLU cc_start: 0.8133 (tp30) cc_final: 0.7713 (tp30) REVERT: G 241 MET cc_start: 0.6345 (ttt) cc_final: 0.6086 (tpp) outliers start: 9 outliers final: 8 residues processed: 144 average time/residue: 0.3400 time to fit residues: 81.4574 Evaluate side-chains 136 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 128 time to evaluate : 2.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 406 ILE Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 260 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 156 optimal weight: 10.0000 chunk 87 optimal weight: 0.4980 chunk 234 optimal weight: 0.8980 chunk 191 optimal weight: 0.1980 chunk 77 optimal weight: 6.9990 chunk 282 optimal weight: 0.9980 chunk 304 optimal weight: 9.9990 chunk 251 optimal weight: 5.9990 chunk 279 optimal weight: 7.9990 chunk 96 optimal weight: 7.9990 chunk 226 optimal weight: 0.0970 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 ASN ** F 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 65 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.0960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 24651 Z= 0.113 Angle : 0.463 7.047 33427 Z= 0.240 Chirality : 0.042 0.142 3852 Planarity : 0.004 0.053 4362 Dihedral : 7.161 89.528 3546 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.58 % Allowed : 6.46 % Favored : 92.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 1.27 (0.15), residues: 3115 helix: 1.77 (0.15), residues: 1243 sheet: 0.86 (0.21), residues: 561 loop : 0.01 (0.17), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 401 PHE 0.015 0.001 PHE G 205 TYR 0.010 0.001 TYR G 171 ARG 0.004 0.000 ARG B 140 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 156 time to evaluate : 2.854 Fit side-chains REVERT: D 56 ASP cc_start: 0.7157 (t0) cc_final: 0.6568 (t0) REVERT: D 74 MET cc_start: 0.8965 (ttm) cc_final: 0.8711 (ttm) REVERT: E 341 TYR cc_start: 0.8240 (m-80) cc_final: 0.7943 (m-80) REVERT: F 170 GLU cc_start: 0.8120 (tp30) cc_final: 0.7669 (tp30) REVERT: G 174 HIS cc_start: 0.6124 (p-80) cc_final: 0.5869 (p-80) outliers start: 15 outliers final: 8 residues processed: 169 average time/residue: 0.3382 time to fit residues: 95.0508 Evaluate side-chains 147 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 139 time to evaluate : 2.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 326 ASP Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain F residue 406 ILE Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 260 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 278 optimal weight: 3.9990 chunk 212 optimal weight: 9.9990 chunk 146 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 134 optimal weight: 4.9990 chunk 189 optimal weight: 1.9990 chunk 283 optimal weight: 4.9990 chunk 299 optimal weight: 0.4980 chunk 147 optimal weight: 2.9990 chunk 268 optimal weight: 8.9990 chunk 80 optimal weight: 0.0370 overall best weight: 1.9064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 189 GLN ** F 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24651 Z= 0.185 Angle : 0.484 7.687 33427 Z= 0.249 Chirality : 0.043 0.152 3852 Planarity : 0.004 0.050 4362 Dihedral : 7.025 88.714 3546 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.93 % Allowed : 7.67 % Favored : 91.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 1.27 (0.15), residues: 3115 helix: 1.76 (0.15), residues: 1245 sheet: 0.86 (0.22), residues: 553 loop : 0.03 (0.18), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 363 PHE 0.012 0.001 PHE B 456 TYR 0.011 0.001 TYR G 169 ARG 0.003 0.000 ARG E 3 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 141 time to evaluate : 2.821 Fit side-chains REVERT: D 56 ASP cc_start: 0.7221 (t0) cc_final: 0.6657 (t0) REVERT: D 74 MET cc_start: 0.8979 (ttm) cc_final: 0.8703 (mtt) REVERT: F 170 GLU cc_start: 0.8145 (tp30) cc_final: 0.7603 (tp30) REVERT: G 273 GLU cc_start: 0.8179 (tp30) cc_final: 0.7968 (tp30) outliers start: 24 outliers final: 16 residues processed: 160 average time/residue: 0.3152 time to fit residues: 84.5338 Evaluate side-chains 150 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 134 time to evaluate : 2.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 469 MET Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 170 MET Chi-restraints excluded: chain G residue 260 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 249 optimal weight: 0.1980 chunk 170 optimal weight: 0.0040 chunk 4 optimal weight: 8.9990 chunk 223 optimal weight: 7.9990 chunk 123 optimal weight: 7.9990 chunk 255 optimal weight: 10.0000 chunk 207 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 153 optimal weight: 6.9990 chunk 268 optimal weight: 7.9990 chunk 75 optimal weight: 9.9990 overall best weight: 4.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 433 GLN C 474 HIS D 253 ASN ** F 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 24651 Z= 0.384 Angle : 0.592 7.183 33427 Z= 0.306 Chirality : 0.047 0.185 3852 Planarity : 0.005 0.051 4362 Dihedral : 7.297 88.677 3546 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.40 % Allowed : 9.15 % Favored : 89.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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 (0.15), residues: 3115 helix: 1.40 (0.15), residues: 1233 sheet: 0.59 (0.22), residues: 548 loop : -0.22 (0.17), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS E 401 PHE 0.016 0.002 PHE A 494 TYR 0.015 0.002 TYR G 78 ARG 0.005 0.000 ARG C 164 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 133 time to evaluate : 3.067 Fit side-chains REVERT: A 397 GLN cc_start: 0.4421 (OUTLIER) cc_final: 0.3636 (pm20) REVERT: D 56 ASP cc_start: 0.7355 (t0) cc_final: 0.6775 (t0) REVERT: D 74 MET cc_start: 0.9023 (ttm) cc_final: 0.8733 (mtt) REVERT: D 271 MET cc_start: 0.8739 (mmm) cc_final: 0.8018 (mtt) REVERT: F 74 MET cc_start: 0.8798 (mtt) cc_final: 0.8579 (mtt) REVERT: F 170 GLU cc_start: 0.8192 (tp30) cc_final: 0.7625 (tp30) outliers start: 36 outliers final: 21 residues processed: 160 average time/residue: 0.3195 time to fit residues: 87.0356 Evaluate side-chains 149 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 127 time to evaluate : 3.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 397 GLN Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 475 ILE Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 253 ASN Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 326 ASP Chi-restraints excluded: chain D residue 382 ASP Chi-restraints excluded: chain D residue 469 MET Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 65 HIS Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 170 MET Chi-restraints excluded: chain G residue 260 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 100 optimal weight: 0.0370 chunk 269 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 175 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 299 optimal weight: 6.9990 chunk 248 optimal weight: 6.9990 chunk 138 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 157 optimal weight: 0.7980 overall best weight: 1.5462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 189 GLN C 433 GLN E 381 GLN ** F 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 24651 Z= 0.160 Angle : 0.485 6.893 33427 Z= 0.251 Chirality : 0.043 0.153 3852 Planarity : 0.004 0.048 4362 Dihedral : 6.981 89.414 3546 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.93 % Allowed : 10.40 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 1.05 (0.15), residues: 3115 helix: 1.61 (0.15), residues: 1246 sheet: 0.70 (0.22), residues: 547 loop : -0.12 (0.17), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 401 PHE 0.013 0.001 PHE B 456 TYR 0.013 0.001 TYR B 389 ARG 0.003 0.000 ARG A 171 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 138 time to evaluate : 2.903 Fit side-chains revert: symmetry clash REVERT: A 397 GLN cc_start: 0.4335 (OUTLIER) cc_final: 0.3549 (pm20) REVERT: D 56 ASP cc_start: 0.7261 (t0) cc_final: 0.6674 (t0) REVERT: D 74 MET cc_start: 0.8954 (ttm) cc_final: 0.8693 (mtt) REVERT: F 74 MET cc_start: 0.8746 (mtt) cc_final: 0.8514 (mtt) REVERT: F 170 GLU cc_start: 0.8137 (tp30) cc_final: 0.7559 (tp30) REVERT: G 65 HIS cc_start: 0.6562 (OUTLIER) cc_final: 0.6299 (m-70) outliers start: 24 outliers final: 17 residues processed: 157 average time/residue: 0.3536 time to fit residues: 92.6098 Evaluate side-chains 148 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 129 time to evaluate : 2.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 397 GLN Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 326 ASP Chi-restraints excluded: chain D residue 469 MET Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 406 ILE Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 65 HIS Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 170 MET Chi-restraints excluded: chain G residue 260 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 289 optimal weight: 0.0050 chunk 33 optimal weight: 0.9980 chunk 170 optimal weight: 10.0000 chunk 219 optimal weight: 10.0000 chunk 169 optimal weight: 0.7980 chunk 252 optimal weight: 9.9990 chunk 167 optimal weight: 10.0000 chunk 298 optimal weight: 5.9990 chunk 186 optimal weight: 9.9990 chunk 182 optimal weight: 0.0270 chunk 137 optimal weight: 1.9990 overall best weight: 0.7654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 433 GLN ** F 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 253 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 24651 Z= 0.121 Angle : 0.460 7.726 33427 Z= 0.236 Chirality : 0.042 0.174 3852 Planarity : 0.004 0.046 4362 Dihedral : 6.558 89.369 3546 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.01 % Allowed : 10.75 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 1.30 (0.16), residues: 3115 helix: 1.83 (0.15), residues: 1244 sheet: 0.83 (0.22), residues: 555 loop : 0.02 (0.18), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 401 PHE 0.012 0.001 PHE B 456 TYR 0.022 0.001 TYR A 251 ARG 0.003 0.000 ARG E 405 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 138 time to evaluate : 2.854 Fit side-chains REVERT: B 435 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8463 (mt) REVERT: D 56 ASP cc_start: 0.7297 (t0) cc_final: 0.6653 (t0) REVERT: D 74 MET cc_start: 0.8903 (ttm) cc_final: 0.8637 (mtt) REVERT: D 271 MET cc_start: 0.8648 (mmm) cc_final: 0.8043 (mtt) REVERT: E 341 TYR cc_start: 0.8249 (m-80) cc_final: 0.7951 (m-80) REVERT: F 170 GLU cc_start: 0.8117 (tp30) cc_final: 0.7556 (tp30) outliers start: 26 outliers final: 17 residues processed: 157 average time/residue: 0.3237 time to fit residues: 85.2664 Evaluate side-chains 150 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 132 time to evaluate : 2.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 202 MET Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 326 ASP Chi-restraints excluded: chain D residue 469 MET Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 170 MET Chi-restraints excluded: chain G residue 260 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 184 optimal weight: 0.9990 chunk 119 optimal weight: 0.0970 chunk 178 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 57 optimal weight: 0.0870 chunk 189 optimal weight: 3.9990 chunk 203 optimal weight: 8.9990 chunk 147 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 234 optimal weight: 9.9990 overall best weight: 1.0362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 433 GLN D 253 ASN ** F 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 24651 Z= 0.129 Angle : 0.456 7.826 33427 Z= 0.233 Chirality : 0.042 0.146 3852 Planarity : 0.004 0.045 4362 Dihedral : 6.404 87.732 3546 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.21 % Allowed : 10.48 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 1.36 (0.16), residues: 3115 helix: 1.86 (0.15), residues: 1245 sheet: 0.90 (0.22), residues: 555 loop : 0.06 (0.18), residues: 1315 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS C 470 PHE 0.019 0.001 PHE A 395 TYR 0.015 0.001 TYR B 389 ARG 0.002 0.000 ARG B 390 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 140 time to evaluate : 2.687 Fit side-chains REVERT: B 272 GLU cc_start: 0.7911 (tt0) cc_final: 0.7641 (tt0) REVERT: B 435 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8459 (mt) REVERT: D 56 ASP cc_start: 0.7297 (t0) cc_final: 0.6659 (t0) REVERT: D 74 MET cc_start: 0.8905 (ttm) cc_final: 0.8660 (mtt) REVERT: D 253 ASN cc_start: 0.8270 (OUTLIER) cc_final: 0.7895 (m110) REVERT: D 271 MET cc_start: 0.8653 (mmm) cc_final: 0.7968 (mtt) REVERT: E 341 TYR cc_start: 0.8208 (m-80) cc_final: 0.7961 (m-80) REVERT: F 74 MET cc_start: 0.8868 (mtt) cc_final: 0.8475 (mtt) REVERT: F 170 GLU cc_start: 0.8128 (tp30) cc_final: 0.7574 (tp30) outliers start: 31 outliers final: 21 residues processed: 166 average time/residue: 0.3145 time to fit residues: 89.1503 Evaluate side-chains 157 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 134 time to evaluate : 2.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 253 ASN Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 326 ASP Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 381 GLN Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 170 MET Chi-restraints excluded: chain G residue 260 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 271 optimal weight: 3.9990 chunk 286 optimal weight: 4.9990 chunk 261 optimal weight: 8.9990 chunk 278 optimal weight: 6.9990 chunk 167 optimal weight: 10.0000 chunk 121 optimal weight: 5.9990 chunk 218 optimal weight: 0.3980 chunk 85 optimal weight: 10.0000 chunk 251 optimal weight: 6.9990 chunk 263 optimal weight: 8.9990 chunk 277 optimal weight: 4.9990 overall best weight: 4.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 189 GLN C 433 GLN D 253 ASN E 401 HIS ** F 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 24651 Z= 0.345 Angle : 0.581 8.187 33427 Z= 0.299 Chirality : 0.046 0.161 3852 Planarity : 0.004 0.047 4362 Dihedral : 6.762 83.216 3546 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.13 % Allowed : 10.83 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.90 (0.15), residues: 3115 helix: 1.47 (0.15), residues: 1239 sheet: 0.58 (0.22), residues: 561 loop : -0.15 (0.17), residues: 1315 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS G 65 PHE 0.016 0.002 PHE A 494 TYR 0.018 0.002 TYR B 389 ARG 0.004 0.000 ARG E 333 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 129 time to evaluate : 2.897 Fit side-chains REVERT: A 250 MET cc_start: 0.8539 (tpp) cc_final: 0.7935 (ttm) REVERT: B 435 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8525 (mt) REVERT: D 56 ASP cc_start: 0.7452 (t0) cc_final: 0.6839 (t0) REVERT: D 74 MET cc_start: 0.8980 (ttm) cc_final: 0.8736 (mtt) REVERT: D 271 MET cc_start: 0.8738 (mmm) cc_final: 0.8002 (mtt) REVERT: E 218 MET cc_start: 0.8494 (mtp) cc_final: 0.8138 (mtt) REVERT: F 74 MET cc_start: 0.8901 (mtt) cc_final: 0.8539 (mtt) REVERT: F 170 GLU cc_start: 0.8231 (tp30) cc_final: 0.7619 (tp30) outliers start: 29 outliers final: 24 residues processed: 154 average time/residue: 0.3269 time to fit residues: 84.8459 Evaluate side-chains 149 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 124 time to evaluate : 2.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 253 ASN Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 326 ASP Chi-restraints excluded: chain D residue 469 MET Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 381 GLN Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 430 VAL Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 170 MET Chi-restraints excluded: chain G residue 260 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 182 optimal weight: 6.9990 chunk 294 optimal weight: 0.8980 chunk 179 optimal weight: 0.8980 chunk 139 optimal weight: 7.9990 chunk 204 optimal weight: 0.4980 chunk 308 optimal weight: 5.9990 chunk 284 optimal weight: 5.9990 chunk 245 optimal weight: 8.9990 chunk 25 optimal weight: 0.6980 chunk 189 optimal weight: 2.9990 chunk 150 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 433 GLN D 253 ASN ** F 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 24651 Z= 0.124 Angle : 0.475 7.483 33427 Z= 0.244 Chirality : 0.042 0.153 3852 Planarity : 0.004 0.046 4362 Dihedral : 6.522 86.728 3546 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.97 % Allowed : 11.06 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 3115 helix: 1.73 (0.15), residues: 1244 sheet: 0.79 (0.22), residues: 549 loop : -0.03 (0.17), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 401 PHE 0.013 0.001 PHE B 456 TYR 0.015 0.001 TYR B 389 ARG 0.003 0.000 ARG E 405 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 130 time to evaluate : 2.849 Fit side-chains REVERT: B 435 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8480 (mt) REVERT: D 56 ASP cc_start: 0.7382 (t0) cc_final: 0.6770 (t0) REVERT: D 74 MET cc_start: 0.8917 (ttm) cc_final: 0.8671 (mtt) REVERT: D 253 ASN cc_start: 0.8381 (OUTLIER) cc_final: 0.8137 (m110) REVERT: F 74 MET cc_start: 0.8906 (mtt) cc_final: 0.8550 (mtt) REVERT: F 170 GLU cc_start: 0.8199 (tp30) cc_final: 0.7626 (tp30) REVERT: G 241 MET cc_start: 0.6594 (tpt) cc_final: 0.6282 (tpt) outliers start: 25 outliers final: 19 residues processed: 151 average time/residue: 0.3200 time to fit residues: 81.4550 Evaluate side-chains 149 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 128 time to evaluate : 2.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 253 ASN Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 326 ASP Chi-restraints excluded: chain D residue 469 MET Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 381 GLN Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 170 MET Chi-restraints excluded: chain G residue 260 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 195 optimal weight: 5.9990 chunk 261 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 226 optimal weight: 0.9980 chunk 36 optimal weight: 7.9990 chunk 68 optimal weight: 5.9990 chunk 246 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 252 optimal weight: 8.9990 chunk 31 optimal weight: 8.9990 chunk 45 optimal weight: 9.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 433 GLN E 372 GLN ** F 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.078735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.062851 restraints weight = 60773.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.064810 restraints weight = 32089.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.066106 restraints weight = 20654.645| |-----------------------------------------------------------------------------| r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 24651 Z= 0.412 Angle : 0.606 7.331 33427 Z= 0.312 Chirality : 0.047 0.168 3852 Planarity : 0.005 0.049 4362 Dihedral : 6.895 85.658 3546 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.01 % Allowed : 11.18 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.67 (0.15), residues: 3115 helix: 1.27 (0.15), residues: 1249 sheet: 0.46 (0.22), residues: 561 loop : -0.27 (0.17), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS E 363 PHE 0.017 0.002 PHE A 494 TYR 0.018 0.002 TYR B 389 ARG 0.004 0.001 ARG E 333 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3758.93 seconds wall clock time: 70 minutes 12.67 seconds (4212.67 seconds total)