Starting phenix.real_space_refine on Mon Feb 19 09:23:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hhc_34760/02_2024/8hhc_34760_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hhc_34760/02_2024/8hhc_34760.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hhc_34760/02_2024/8hhc_34760.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hhc_34760/02_2024/8hhc_34760.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hhc_34760/02_2024/8hhc_34760_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hhc_34760/02_2024/8hhc_34760_updated.pdb" } resolution = 3.3 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 16 5.49 5 Mg 5 5.21 5 S 77 5.16 5 C 15277 2.51 5 N 4214 2.21 5 O 4660 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 GLU 492": "OE1" <-> "OE2" Residue "D GLU 362": "OE1" <-> "OE2" Residue "D GLU 461": "OE1" <-> "OE2" Residue "E GLU 439": "OE1" <-> "OE2" Residue "F GLU 89": "OE1" <-> "OE2" Residue "F GLU 290": "OE1" <-> "OE2" Residue "G GLU 112": "OE1" <-> "OE2" Residue "G PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 222": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 24249 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: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 272} Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {' MG': 1, 'ATP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 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: 11.17, per 1000 atoms: 0.46 Number of scatterers: 24249 At special positions: 0 Unit cell: (127.6, 121.44, 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 16 15.00 Mg 5 11.99 O 4660 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: 9.97 Conformation dependent library (CDL) restraints added in 4.4 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: 119 helices and 22 sheets defined 42.1% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.82 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 101 through 103 No H-bonds generated for 'chain 'A' and resid 101 through 103' Processing helix chain 'A' and resid 136 through 138 No H-bonds generated for 'chain 'A' and resid 136 through 138' Processing helix chain 'A' and resid 151 through 154 No H-bonds generated for 'chain 'A' and resid 151 through 154' Processing helix chain 'A' and resid 175 through 186 removed outlier: 3.552A pdb=" N GLN A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 215 Processing helix chain 'A' and resid 217 through 219 No H-bonds generated for 'chain 'A' and resid 217 through 219' Processing helix chain 'A' and resid 232 through 251 Proline residue: A 239 - end of helix removed outlier: 3.702A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 277 Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 290 through 298 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 378 Processing helix chain 'A' and resid 380 through 395 removed outlier: 4.426A pdb=" N LEU A 384 " --> pdb=" O GLY A 380 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N ALA A 394 " --> pdb=" O ARG A 390 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N PHE A 395 " --> pdb=" O GLU A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 420 removed outlier: 4.287A pdb=" N ALA A 411 " --> pdb=" O GLN A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 441 Processing helix chain 'A' and resid 450 through 467 removed outlier: 4.547A pdb=" N ARG A 454 " --> pdb=" O VAL A 450 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ARG A 455 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLN A 466 " --> pdb=" O LEU A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 478 removed outlier: 3.919A pdb=" N HIS A 474 " --> pdb=" O HIS A 470 " (cutoff:3.500A) 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 151 through 156 Processing helix chain 'B' and resid 175 through 187 removed outlier: 3.552A pdb=" N GLN B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N LYS B 187 " --> pdb=" O ILE B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 215 Processing helix chain 'B' and resid 217 through 219 No H-bonds generated for 'chain 'B' and resid 217 through 219' Processing helix chain 'B' and resid 232 through 252 Proline residue: B 239 - end of helix removed outlier: 3.628A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS B 252 " --> pdb=" O TYR B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 276 Processing helix chain 'B' and resid 283 through 285 No H-bonds generated for 'chain 'B' and resid 283 through 285' Processing helix chain 'B' and resid 288 through 300 removed outlier: 4.202A pdb=" N PHE B 291 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU B 293 " --> pdb=" O ILE B 290 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER B 295 " --> pdb=" O TYR B 292 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ARG B 296 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLU B 299 " --> 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 350 Processing helix chain 'B' and resid 373 through 398 removed outlier: 3.795A pdb=" N LYS B 377 " --> pdb=" O LYS B 373 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N VAL B 378 " --> pdb=" O ALA B 374 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY B 380 " --> pdb=" O LYS B 376 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N THR B 381 " --> pdb=" O LYS B 377 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU B 384 " --> pdb=" O GLY B 380 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU B 391 " --> pdb=" O ALA B 387 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU B 392 " --> pdb=" O ALA B 388 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ALA B 394 " --> pdb=" O ARG B 390 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N PHE B 395 " --> pdb=" O GLU B 391 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN B 397 " --> pdb=" O GLU B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 419 removed outlier: 3.598A pdb=" N ALA B 408 " --> pdb=" O LYS B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 442 Processing helix chain 'B' and resid 453 through 467 removed outlier: 3.715A pdb=" N LEU B 462 " --> pdb=" O LYS B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 478 Processing helix chain 'B' and resid 484 through 497 Processing helix chain 'C' and resid 79 through 81 No H-bonds generated for 'chain 'C' and resid 79 through 81' 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: 3.624A pdb=" N GLN C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N LYS C 187 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 5.876A 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 217 through 220 Processing helix chain 'C' and resid 232 through 252 Proline residue: C 239 - end of helix removed outlier: 3.597A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 4.066A 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 288 through 300 removed outlier: 4.485A pdb=" N PHE C 291 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU C 299 " --> pdb=" O ARG C 296 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG C 300 " --> pdb=" O LEU C 297 " (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 395 removed outlier: 3.906A pdb=" N VAL C 378 " --> pdb=" O ALA C 374 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLY C 380 " --> pdb=" O LYS C 376 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N THR C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 420 removed outlier: 3.727A pdb=" N LYS C 409 " --> pdb=" O ALA C 405 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG C 412 " --> pdb=" O ALA C 408 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY C 413 " --> pdb=" O LYS C 409 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA C 414 " --> pdb=" O LEU C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 441 removed outlier: 4.038A pdb=" N LEU C 435 " --> pdb=" O GLU C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 467 removed outlier: 4.650A pdb=" N ARG C 454 " --> pdb=" O VAL C 450 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N ARG C 455 " --> pdb=" O GLU C 451 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU C 462 " --> pdb=" O LYS C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 478 Processing helix chain 'C' and resid 484 through 497 Processing helix chain 'D' and resid 89 through 91 No H-bonds generated for 'chain 'D' and resid 89 through 91' Processing helix chain 'D' and resid 140 through 145 Processing helix chain 'D' and resid 164 through 178 removed outlier: 3.764A pdb=" N HIS D 173 " --> pdb=" O GLN D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 205 Processing helix chain 'D' and resid 207 through 210 Processing helix chain 'D' and resid 222 through 243 removed outlier: 5.142A pdb=" N ALA D 229 " --> pdb=" O ARG D 225 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N LEU D 230 " --> pdb=" O MET D 226 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR D 238 " --> pdb=" O THR D 234 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE D 239 " --> pdb=" O MET D 235 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN D 243 " --> pdb=" O PHE D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 268 removed outlier: 3.658A pdb=" N GLY D 261 " --> pdb=" O PHE D 257 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA D 266 " --> pdb=" O SER D 262 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU D 267 " --> pdb=" O GLU D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 291 removed outlier: 4.503A 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: 4.193A pdb=" N SER D 323 " --> pdb=" O ALA D 319 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N HIS D 324 " --> pdb=" O THR D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 337 Processing helix chain 'D' and resid 356 through 359 No H-bonds generated for 'chain 'D' and resid 356 through 359' Processing helix chain 'D' and resid 361 through 387 removed outlier: 3.788A pdb=" N LYS D 378 " --> pdb=" O LEU D 374 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLU D 379 " --> pdb=" O GLN D 375 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU D 380 " --> pdb=" O ARG D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 409 removed outlier: 4.435A pdb=" N ARG D 404 " --> pdb=" O VAL D 400 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLN D 407 " --> pdb=" O ALA D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 421 removed outlier: 4.120A pdb=" N GLN D 419 " --> pdb=" O VAL D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 442 Processing helix chain 'D' and resid 450 through 453 removed outlier: 3.637A pdb=" N PHE D 453 " --> pdb=" O GLU D 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 450 through 453' Processing helix chain 'D' and resid 460 through 469 removed outlier: 4.466A pdb=" N GLU D 464 " --> pdb=" O GLU D 460 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 91 No H-bonds generated for 'chain 'E' and resid 89 through 91' Processing helix chain 'E' and resid 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 208 through 210 No H-bonds generated for 'chain 'E' and resid 208 through 210' Processing helix chain 'E' and resid 222 through 242 removed outlier: 5.406A pdb=" N ALA E 229 " --> pdb=" O ARG E 225 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N LEU E 230 " --> pdb=" O MET E 226 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N PHE E 239 " --> pdb=" O MET E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 268 Processing helix chain 'E' and resid 274 through 276 No H-bonds generated for 'chain 'E' and resid 274 through 276' Processing helix chain 'E' and resid 281 through 291 removed outlier: 4.564A pdb=" N ARG E 291 " --> pdb=" O GLN E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 311 No H-bonds generated for 'chain 'E' and resid 309 through 311' Processing helix chain 'E' and resid 316 through 323 removed outlier: 3.545A pdb=" N SER E 323 " --> pdb=" O ALA E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 338 Processing helix chain 'E' and resid 361 through 386 removed outlier: 3.515A pdb=" N GLN E 381 " --> pdb=" O TYR E 377 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N ASP E 382 " --> pdb=" O LYS E 378 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N ILE E 383 " --> pdb=" O GLU E 379 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 391 No H-bonds generated for 'chain 'E' and resid 389 through 391' Processing helix chain 'E' and resid 394 through 409 removed outlier: 3.568A pdb=" N ARG E 404 " --> pdb=" O VAL E 400 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 415 through 421 removed outlier: 4.211A pdb=" N GLN E 419 " --> pdb=" O VAL E 416 " (cutoff:3.500A) Processing helix chain 'E' and resid 430 through 441 Processing helix chain 'E' and resid 450 through 453 Processing helix chain 'E' and resid 459 through 469 removed outlier: 3.887A pdb=" N VAL E 463 " --> pdb=" O ILE E 459 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 91 No H-bonds generated for 'chain 'F' and resid 89 through 91' Processing helix chain 'F' and resid 125 through 127 No H-bonds generated for 'chain 'F' and resid 125 through 127' Processing helix chain 'F' and resid 140 through 145 Processing helix chain 'F' and resid 164 through 178 removed outlier: 4.297A pdb=" N GLN F 177 " --> pdb=" O HIS F 173 " (cutoff:3.500A) removed outlier: 5.444A 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 241 removed outlier: 5.003A pdb=" N ALA F 229 " --> pdb=" O ARG F 225 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N LEU F 230 " --> pdb=" O MET F 226 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE F 239 " --> pdb=" O MET F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 265 Processing helix chain 'F' and resid 281 through 291 removed outlier: 4.415A pdb=" N ARG F 291 " --> pdb=" O GLN F 287 " (cutoff:3.500A) Processing helix chain 'F' and resid 309 through 311 No H-bonds generated for 'chain 'F' and resid 309 through 311' Processing helix chain 'F' and resid 316 through 324 removed outlier: 3.553A pdb=" N THR F 321 " --> pdb=" O ALA F 317 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE F 322 " --> pdb=" O PRO F 318 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N SER F 323 " --> pdb=" O ALA F 319 " (cutoff:3.500A) removed outlier: 4.715A 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: 3.520A pdb=" N GLN F 381 " --> pdb=" O TYR F 377 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ASP F 382 " --> pdb=" O LYS F 378 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ILE F 383 " --> pdb=" O GLU F 379 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 391 No H-bonds generated for 'chain 'F' and resid 389 through 391' Processing helix chain 'F' and resid 394 through 409 removed outlier: 3.717A 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 466 removed outlier: 3.584A pdb=" N VAL F 463 " --> pdb=" O ILE F 459 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 57 removed outlier: 3.758A pdb=" N THR G 17 " --> pdb=" O ALA G 13 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN G 19 " --> pdb=" O LYS G 15 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILE G 20 " --> pdb=" O LYS G 16 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS G 31 " --> pdb=" O VAL G 27 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL G 43 " --> pdb=" O ALA G 39 " (cutoff:3.500A) Proline residue: G 44 - end of helix Processing helix chain 'G' and resid 91 through 106 removed outlier: 3.841A pdb=" N VAL G 95 " --> pdb=" O TYR G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 120 through 128 Processing helix chain 'G' and resid 146 through 161 removed outlier: 4.882A pdb=" N GLU G 151 " --> pdb=" O ALA G 147 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ILE G 152 " --> pdb=" O ASP G 148 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU G 159 " --> pdb=" O LYS G 155 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE G 160 " --> pdb=" O THR G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 212 through 282 Proline residue: G 218 - end of helix removed outlier: 3.871A pdb=" N ALA G 228 " --> pdb=" O LEU G 224 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 28 through 30 removed outlier: 4.401A pdb=" N MET A 60 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N GLY A 72 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN A 33 " --> pdb=" O ARG A 40 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N HIS A 42 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N VAL A 31 " --> pdb=" O HIS A 42 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 96 through 99 removed outlier: 3.994A 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: 8.564A pdb=" N VAL A 108 " --> pdb=" O THR A 221 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N VAL A 223 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 8.958A pdb=" N ILE A 222 " --> pdb=" O MET A 191 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N SER A 193 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N VAL A 224 " --> pdb=" O SER A 193 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TYR A 195 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N ALA A 226 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ALA A 197 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N HIS A 255 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ILE A 194 " --> pdb=" O HIS A 255 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LEU A 257 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL A 196 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N VAL A 259 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ILE A 198 " --> pdb=" O VAL A 259 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N SER A 312 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N VAL A 258 " --> pdb=" O SER A 312 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N THR A 314 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N TYR A 260 " --> pdb=" O THR A 314 " (cutoff:3.500A) removed outlier: 6.685A 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 341 through 344 removed outlier: 6.936A pdb=" N LEU A 166 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N LEU A 344 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ILE A 168 " --> pdb=" O LEU A 344 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 28 through 30 removed outlier: 6.555A pdb=" N GLY B 72 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N LEU B 66 " --> pdb=" O ASN B 70 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ASN B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N HIS B 42 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N VAL B 31 " --> pdb=" O HIS B 42 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 96 through 99 removed outlier: 4.228A 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 343 removed outlier: 6.515A pdb=" N LEU B 166 " --> pdb=" O ILE B 342 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 221 through 226 removed outlier: 6.661A pdb=" N SER B 193 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N VAL B 224 " --> pdb=" O SER B 193 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N TYR B 195 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N ALA B 226 " --> pdb=" O TYR B 195 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA B 197 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N SER B 312 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N VAL B 258 " --> pdb=" O SER B 312 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N THR B 314 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N TYR B 260 " --> pdb=" O THR B 314 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU B 316 " --> pdb=" O TYR B 260 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 87 through 89 removed outlier: 6.394A pdb=" N ARG C 40 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N VAL C 34 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ILE C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN C 65 " --> pdb=" O GLY C 72 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL C 74 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N ALA C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 96 through 99 removed outlier: 3.826A pdb=" N GLU C 125 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 341 through 344 removed outlier: 6.872A pdb=" N LEU C 166 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N LEU C 344 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE C 168 " --> pdb=" O LEU C 344 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 221 through 226 removed outlier: 6.520A pdb=" N SER C 193 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N VAL C 224 " --> pdb=" O SER C 193 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N TYR C 195 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N ALA C 226 " --> pdb=" O TYR C 195 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ALA C 197 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N SER C 312 " --> pdb=" O VAL C 256 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N VAL C 258 " --> pdb=" O SER C 312 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N THR C 314 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N TYR C 260 " --> pdb=" O THR C 314 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU C 316 " --> pdb=" O TYR C 260 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 75 through 77 removed outlier: 6.636A pdb=" N ASP D 15 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N VAL D 9 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N VAL D 13 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE D 62 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 5.839A 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 94 through 96 removed outlier: 3.932A pdb=" N ARG D 94 " --> pdb=" O THR D 211 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N SER D 183 " --> pdb=" O ALA D 212 " (cutoff:3.500A) removed outlier: 8.541A pdb=" N VAL D 214 " --> pdb=" O SER D 183 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N PHE D 185 " --> pdb=" O VAL D 214 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE D 182 " --> pdb=" O ASP D 246 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N SER D 299 " --> pdb=" O VAL D 247 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N LEU D 249 " --> pdb=" O SER D 299 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N THR D 301 " --> pdb=" O LEU D 249 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ILE D 251 " --> pdb=" O THR D 301 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ILE D 303 " --> pdb=" O ILE D 251 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ALA D 327 " --> pdb=" O GLY D 155 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N PHE D 157 " --> pdb=" O ALA D 327 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N THR D 329 " --> pdb=" O PHE D 157 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 75 through 77 removed outlier: 6.779A pdb=" N ASP E 15 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N VAL E 9 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N VAL E 13 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N ILE E 62 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N VAL E 50 " --> pdb=" O ILE E 62 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 84 through 86 Processing sheet with id= R, first strand: chain 'E' and resid 327 through 330 removed outlier: 8.480A pdb=" N ILE E 154 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N SER E 302 " --> pdb=" O ILE E 154 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N LEU E 156 " --> pdb=" O SER E 302 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLN E 304 " --> pdb=" O LEU E 156 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 4 through 10 removed outlier: 6.539A pdb=" N ASP F 15 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N VAL F 9 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL F 13 " --> pdb=" O VAL F 9 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ILE F 62 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N VAL F 50 " --> pdb=" O ILE F 62 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 84 through 86 Processing sheet with id= U, first strand: chain 'F' and resid 327 through 330 removed outlier: 7.898A pdb=" N ILE F 154 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N SER F 302 " --> pdb=" O ILE F 154 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N LEU F 156 " --> pdb=" O SER F 302 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N GLN F 304 " --> pdb=" O LEU F 156 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N GLY F 158 " --> pdb=" O GLN F 304 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ILE F 306 " --> pdb=" O GLY F 158 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE F 182 " --> pdb=" O LEU F 248 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N PHE F 250 " --> pdb=" O ILE F 182 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL F 184 " --> pdb=" O PHE F 250 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'G' and resid 181 through 189 removed outlier: 6.302A pdb=" N LEU G 168 " --> pdb=" O LEU G 188 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N ASN G 173 " --> pdb=" O ILE G 81 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N VAL G 117 " --> pdb=" O ILE G 134 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ASP G 136 " --> pdb=" O VAL G 117 " (cutoff:3.500A) 941 hydrogen bonds defined for protein. 2724 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: 8.59 Time building geometry restraints manager: 10.50 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: 8239 1.34 - 1.46: 4727 1.46 - 1.58: 11519 1.58 - 1.70: 16 1.70 - 1.81: 154 Bond restraints: 24655 Sorted by residual: bond pdb=" CB PRO G 207 " pdb=" CG PRO G 207 " ideal model delta sigma weight residual 1.492 1.641 -0.149 5.00e-02 4.00e+02 8.90e+00 bond pdb=" O3 PO4 A 603 " pdb=" P PO4 A 603 " ideal model delta sigma weight residual 1.569 1.510 0.059 2.00e-02 2.50e+03 8.82e+00 bond pdb=" O4 PO4 A 603 " pdb=" P PO4 A 603 " ideal model delta sigma weight residual 1.568 1.510 0.058 2.00e-02 2.50e+03 8.34e+00 bond pdb=" O2 PO4 A 603 " pdb=" P PO4 A 603 " ideal model delta sigma weight residual 1.567 1.509 0.058 2.00e-02 2.50e+03 8.27e+00 bond pdb=" O1 PO4 A 603 " pdb=" P PO4 A 603 " ideal model delta sigma weight residual 1.565 1.511 0.054 2.00e-02 2.50e+03 7.23e+00 ... (remaining 24650 not shown) Histogram of bond angle deviations from ideal: 95.84 - 104.65: 509 104.65 - 113.46: 14100 113.46 - 122.27: 15260 122.27 - 131.07: 3488 131.07 - 139.88: 77 Bond angle restraints: 33434 Sorted by residual: angle pdb=" CA PRO G 207 " pdb=" N PRO G 207 " pdb=" CD PRO G 207 " ideal model delta sigma weight residual 112.00 99.09 12.91 1.40e+00 5.10e-01 8.51e+01 angle pdb=" C SER D 393 " pdb=" N ASP D 394 " pdb=" CA ASP D 394 " ideal model delta sigma weight residual 121.54 132.21 -10.67 1.91e+00 2.74e-01 3.12e+01 angle pdb=" N PRO G 207 " pdb=" CD PRO G 207 " pdb=" CG PRO G 207 " ideal model delta sigma weight residual 103.20 95.84 7.36 1.50e+00 4.44e-01 2.41e+01 angle pdb=" C PHE G 42 " pdb=" N VAL G 43 " pdb=" CA VAL G 43 " ideal model delta sigma weight residual 120.33 123.65 -3.32 8.00e-01 1.56e+00 1.73e+01 angle pdb=" C LEU F 455 " pdb=" N VAL F 456 " pdb=" CA VAL F 456 " ideal model delta sigma weight residual 123.08 119.08 4.00 1.01e+00 9.80e-01 1.57e+01 ... (remaining 33429 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 13863 17.71 - 35.42: 925 35.42 - 53.13: 207 53.13 - 70.84: 61 70.84 - 88.54: 26 Dihedral angle restraints: 15082 sinusoidal: 6157 harmonic: 8925 Sorted by residual: dihedral pdb=" CA ARG C 164 " pdb=" C ARG C 164 " pdb=" N GLU C 165 " pdb=" CA GLU C 165 " ideal model delta harmonic sigma weight residual 180.00 -159.64 -20.36 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA GLN C 397 " pdb=" C GLN C 397 " pdb=" N PHE C 398 " pdb=" CA PHE C 398 " ideal model delta harmonic sigma weight residual 180.00 160.35 19.65 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA PHE F 215 " pdb=" C PHE F 215 " pdb=" N GLY F 216 " pdb=" CA GLY F 216 " ideal model delta harmonic sigma weight residual 180.00 161.18 18.82 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 15079 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 2476 0.039 - 0.078: 976 0.078 - 0.117: 340 0.117 - 0.156: 58 0.156 - 0.195: 2 Chirality restraints: 3852 Sorted by residual: chirality pdb=" CB ILE D 172 " pdb=" CA ILE D 172 " pdb=" CG1 ILE D 172 " pdb=" CG2 ILE D 172 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.53e-01 chirality pdb=" CA ARG C 164 " pdb=" N ARG C 164 " pdb=" C ARG C 164 " pdb=" CB ARG C 164 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.14e-01 chirality pdb=" CA PHE D 215 " pdb=" N PHE D 215 " pdb=" C PHE D 215 " pdb=" CB PHE D 215 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.16 2.00e-01 2.50e+01 6.02e-01 ... (remaining 3849 not shown) Planarity restraints: 4362 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU G 206 " -0.086 5.00e-02 4.00e+02 1.21e-01 2.35e+01 pdb=" N PRO G 207 " 0.209 5.00e-02 4.00e+02 pdb=" CA PRO G 207 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO G 207 " -0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER D 393 " -0.012 2.00e-02 2.50e+03 2.39e-02 5.72e+00 pdb=" C SER D 393 " 0.041 2.00e-02 2.50e+03 pdb=" O SER D 393 " -0.016 2.00e-02 2.50e+03 pdb=" N ASP D 394 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG G 71 " 0.032 5.00e-02 4.00e+02 4.82e-02 3.72e+00 pdb=" N PRO G 72 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO G 72 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO G 72 " 0.027 5.00e-02 4.00e+02 ... (remaining 4359 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.40: 66 2.40 - 3.03: 14727 3.03 - 3.65: 35531 3.65 - 4.28: 53966 4.28 - 4.90: 92382 Nonbonded interactions: 196672 Sorted by model distance: nonbonded pdb=" OG1 THR D 165 " pdb="MG MG D 502 " model vdw 1.776 2.170 nonbonded pdb="MG MG F 601 " pdb=" O3G ATP F 602 " model vdw 1.914 2.170 nonbonded pdb=" OG1 THR F 165 " pdb="MG MG F 601 " model vdw 1.959 2.170 nonbonded pdb=" O3B ATP D 501 " pdb="MG MG D 502 " model vdw 1.964 2.170 nonbonded pdb=" O2B ATP C 600 " pdb="MG MG C 601 " model vdw 1.967 2.170 ... (remaining 196667 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 or resid 601 through 602)) selection = chain 'B' selection = chain 'C' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.580 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: 11.160 Check model and map are aligned: 0.390 Set scattering table: 0.240 Process input model: 62.890 Find NCS groups from input model: 1.800 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 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 : 0.005 0.149 24655 Z= 0.362 Angle : 0.653 12.913 33434 Z= 0.367 Chirality : 0.046 0.195 3852 Planarity : 0.005 0.121 4362 Dihedral : 13.661 88.544 9370 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.86 % Favored : 97.11 % Rotamer: Outliers : 0.04 % Allowed : 0.23 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % 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: 0.83 (0.15), residues: 3115 helix: 1.18 (0.15), residues: 1236 sheet: 0.93 (0.23), residues: 510 loop : -0.08 (0.17), residues: 1369 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS F 363 PHE 0.017 0.002 PHE A 494 TYR 0.012 0.001 TYR A 286 ARG 0.008 0.000 ARG B 89 *********************** 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 118 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 117 time to evaluate : 3.044 Fit side-chains REVERT: G 46 MET cc_start: 0.5592 (mmm) cc_final: 0.5313 (tpp) outliers start: 1 outliers final: 0 residues processed: 118 average time/residue: 0.3191 time to fit residues: 64.8824 Evaluate side-chains 107 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 3.085 ------------------------------------------------------------------------------- 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: 5.9990 chunk 234 optimal weight: 6.9990 chunk 130 optimal weight: 10.0000 chunk 80 optimal weight: 8.9990 chunk 158 optimal weight: 5.9990 chunk 125 optimal weight: 4.9990 chunk 242 optimal weight: 4.9990 chunk 94 optimal weight: 10.0000 chunk 147 optimal weight: 4.9990 chunk 180 optimal weight: 2.9990 chunk 281 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 GLN ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 173 ASN ** G 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.0590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 24655 Z= 0.404 Angle : 0.594 8.660 33434 Z= 0.309 Chirality : 0.047 0.168 3852 Planarity : 0.005 0.045 4362 Dihedral : 7.928 86.926 3569 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.55 % Allowed : 4.05 % Favored : 95.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % 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: 0.64 (0.15), residues: 3115 helix: 1.11 (0.15), residues: 1248 sheet: 0.73 (0.22), residues: 522 loop : -0.26 (0.17), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS F 363 PHE 0.018 0.002 PHE F 257 TYR 0.013 0.002 TYR A 195 ARG 0.004 0.000 ARG B 89 *********************** 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 121 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 107 time to evaluate : 2.539 Fit side-chains REVERT: E 338 MET cc_start: 0.8036 (ttm) cc_final: 0.7811 (ttm) outliers start: 14 outliers final: 12 residues processed: 114 average time/residue: 0.3104 time to fit residues: 61.4189 Evaluate side-chains 115 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 103 time to evaluate : 2.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 469 MET Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain G residue 24 MET Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 244 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 156 optimal weight: 7.9990 chunk 87 optimal weight: 0.9980 chunk 234 optimal weight: 10.0000 chunk 191 optimal weight: 9.9990 chunk 77 optimal weight: 2.9990 chunk 282 optimal weight: 4.9990 chunk 304 optimal weight: 10.0000 chunk 251 optimal weight: 0.4980 chunk 279 optimal weight: 6.9990 chunk 96 optimal weight: 8.9990 chunk 226 optimal weight: 4.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 HIS F 179 HIS G 174 HIS ** G 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.0764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 24655 Z= 0.254 Angle : 0.512 7.764 33434 Z= 0.265 Chirality : 0.044 0.148 3852 Planarity : 0.004 0.045 4362 Dihedral : 7.473 89.853 3569 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.93 % Allowed : 6.11 % Favored : 92.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % 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: 0.78 (0.15), residues: 3115 helix: 1.30 (0.15), residues: 1243 sheet: 0.70 (0.22), residues: 520 loop : -0.21 (0.17), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS F 363 PHE 0.022 0.001 PHE G 146 TYR 0.009 0.001 TYR A 195 ARG 0.002 0.000 ARG A 139 *********************** 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 133 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 109 time to evaluate : 2.944 Fit side-chains REVERT: A 357 ILE cc_start: 0.8976 (OUTLIER) cc_final: 0.8706 (mp) REVERT: D 392 LEU cc_start: 0.2472 (mm) cc_final: 0.2242 (tt) REVERT: E 226 MET cc_start: 0.8623 (ttp) cc_final: 0.8404 (ttp) outliers start: 24 outliers final: 17 residues processed: 125 average time/residue: 0.3263 time to fit residues: 70.0844 Evaluate side-chains 125 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 107 time to evaluate : 2.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 469 MET Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain G residue 24 MET Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain G residue 244 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 278 optimal weight: 4.9990 chunk 212 optimal weight: 7.9990 chunk 146 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 chunk 134 optimal weight: 0.8980 chunk 189 optimal weight: 9.9990 chunk 283 optimal weight: 10.0000 chunk 299 optimal weight: 10.0000 chunk 147 optimal weight: 1.9990 chunk 268 optimal weight: 6.9990 chunk 80 optimal weight: 0.0980 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.0915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 24655 Z= 0.265 Angle : 0.512 7.928 33434 Z= 0.263 Chirality : 0.044 0.146 3852 Planarity : 0.004 0.044 4362 Dihedral : 7.228 87.358 3569 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.64 % Allowed : 6.74 % Favored : 91.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % 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: 0.80 (0.15), residues: 3115 helix: 1.30 (0.15), residues: 1253 sheet: 0.71 (0.23), residues: 519 loop : -0.19 (0.17), residues: 1343 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 363 PHE 0.022 0.001 PHE G 146 TYR 0.010 0.001 TYR A 195 ARG 0.002 0.000 ARG A 354 *********************** 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 153 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 111 time to evaluate : 2.821 Fit side-chains REVERT: A 357 ILE cc_start: 0.8974 (OUTLIER) cc_final: 0.8692 (mp) REVERT: C 164 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.7139 (pmt-80) REVERT: G 46 MET cc_start: 0.6275 (tpp) cc_final: 0.5987 (tpp) REVERT: G 168 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7563 (tt) outliers start: 42 outliers final: 28 residues processed: 141 average time/residue: 0.3125 time to fit residues: 75.5932 Evaluate side-chains 136 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 105 time to evaluate : 2.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 164 ARG Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 469 MET Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain G residue 24 MET Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 136 ASP Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain G residue 244 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 249 optimal weight: 3.9990 chunk 170 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 223 optimal weight: 2.9990 chunk 123 optimal weight: 6.9990 chunk 255 optimal weight: 1.9990 chunk 207 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 153 optimal weight: 9.9990 chunk 268 optimal weight: 0.9980 chunk 75 optimal weight: 9.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 174 HIS ** G 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 24655 Z= 0.263 Angle : 0.512 10.935 33434 Z= 0.262 Chirality : 0.044 0.146 3852 Planarity : 0.004 0.044 4362 Dihedral : 7.056 88.868 3569 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.99 % Allowed : 7.52 % Favored : 90.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % 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: 0.83 (0.15), residues: 3115 helix: 1.33 (0.15), residues: 1253 sheet: 0.73 (0.22), residues: 529 loop : -0.18 (0.17), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS G 174 PHE 0.026 0.001 PHE C 460 TYR 0.011 0.001 TYR D 341 ARG 0.002 0.000 ARG A 354 *********************** 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 158 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 107 time to evaluate : 3.100 Fit side-chains REVERT: A 357 ILE cc_start: 0.8976 (OUTLIER) cc_final: 0.8701 (mp) REVERT: C 164 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.7195 (pmt-80) REVERT: G 168 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7551 (tt) REVERT: G 206 GLU cc_start: 0.3481 (OUTLIER) cc_final: 0.3263 (pt0) outliers start: 51 outliers final: 31 residues processed: 144 average time/residue: 0.3127 time to fit residues: 77.9532 Evaluate side-chains 140 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 105 time to evaluate : 2.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 164 ARG Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 384 ILE Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain G residue 24 MET Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 136 ASP Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain G residue 206 GLU Chi-restraints excluded: chain G residue 244 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 100 optimal weight: 8.9990 chunk 269 optimal weight: 0.0980 chunk 59 optimal weight: 0.8980 chunk 175 optimal weight: 0.0870 chunk 73 optimal weight: 6.9990 chunk 299 optimal weight: 20.0000 chunk 248 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 chunk 24 optimal weight: 9.9990 chunk 99 optimal weight: 5.9990 chunk 157 optimal weight: 2.9990 overall best weight: 1.4162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 24655 Z= 0.153 Angle : 0.462 11.505 33434 Z= 0.236 Chirality : 0.042 0.147 3852 Planarity : 0.003 0.043 4362 Dihedral : 6.635 87.697 3569 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.29 % Allowed : 8.41 % Favored : 90.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % 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: 1.10 (0.15), residues: 3115 helix: 1.60 (0.15), residues: 1248 sheet: 0.97 (0.23), residues: 500 loop : -0.10 (0.17), residues: 1367 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS F 363 PHE 0.028 0.001 PHE G 146 TYR 0.012 0.001 TYR D 341 ARG 0.003 0.000 ARG E 227 *********************** 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 146 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 113 time to evaluate : 2.823 Fit side-chains revert: symmetry clash REVERT: A 357 ILE cc_start: 0.8895 (OUTLIER) cc_final: 0.8620 (mp) REVERT: C 419 VAL cc_start: 0.8879 (OUTLIER) cc_final: 0.8667 (p) outliers start: 33 outliers final: 20 residues processed: 138 average time/residue: 0.3138 time to fit residues: 73.8748 Evaluate side-chains 130 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 108 time to evaluate : 2.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain C residue 164 ARG Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 469 MET Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 384 ILE Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 244 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 289 optimal weight: 0.0060 chunk 33 optimal weight: 9.9990 chunk 170 optimal weight: 10.0000 chunk 219 optimal weight: 0.9990 chunk 169 optimal weight: 3.9990 chunk 252 optimal weight: 2.9990 chunk 167 optimal weight: 10.0000 chunk 298 optimal weight: 0.9980 chunk 186 optimal weight: 20.0000 chunk 182 optimal weight: 2.9990 chunk 137 optimal weight: 0.9990 overall best weight: 1.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 174 HIS ** G 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 24655 Z= 0.141 Angle : 0.452 10.636 33434 Z= 0.230 Chirality : 0.042 0.145 3852 Planarity : 0.003 0.043 4362 Dihedral : 6.340 85.818 3569 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.32 % Allowed : 8.41 % Favored : 90.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % 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: 1.28 (0.15), residues: 3115 helix: 1.75 (0.15), residues: 1241 sheet: 1.06 (0.23), residues: 524 loop : -0.01 (0.17), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS G 174 PHE 0.020 0.001 PHE G 146 TYR 0.011 0.001 TYR D 341 ARG 0.002 0.000 ARG A 139 *********************** 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 146 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 112 time to evaluate : 2.626 Fit side-chains REVERT: A 357 ILE cc_start: 0.8872 (OUTLIER) cc_final: 0.8619 (mp) REVERT: C 164 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.7163 (pmt-80) REVERT: C 419 VAL cc_start: 0.8818 (OUTLIER) cc_final: 0.8617 (p) REVERT: F 10 MET cc_start: 0.7643 (mtp) cc_final: 0.7365 (mtm) REVERT: G 46 MET cc_start: 0.5772 (tpp) cc_final: 0.5495 (tpp) REVERT: G 131 MET cc_start: 0.4998 (OUTLIER) cc_final: 0.4086 (mpt) outliers start: 34 outliers final: 20 residues processed: 138 average time/residue: 0.3387 time to fit residues: 79.3556 Evaluate side-chains 133 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 109 time to evaluate : 2.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 164 ARG Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 469 MET Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 384 ILE Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain G residue 244 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 184 optimal weight: 8.9990 chunk 119 optimal weight: 0.6980 chunk 178 optimal weight: 10.0000 chunk 90 optimal weight: 8.9990 chunk 58 optimal weight: 8.9990 chunk 57 optimal weight: 0.7980 chunk 189 optimal weight: 0.4980 chunk 203 optimal weight: 8.9990 chunk 147 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 234 optimal weight: 6.9990 overall best weight: 2.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 GLN ** G 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 24655 Z= 0.248 Angle : 0.502 9.957 33434 Z= 0.254 Chirality : 0.043 0.144 3852 Planarity : 0.004 0.042 4362 Dihedral : 6.434 82.800 3569 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.71 % Allowed : 8.57 % Favored : 89.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % 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: 1.15 (0.15), residues: 3115 helix: 1.63 (0.15), residues: 1248 sheet: 0.95 (0.23), residues: 514 loop : -0.07 (0.17), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 363 PHE 0.032 0.001 PHE G 146 TYR 0.012 0.001 TYR D 341 ARG 0.002 0.000 ARG B 365 *********************** 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 152 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 108 time to evaluate : 2.592 Fit side-chains REVERT: A 357 ILE cc_start: 0.8881 (OUTLIER) cc_final: 0.8633 (mp) REVERT: C 164 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.7331 (pmt-80) REVERT: G 131 MET cc_start: 0.4991 (OUTLIER) cc_final: 0.4007 (mpt) outliers start: 44 outliers final: 34 residues processed: 143 average time/residue: 0.3034 time to fit residues: 74.0945 Evaluate side-chains 145 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 108 time to evaluate : 2.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 164 ARG Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 384 ILE Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 384 ILE Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain G residue 24 MET Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 244 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 271 optimal weight: 6.9990 chunk 286 optimal weight: 8.9990 chunk 261 optimal weight: 6.9990 chunk 278 optimal weight: 7.9990 chunk 167 optimal weight: 4.9990 chunk 121 optimal weight: 8.9990 chunk 218 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 251 optimal weight: 0.0470 chunk 263 optimal weight: 0.6980 chunk 277 optimal weight: 4.9990 overall best weight: 3.1484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 24655 Z= 0.272 Angle : 0.514 10.411 33434 Z= 0.261 Chirality : 0.044 0.144 3852 Planarity : 0.004 0.042 4362 Dihedral : 6.495 82.041 3569 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.71 % Allowed : 8.84 % Favored : 89.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % 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: 1.04 (0.15), residues: 3115 helix: 1.54 (0.15), residues: 1252 sheet: 0.88 (0.23), residues: 507 loop : -0.11 (0.17), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 363 PHE 0.029 0.001 PHE G 146 TYR 0.014 0.001 TYR D 341 ARG 0.003 0.000 ARG B 365 *********************** 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 154 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 110 time to evaluate : 2.944 Fit side-chains REVERT: A 357 ILE cc_start: 0.8908 (OUTLIER) cc_final: 0.8660 (mp) REVERT: C 164 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.7290 (pmt-80) REVERT: G 131 MET cc_start: 0.4989 (OUTLIER) cc_final: 0.3996 (mpt) outliers start: 44 outliers final: 37 residues processed: 142 average time/residue: 0.3249 time to fit residues: 79.1017 Evaluate side-chains 148 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 108 time to evaluate : 2.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 164 ARG Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 384 ILE Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 384 ILE Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain G residue 24 MET Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain G residue 136 ASP Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain G residue 244 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 182 optimal weight: 20.0000 chunk 294 optimal weight: 0.8980 chunk 179 optimal weight: 7.9990 chunk 139 optimal weight: 10.0000 chunk 204 optimal weight: 5.9990 chunk 308 optimal weight: 1.9990 chunk 284 optimal weight: 9.9990 chunk 245 optimal weight: 0.0770 chunk 25 optimal weight: 8.9990 chunk 189 optimal weight: 0.9990 chunk 150 optimal weight: 0.0010 overall best weight: 0.7948 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 8 GLN ** G 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 24655 Z= 0.123 Angle : 0.455 11.557 33434 Z= 0.229 Chirality : 0.042 0.145 3852 Planarity : 0.003 0.042 4362 Dihedral : 6.177 84.111 3569 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.17 % Allowed : 9.35 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % 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 (0.15), residues: 3115 helix: 1.77 (0.15), residues: 1247 sheet: 1.06 (0.23), residues: 510 loop : 0.00 (0.17), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS F 363 PHE 0.027 0.001 PHE G 146 TYR 0.010 0.001 TYR D 341 ARG 0.002 0.000 ARG B 365 ********************** 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 143 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 113 time to evaluate : 2.963 Fit side-chains REVERT: A 357 ILE cc_start: 0.8889 (OUTLIER) cc_final: 0.8622 (mp) REVERT: C 164 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.7099 (pmt-80) REVERT: C 419 VAL cc_start: 0.8829 (OUTLIER) cc_final: 0.8627 (p) REVERT: G 131 MET cc_start: 0.4938 (OUTLIER) cc_final: 0.3996 (mpt) outliers start: 30 outliers final: 25 residues processed: 136 average time/residue: 0.3337 time to fit residues: 77.0441 Evaluate side-chains 139 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 110 time to evaluate : 2.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 164 ARG Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 384 ILE Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 384 ILE Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain G residue 136 ASP Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain G residue 244 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 195 optimal weight: 8.9990 chunk 261 optimal weight: 5.9990 chunk 75 optimal weight: 0.0170 chunk 226 optimal weight: 0.6980 chunk 36 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 246 optimal weight: 0.4980 chunk 103 optimal weight: 0.0570 chunk 252 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 200 GLN ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 8 GLN G 174 HIS G 219 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.076757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.057646 restraints weight = 68433.394| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 2.79 r_work: 0.2839 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 24655 Z= 0.109 Angle : 0.443 12.125 33434 Z= 0.221 Chirality : 0.041 0.142 3852 Planarity : 0.003 0.042 4362 Dihedral : 5.797 81.553 3569 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.05 % Allowed : 9.62 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % 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: 1.55 (0.16), residues: 3115 helix: 1.94 (0.15), residues: 1249 sheet: 1.24 (0.23), residues: 531 loop : 0.12 (0.17), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS G 174 PHE 0.027 0.001 PHE G 146 TYR 0.010 0.001 TYR D 341 ARG 0.002 0.000 ARG C 139 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3803.12 seconds wall clock time: 70 minutes 55.19 seconds (4255.19 seconds total)