Starting phenix.real_space_refine (version: dev) on Thu Apr 7 01:37:51 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1r_23116/04_2022/7l1r_23116_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1r_23116/04_2022/7l1r_23116.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1r_23116/04_2022/7l1r_23116.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1r_23116/04_2022/7l1r_23116.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1r_23116/04_2022/7l1r_23116_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1r_23116/04_2022/7l1r_23116_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.005 sd= 0.050 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 24199 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3636 Classifications: {'peptide': 474} Link IDs: {'PTRANS': 21, 'TRANS': 451, 'PCIS': 1} Chain: "B" Number of atoms: 3643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3643 Classifications: {'peptide': 475} Link IDs: {'PTRANS': 21, 'TRANS': 452, 'PCIS': 1} Chain: "C" Number of atoms: 3649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3649 Classifications: {'peptide': 476} Link IDs: {'PTRANS': 21, 'TRANS': 453, 'PCIS': 1} Chain: "D" Number of atoms: 3621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3621 Classifications: {'peptide': 470} Link IDs: {'PTRANS': 22, 'TRANS': 446, 'PCIS': 1} Chain: "E" Number of atoms: 3622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3622 Classifications: {'peptide': 470} Link IDs: {'PTRANS': 22, 'TRANS': 446, 'PCIS': 1} Chain: "F" Number of atoms: 3629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3629 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 22, 'TRANS': 447, 'PCIS': 1} Chain: "G" Number of atoms: 2211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2211 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 9, 'TRANS': 271, 'PCIS': 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 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: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: 13.78, per 1000 atoms: 0.57 Number of scatterers: 24199 At special positions: 0 Unit cell: (152.88, 123.48, 126, 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 78 16.00 P 17 15.00 Mg 6 11.99 O 4649 8.00 N 4214 7.00 C 15235 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: 9.87 Conformation dependent library (CDL) restraints added in 3.8 seconds 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5690 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 114 helices and 22 sheets defined 42.0% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.77 Creating SS restraints... Processing helix chain 'A' and resid 101 through 103 No H-bonds generated for 'chain 'A' and resid 101 through 103' Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'A' and resid 176 through 186 Processing helix chain 'A' and resid 202 through 214 Processing helix chain 'A' and resid 217 through 220 Processing helix chain 'A' and resid 232 through 252 Proline residue: A 239 - end of helix removed outlier: 3.845A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 276 Processing helix chain 'A' and resid 290 through 298 Processing helix chain 'A' and resid 322 through 324 No H-bonds generated for 'chain 'A' and resid 322 through 324' Processing helix chain 'A' and resid 329 through 337 removed outlier: 3.671A pdb=" N SER A 336 " --> pdb=" O THR A 332 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE A 337 " --> pdb=" O ASN A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 351 Processing helix chain 'A' and resid 373 through 396 removed outlier: 3.931A pdb=" N LYS A 377 " --> pdb=" O LYS A 373 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL A 378 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N THR A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU A 384 " --> pdb=" O GLY A 380 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU A 392 " --> pdb=" O ALA A 388 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N PHE A 395 " --> pdb=" O GLU A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 419 Processing helix chain 'A' and resid 430 through 441 Processing helix chain 'A' and resid 450 through 466 removed outlier: 3.988A pdb=" N ARG A 454 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE A 456 " --> pdb=" O VAL A 453 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLU A 457 " --> pdb=" O ARG A 454 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU A 459 " --> pdb=" O PHE A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 478 removed outlier: 3.565A pdb=" N HIS A 474 " --> pdb=" O HIS A 470 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE A 475 " --> pdb=" O LEU A 471 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG A 476 " --> pdb=" O LEU A 472 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR A 477 " --> pdb=" O GLU A 473 " (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: 3.516A pdb=" N ALA B 179 " --> pdb=" O LYS B 175 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS B 187 " --> pdb=" O ILE B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 214 Processing helix chain 'B' and resid 217 through 220 Processing helix chain 'B' and resid 232 through 252 Proline residue: B 239 - end of helix removed outlier: 3.845A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 275 Processing helix chain 'B' and resid 288 through 300 removed outlier: 3.923A pdb=" N PHE B 291 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR B 292 " --> pdb=" O ASP B 289 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N HIS B 294 " --> pdb=" O PHE B 291 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER B 295 " --> pdb=" O TYR B 292 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLU B 299 " --> pdb=" O ARG B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 324 No H-bonds generated for 'chain 'B' and resid 322 through 324' Processing helix chain 'B' and resid 329 through 337 removed outlier: 3.510A pdb=" N ILE B 337 " --> pdb=" O ASN B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 351 Processing helix chain 'B' and resid 373 through 379 Processing helix chain 'B' and resid 382 through 398 removed outlier: 3.519A pdb=" N ALA B 387 " --> pdb=" O ARG B 383 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA B 388 " --> pdb=" O LEU B 384 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU B 391 " --> pdb=" O ALA B 387 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE B 398 " --> pdb=" O ALA B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 419 removed outlier: 3.516A pdb=" N LYS B 409 " --> pdb=" O ALA B 405 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA B 414 " --> pdb=" O LEU B 410 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG B 415 " --> pdb=" O ALA B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 442 Processing helix chain 'B' and resid 444 through 446 No H-bonds generated for 'chain 'B' and resid 444 through 446' Processing helix chain 'B' and resid 450 through 466 removed outlier: 3.833A pdb=" N ARG B 454 " --> pdb=" O GLU B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 478 removed outlier: 3.813A pdb=" N ARG B 476 " --> pdb=" O LEU B 472 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR B 477 " --> pdb=" O GLU B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 497 removed outlier: 3.607A pdb=" N THR B 497 " --> pdb=" O ALA B 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 103 No H-bonds generated for 'chain 'C' and resid 101 through 103' Processing helix chain 'C' and resid 151 through 156 Processing helix chain 'C' and resid 175 through 186 Processing helix chain 'C' and resid 202 through 214 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: 3.845A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 276 Processing helix chain 'C' and resid 288 through 300 removed outlier: 3.930A pdb=" N PHE C 291 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR C 292 " --> pdb=" O ASP C 289 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N HIS C 294 " --> pdb=" O PHE C 291 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLU C 299 " --> pdb=" O ARG C 296 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG C 300 " --> pdb=" O LEU C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 324 No H-bonds generated for 'chain 'C' and resid 322 through 324' Processing helix chain 'C' and resid 329 through 337 Processing helix chain 'C' and resid 346 through 351 Processing helix chain 'C' and resid 373 through 378 Processing helix chain 'C' and resid 382 through 398 removed outlier: 4.003A pdb=" N PHE C 398 " --> pdb=" O ALA C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 419 Processing helix chain 'C' and resid 430 through 442 Processing helix chain 'C' and resid 450 through 466 removed outlier: 4.364A pdb=" N ARG C 454 " --> pdb=" O GLU C 451 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU C 459 " --> pdb=" O PHE C 456 " (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 165 through 178 removed outlier: 3.867A pdb=" N GLU D 170 " --> pdb=" O VAL D 166 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLN D 177 " --> pdb=" O HIS D 173 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLU D 178 " --> pdb=" O ASN D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 205 removed outlier: 3.801A pdb=" N ASN D 196 " --> pdb=" O THR D 192 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP D 197 " --> pdb=" O ARG D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 210 Processing helix chain 'D' and resid 222 through 241 removed outlier: 4.662A pdb=" N ALA D 229 " --> pdb=" O ARG D 225 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N LEU D 230 " --> pdb=" O MET D 226 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR D 231 " --> pdb=" O ARG D 227 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY D 232 " --> pdb=" O VAL D 228 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET D 235 " --> pdb=" O THR D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 268 removed outlier: 3.611A pdb=" N THR D 258 " --> pdb=" O ILE D 254 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY D 261 " --> pdb=" O PHE D 257 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER D 262 " --> pdb=" O THR D 258 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU D 263 " --> pdb=" O GLN D 259 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA D 266 " --> pdb=" O SER D 262 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N LEU D 267 " --> pdb=" O GLU D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 291 removed outlier: 3.897A pdb=" N ARG D 291 " --> pdb=" O GLN D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 324 removed outlier: 4.003A pdb=" N SER D 323 " --> pdb=" O ALA D 319 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N HIS D 324 " --> pdb=" O THR D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 338 Processing helix chain 'D' and resid 356 through 359 No H-bonds generated for 'chain 'D' and resid 356 through 359' Processing helix chain 'D' and resid 361 through 387 removed outlier: 4.149A pdb=" N ASP D 382 " --> pdb=" O LYS D 378 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ILE D 383 " --> pdb=" O GLU D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 391 No H-bonds generated for 'chain 'D' and resid 389 through 391' Processing helix chain 'D' and resid 394 through 409 removed outlier: 3.622A pdb=" N ARG D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 421 removed outlier: 3.838A pdb=" N GLN D 419 " --> pdb=" O VAL D 416 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR D 421 " --> pdb=" O GLU D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 442 Processing helix chain 'D' and resid 450 through 453 Processing helix chain 'D' and resid 459 through 469 removed outlier: 3.550A pdb=" N GLU D 464 " --> pdb=" O GLU D 460 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N MET D 469 " --> pdb=" O LYS D 465 " (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 177 Processing helix chain 'E' and resid 192 through 204 removed outlier: 3.797A pdb=" N ASN E 196 " --> pdb=" O THR E 192 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASP E 197 " --> pdb=" O ARG E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 210 Processing helix chain 'E' and resid 222 through 241 removed outlier: 4.960A pdb=" N ALA E 229 " --> pdb=" O ARG E 225 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N LEU E 230 " --> pdb=" O MET E 226 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR E 238 " --> pdb=" O THR E 234 " (cutoff:3.500A) removed outlier: 3.702A 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: 4.728A pdb=" N ARG E 291 " --> pdb=" O GLN E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 316 through 324 removed outlier: 3.586A pdb=" N THR E 320 " --> pdb=" O PRO E 316 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N HIS E 324 " --> pdb=" O THR E 320 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 338 Processing helix chain 'E' and resid 356 through 359 No H-bonds generated for 'chain 'E' and resid 356 through 359' Processing helix chain 'E' and resid 361 through 386 removed outlier: 4.098A pdb=" N ASP E 382 " --> pdb=" O LYS E 378 " (cutoff:3.500A) removed outlier: 3.908A 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 410 removed outlier: 3.962A pdb=" N ARG E 402 " --> pdb=" O LEU E 398 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 419 removed outlier: 3.766A pdb=" N GLN E 419 " --> pdb=" O VAL E 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 416 through 419' Processing helix chain 'E' and resid 430 through 442 Processing helix chain 'E' and resid 450 through 453 Processing helix chain 'E' and resid 459 through 469 removed outlier: 3.632A pdb=" N VAL E 463 " --> pdb=" O ILE E 459 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N MET E 469 " --> pdb=" O LYS E 465 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 91 No H-bonds generated for 'chain 'F' and resid 89 through 91' Processing helix chain 'F' and resid 140 through 145 Processing helix chain 'F' and resid 164 through 178 removed outlier: 3.816A pdb=" N GLN F 177 " --> pdb=" O HIS F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 205 Processing helix chain 'F' and resid 207 through 210 Processing helix chain 'F' and resid 222 through 241 removed outlier: 3.531A pdb=" N MET F 226 " --> pdb=" O PRO F 222 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG F 227 " --> pdb=" O GLY F 223 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA F 229 " --> pdb=" O ARG F 225 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LEU F 230 " --> pdb=" O MET F 226 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N MET F 235 " --> pdb=" O THR F 231 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 268 removed outlier: 3.788A pdb=" N ALA F 266 " --> pdb=" O SER F 262 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEU F 267 " --> pdb=" O GLU F 263 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 291 removed outlier: 3.614A pdb=" N LEU F 288 " --> pdb=" O GLU F 284 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ARG F 291 " --> pdb=" O GLN F 287 " (cutoff:3.500A) Processing helix chain 'F' and resid 316 through 324 removed outlier: 3.549A pdb=" N THR F 320 " --> pdb=" O PRO F 316 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER F 323 " --> pdb=" O ALA F 319 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N HIS F 324 " --> pdb=" O THR F 320 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 338 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 384 removed outlier: 4.986A pdb=" N ASP F 382 " --> pdb=" O LYS F 378 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ILE F 383 " --> pdb=" O GLU F 379 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 through 409 removed outlier: 3.530A pdb=" N VAL F 399 " --> pdb=" O ASP F 396 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE F 408 " --> pdb=" O ARG F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 417 No H-bonds generated for 'chain 'F' and resid 415 through 417' Processing helix chain 'F' and resid 430 through 442 Processing helix chain 'F' and resid 450 through 453 Processing helix chain 'F' and resid 459 through 469 removed outlier: 3.550A pdb=" N MET F 469 " --> pdb=" O LYS F 465 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 61 Proline residue: G 47 - end of helix Processing helix chain 'G' and resid 94 through 109 removed outlier: 3.569A pdb=" N VAL G 98 " --> pdb=" O TYR G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'G' and resid 123 through 130 Processing helix chain 'G' and resid 149 through 164 removed outlier: 3.930A pdb=" N GLU G 154 " --> pdb=" O ALA G 150 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ILE G 155 " --> pdb=" O ASP G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 212 through 286 removed outlier: 3.596A pdb=" N VAL G 218 " --> pdb=" O GLU G 214 " (cutoff:3.500A) Proline residue: G 221 - end of helix removed outlier: 3.523A pdb=" N SER G 264 " --> pdb=" O THR G 260 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE G 277 " --> pdb=" O ILE G 273 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 28 through 30 removed outlier: 6.853A pdb=" N GLY A 72 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N LEU A 66 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ASN A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN A 33 " --> pdb=" O ARG A 40 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N HIS A 42 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 5.736A 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 Processing sheet with id= C, first strand: chain 'A' and resid 341 through 344 removed outlier: 6.656A pdb=" N LEU A 166 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N LEU A 344 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ILE A 168 " --> pdb=" O LEU A 344 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 221 through 226 removed outlier: 7.020A pdb=" N SER A 193 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N VAL A 224 " --> pdb=" O SER A 193 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N TYR A 195 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ALA A 226 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ALA A 197 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N SER A 312 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N VAL A 258 " --> pdb=" O SER A 312 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N THR A 314 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N TYR A 260 " --> pdb=" O THR A 314 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU A 316 " --> pdb=" O TYR A 260 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 38 through 41 removed outlier: 3.604A pdb=" N ILE B 73 " --> pdb=" O ALA B 39 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N VAL B 74 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N ALA B 63 " --> pdb=" O VAL B 74 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 96 through 99 Processing sheet with id= G, first strand: chain 'B' and resid 341 through 343 removed outlier: 6.573A 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: 6.939A pdb=" N SER B 193 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N VAL B 224 " --> pdb=" O SER B 193 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N TYR B 195 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N ALA B 226 " --> pdb=" O TYR B 195 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ALA B 197 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TYR B 260 " --> pdb=" O LEU B 316 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 28 through 30 removed outlier: 6.873A pdb=" N GLY C 72 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N LEU C 66 " --> pdb=" O ASN C 70 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ASN C 70 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN C 33 " --> pdb=" O ARG C 40 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N HIS C 42 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N VAL C 31 " --> pdb=" O HIS C 42 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 96 through 99 Processing sheet with id= K, first strand: chain 'C' and resid 107 through 109 removed outlier: 8.827A pdb=" N VAL C 108 " --> pdb=" O THR C 221 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL C 223 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N ILE C 222 " --> pdb=" O MET C 191 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N SER C 193 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N VAL C 224 " --> pdb=" O SER C 193 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N TYR C 195 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N ALA C 226 " --> pdb=" O TYR C 195 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ALA C 197 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N HIS C 255 " --> pdb=" O ILE C 192 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N ILE C 194 " --> pdb=" O HIS C 255 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU C 257 " --> pdb=" O ILE C 194 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N VAL C 196 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL C 259 " --> pdb=" O VAL C 196 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ILE C 198 " --> pdb=" O VAL C 259 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 318 through 320 removed outlier: 6.578A pdb=" N ILE C 167 " --> pdb=" O VAL C 319 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ILE C 342 " --> pdb=" O ILE C 168 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'D' and resid 5 through 10 removed outlier: 6.728A pdb=" N ASP D 15 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N VAL D 9 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N VAL D 13 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU D 52 " --> pdb=" O ARG D 60 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ILE D 62 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N VAL D 50 " --> pdb=" O ILE D 62 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 84 through 86 Processing sheet with id= O, first strand: chain 'D' and resid 327 through 331 removed outlier: 7.687A pdb=" N ILE D 154 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N SER D 302 " --> pdb=" O ILE D 154 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N LEU D 156 " --> pdb=" O SER D 302 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N GLN D 304 " --> pdb=" O LEU D 156 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N GLY D 158 " --> pdb=" O GLN D 304 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ILE D 306 " --> pdb=" O GLY D 158 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL D 247 " --> pdb=" O THR D 301 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N ILE D 303 " --> pdb=" O VAL D 247 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LEU D 249 " --> pdb=" O ILE D 303 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N ALA D 305 " --> pdb=" O LEU D 249 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ILE D 251 " --> pdb=" O ALA D 305 " (cutoff:3.500A) removed outlier: 8.552A pdb=" N TYR D 307 " --> pdb=" O ILE D 251 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 5 through 10 removed outlier: 6.426A pdb=" N ASP E 15 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N VAL E 9 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N VAL E 13 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N ILE E 62 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N VAL E 50 " --> pdb=" O ILE E 62 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 84 through 86 Processing sheet with id= R, first strand: chain 'E' and resid 327 through 331 removed outlier: 3.524A pdb=" N ALA E 327 " --> pdb=" O LYS E 153 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N ILE E 154 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N SER E 302 " --> pdb=" O ILE E 154 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N LEU E 156 " --> pdb=" O SER E 302 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLN E 304 " --> pdb=" O LEU E 156 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N GLY E 158 " --> pdb=" O GLN E 304 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL E 247 " --> pdb=" O THR E 301 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N ILE E 303 " --> pdb=" O VAL E 247 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU E 249 " --> pdb=" O ILE E 303 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N ALA E 305 " --> pdb=" O LEU E 249 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ILE E 251 " --> pdb=" O ALA E 305 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 5 through 10 removed outlier: 6.621A pdb=" N ASP F 15 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N VAL F 9 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N VAL F 13 " --> pdb=" O VAL F 9 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ILE F 62 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N VAL F 50 " --> pdb=" O ILE F 62 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 84 through 86 Processing sheet with id= U, first strand: chain 'F' and resid 327 through 330 removed outlier: 8.098A pdb=" N ILE F 154 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N SER F 302 " --> pdb=" O ILE F 154 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N LEU F 156 " --> pdb=" O SER F 302 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N GLN F 304 " --> pdb=" O LEU F 156 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N GLY F 158 " --> pdb=" O GLN F 304 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ILE F 306 " --> pdb=" O GLY F 158 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL F 247 " --> pdb=" O THR F 301 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N ILE F 303 " --> pdb=" O VAL F 247 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LEU F 249 " --> pdb=" O ILE F 303 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N ALA F 305 " --> pdb=" O LEU F 249 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N ILE F 251 " --> pdb=" O ALA F 305 " (cutoff:3.500A) removed outlier: 8.547A pdb=" N TYR F 307 " --> pdb=" O ILE F 251 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ILE F 182 " --> pdb=" O LEU F 248 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N PHE F 250 " --> pdb=" O ILE F 182 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL F 184 " --> pdb=" O PHE F 250 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'G' and resid 184 through 192 removed outlier: 7.301A pdb=" N LEU G 171 " --> pdb=" O LEU G 191 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N ASN G 176 " --> pdb=" O ILE G 84 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU G 138 " --> pdb=" O VAL G 120 " (cutoff:3.500A) 927 hydrogen bonds defined for protein. 2538 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.94 Time building geometry restraints manager: 10.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4272 1.31 - 1.44: 5802 1.44 - 1.57: 14343 1.57 - 1.69: 33 1.69 - 1.82: 154 Bond restraints: 24604 Sorted by residual: bond pdb=" C PRO B 280 " pdb=" O PRO B 280 " ideal model delta sigma weight residual 1.246 1.196 0.049 8.50e-03 1.38e+04 3.34e+01 bond pdb=" C4 ADP E 501 " pdb=" C5 ADP E 501 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.10e+01 bond pdb=" CA SER A 295 " pdb=" CB SER A 295 " ideal model delta sigma weight residual 1.528 1.463 0.066 1.56e-02 4.11e+03 1.76e+01 bond pdb=" C5 ADP E 501 " pdb=" C6 ADP E 501 " ideal model delta sigma weight residual 1.490 1.407 0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" C ARG B 40 " pdb=" O ARG B 40 " ideal model delta sigma weight residual 1.234 1.184 0.050 1.22e-02 6.72e+03 1.71e+01 ... (remaining 24599 not shown) Histogram of bond angle deviations from ideal: 98.12 - 105.06: 612 105.06 - 111.99: 9833 111.99 - 118.93: 10046 118.93 - 125.86: 12521 125.86 - 132.80: 352 Bond angle restraints: 33364 Sorted by residual: angle pdb=" PB ATP D 500 " pdb=" O3B ATP D 500 " pdb=" PG ATP D 500 " ideal model delta sigma weight residual 139.87 123.33 16.54 1.00e+00 1.00e+00 2.74e+02 angle pdb=" PB ATP C 600 " pdb=" O3B ATP C 600 " pdb=" PG ATP C 600 " ideal model delta sigma weight residual 139.87 125.52 14.35 1.00e+00 1.00e+00 2.06e+02 angle pdb=" PB ATP F 500 " pdb=" O3B ATP F 500 " pdb=" PG ATP F 500 " ideal model delta sigma weight residual 139.87 126.51 13.36 1.00e+00 1.00e+00 1.78e+02 angle pdb=" PA ATP D 500 " pdb=" O3A ATP D 500 " pdb=" PB ATP D 500 " ideal model delta sigma weight residual 136.83 123.69 13.14 1.00e+00 1.00e+00 1.73e+02 angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 127.16 12.71 1.00e+00 1.00e+00 1.62e+02 ... (remaining 33359 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.03: 14421 30.03 - 60.07: 432 60.07 - 90.10: 34 90.10 - 120.13: 0 120.13 - 150.16: 2 Dihedral angle restraints: 14889 sinusoidal: 5997 harmonic: 8892 Sorted by residual: dihedral pdb=" C ARG A 283 " pdb=" N ARG A 283 " pdb=" CA ARG A 283 " pdb=" CB ARG A 283 " ideal model delta harmonic sigma weight residual -122.60 -140.28 17.68 0 2.50e+00 1.60e-01 5.00e+01 dihedral pdb=" C ASP C 261 " pdb=" N ASP C 261 " pdb=" CA ASP C 261 " pdb=" CB ASP C 261 " ideal model delta harmonic sigma weight residual -122.60 -139.55 16.95 0 2.50e+00 1.60e-01 4.60e+01 dihedral pdb=" O1B ADP E 501 " pdb=" O3A ADP E 501 " pdb=" PB ADP E 501 " pdb=" PA ADP E 501 " ideal model delta sinusoidal sigma weight residual 300.00 149.83 150.16 1 2.00e+01 2.50e-03 4.48e+01 ... (remaining 14886 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.133: 3061 0.133 - 0.266: 685 0.266 - 0.399: 76 0.399 - 0.531: 15 0.531 - 0.664: 3 Chirality restraints: 3840 Sorted by residual: chirality pdb=" CA ASP C 261 " pdb=" N ASP C 261 " pdb=" C ASP C 261 " pdb=" CB ASP C 261 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.10e+01 chirality pdb=" CA ARG A 283 " pdb=" N ARG A 283 " pdb=" C ARG A 283 " pdb=" CB ARG A 283 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.08e+01 chirality pdb=" CA TYR D 27 " pdb=" N TYR D 27 " pdb=" C TYR D 27 " pdb=" CB TYR D 27 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.58e+00 ... (remaining 3837 not shown) Planarity restraints: 4349 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 220 " -0.101 2.00e-02 2.50e+03 6.26e-02 7.84e+01 pdb=" CG TYR A 220 " 0.001 2.00e-02 2.50e+03 pdb=" CD1 TYR A 220 " 0.040 2.00e-02 2.50e+03 pdb=" CD2 TYR A 220 " 0.072 2.00e-02 2.50e+03 pdb=" CE1 TYR A 220 " 0.052 2.00e-02 2.50e+03 pdb=" CE2 TYR A 220 " 0.030 2.00e-02 2.50e+03 pdb=" CZ TYR A 220 " 0.008 2.00e-02 2.50e+03 pdb=" OH TYR A 220 " -0.103 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 199 " 0.110 2.00e-02 2.50e+03 6.02e-02 7.25e+01 pdb=" CG TYR D 199 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR D 199 " -0.044 2.00e-02 2.50e+03 pdb=" CD2 TYR D 199 " -0.042 2.00e-02 2.50e+03 pdb=" CE1 TYR D 199 " -0.034 2.00e-02 2.50e+03 pdb=" CE2 TYR D 199 " -0.039 2.00e-02 2.50e+03 pdb=" CZ TYR D 199 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR D 199 " 0.095 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 313 " 0.081 2.00e-02 2.50e+03 5.47e-02 5.97e+01 pdb=" CG TYR D 313 " -0.003 2.00e-02 2.50e+03 pdb=" CD1 TYR D 313 " -0.041 2.00e-02 2.50e+03 pdb=" CD2 TYR D 313 " -0.028 2.00e-02 2.50e+03 pdb=" CE1 TYR D 313 " -0.034 2.00e-02 2.50e+03 pdb=" CE2 TYR D 313 " -0.050 2.00e-02 2.50e+03 pdb=" CZ TYR D 313 " -0.026 2.00e-02 2.50e+03 pdb=" OH TYR D 313 " 0.102 2.00e-02 2.50e+03 ... (remaining 4346 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 99 2.55 - 3.14: 18833 3.14 - 3.73: 34567 3.73 - 4.31: 51288 4.31 - 4.90: 84644 Nonbonded interactions: 189431 Sorted by model distance: nonbonded pdb=" O2G ATP C 600 " pdb="MG MG C 601 " model vdw 1.965 2.170 nonbonded pdb=" O THR F 192 " pdb=" OG1 THR F 192 " model vdw 2.043 2.440 nonbonded pdb=" O1G ATP D 500 " pdb="MG MG D 501 " model vdw 2.098 2.170 nonbonded pdb=" O1G ATP F 500 " pdb="MG MG F 501 " model vdw 2.107 2.170 nonbonded pdb=" OG1 THR B 176 " pdb="MG MG B 601 " model vdw 2.201 2.170 ... (remaining 189426 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 27 through 499 or resid 600 through 601)) selection = (chain 'B' and (resid 27 through 499 or resid 600 through 601)) selection = (chain 'C' and (resid 27 through 499 or resid 600 through 601)) } ncs_group { reference = (chain 'D' and (resid 2 through 470 or resid 501)) selection = (chain 'E' and (resid 2 through 470 or resid 502)) selection = (chain 'F' and (resid 2 through 470 or resid 501)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 17 5.49 5 Mg 6 5.21 5 S 78 5.16 5 C 15235 2.51 5 N 4214 2.21 5 O 4649 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.630 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: 5.930 Check model and map are aligned: 0.360 Convert atoms to be neutral: 0.230 Process input model: 61.910 Find NCS groups from input model: 1.870 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 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 : 0.011 0.111 24604 Z= 0.749 Angle : 1.763 16.538 33364 Z= 1.202 Chirality : 0.111 0.664 3840 Planarity : 0.010 0.089 4349 Dihedral : 14.028 150.162 9199 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.25 % Favored : 96.71 % Rotamer Outliers : 3.32 % Cbeta Deviations : 0.98 % Peptide Plane: Cis-proline : 4.83 % 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: -0.59 (0.14), residues: 3104 helix: -0.08 (0.14), residues: 1225 sheet: 0.26 (0.24), residues: 461 loop : -0.79 (0.16), residues: 1418 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1294 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 1209 time to evaluate : 2.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 85 outliers final: 23 residues processed: 1251 average time/residue: 0.4257 time to fit residues: 776.9319 Evaluate side-chains 1102 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 1079 time to evaluate : 2.833 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.2925 time to fit residues: 15.1871 ------------------------------------------------------------------------------- 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: 0.8980 chunk 234 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 chunk 242 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 147 optimal weight: 0.8980 chunk 180 optimal weight: 1.9990 chunk 281 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN A 186 GLN A 200 GLN A 266 GLN ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 GLN A 425 HIS A 466 GLN A 488 ASN B 33 GLN B 163 GLN B 186 GLN B 230 GLN B 371 GLN B 397 GLN B 469 GLN B 488 ASN C 46 ASN C 147 GLN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 345 GLN C 397 GLN C 407 GLN C 422 GLN C 425 HIS C 466 GLN C 488 ASN D 8 GLN D 33 GLN D 169 GLN D 253 ASN D 304 GLN D 365 GLN E 33 GLN E 119 HIS E 169 GLN E 363 HIS E 365 GLN ** E 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 412 GLN E 423 GLN F 8 GLN F 33 GLN F 173 HIS F 217 GLN F 324 HIS F 371 GLN F 372 GLN F 423 GLN ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 41 ASN ** G 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 183 GLN G 184 GLN G 240 HIS G 249 ASN G 253 ASN G 266 ASN G 285 ASN Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.085 24604 Z= 0.221 Angle : 0.670 10.097 33364 Z= 0.359 Chirality : 0.046 0.185 3840 Planarity : 0.007 0.119 4349 Dihedral : 6.727 137.824 3417 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer Outliers : 3.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.83 % 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: 0.18 (0.15), residues: 3104 helix: 0.93 (0.14), residues: 1235 sheet: 0.30 (0.23), residues: 499 loop : -0.63 (0.16), residues: 1370 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1182 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 1089 time to evaluate : 2.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 93 outliers final: 51 residues processed: 1125 average time/residue: 0.4302 time to fit residues: 717.9901 Evaluate side-chains 1088 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 1037 time to evaluate : 2.593 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 0 residues processed: 51 average time/residue: 0.2404 time to fit residues: 25.5183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 156 optimal weight: 6.9990 chunk 87 optimal weight: 8.9990 chunk 234 optimal weight: 9.9990 chunk 191 optimal weight: 8.9990 chunk 77 optimal weight: 0.4980 chunk 282 optimal weight: 0.9980 chunk 304 optimal weight: 9.9990 chunk 251 optimal weight: 5.9990 chunk 279 optimal weight: 8.9990 chunk 96 optimal weight: 9.9990 chunk 226 optimal weight: 4.9990 overall best weight: 3.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 HIS A 163 GLN A 215 HIS A 294 HIS ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 GLN A 469 GLN ** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 345 GLN C 358 ASN C 470 HIS C 474 HIS D 119 HIS D 219 ASN D 304 GLN ** E 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 401 HIS E 412 GLN ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 95 ASN ** G 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.098 24604 Z= 0.455 Angle : 0.771 7.660 33364 Z= 0.414 Chirality : 0.053 0.239 3840 Planarity : 0.007 0.124 4349 Dihedral : 6.961 139.952 3417 Min Nonbonded Distance : 1.728 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer Outliers : 4.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.83 % 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: -0.40 (0.14), residues: 3104 helix: 0.43 (0.14), residues: 1237 sheet: 0.04 (0.23), residues: 521 loop : -0.97 (0.16), residues: 1346 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1215 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 1104 time to evaluate : 2.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 111 outliers final: 60 residues processed: 1142 average time/residue: 0.4269 time to fit residues: 727.0585 Evaluate side-chains 1143 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 1083 time to evaluate : 2.705 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 0 residues processed: 60 average time/residue: 0.2672 time to fit residues: 31.3391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 278 optimal weight: 2.9990 chunk 212 optimal weight: 4.9990 chunk 146 optimal weight: 7.9990 chunk 31 optimal weight: 4.9990 chunk 134 optimal weight: 0.6980 chunk 189 optimal weight: 0.7980 chunk 283 optimal weight: 5.9990 chunk 299 optimal weight: 0.9980 chunk 147 optimal weight: 0.9990 chunk 268 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 HIS A 345 GLN A 407 GLN B 333 ASN B 345 GLN C 172 GLN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 GLN C 474 HIS D 304 GLN D 401 HIS E 381 GLN ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 119 HIS ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.4152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.122 24604 Z= 0.220 Angle : 0.598 7.667 33364 Z= 0.316 Chirality : 0.045 0.221 3840 Planarity : 0.006 0.095 4349 Dihedral : 6.280 127.028 3417 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer Outliers : 2.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.83 % 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: 0.07 (0.15), residues: 3104 helix: 0.90 (0.14), residues: 1231 sheet: 0.32 (0.22), residues: 530 loop : -0.82 (0.17), residues: 1343 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1123 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 1062 time to evaluate : 2.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 33 residues processed: 1082 average time/residue: 0.4285 time to fit residues: 682.4671 Evaluate side-chains 1087 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 1054 time to evaluate : 2.968 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.2529 time to fit residues: 18.8023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 249 optimal weight: 5.9990 chunk 170 optimal weight: 8.9990 chunk 4 optimal weight: 0.0980 chunk 223 optimal weight: 0.0570 chunk 123 optimal weight: 0.4980 chunk 255 optimal weight: 0.0060 chunk 207 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 153 optimal weight: 6.9990 chunk 268 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 overall best weight: 0.5316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 GLN ** C 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 375 GLN E 401 HIS ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.4430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.109 24604 Z= 0.185 Angle : 0.574 7.549 33364 Z= 0.299 Chirality : 0.043 0.156 3840 Planarity : 0.006 0.097 4349 Dihedral : 5.794 113.233 3417 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer Outliers : 2.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.83 % 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: 0.33 (0.15), residues: 3104 helix: 1.14 (0.15), residues: 1244 sheet: 0.41 (0.22), residues: 542 loop : -0.71 (0.17), residues: 1318 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1102 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 1045 time to evaluate : 2.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 30 residues processed: 1055 average time/residue: 0.4161 time to fit residues: 641.2252 Evaluate side-chains 1059 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 1029 time to evaluate : 2.891 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.2597 time to fit residues: 17.5333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 100 optimal weight: 9.9990 chunk 269 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 175 optimal weight: 7.9990 chunk 73 optimal weight: 0.6980 chunk 299 optimal weight: 5.9990 chunk 248 optimal weight: 10.0000 chunk 138 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 99 optimal weight: 0.2980 chunk 157 optimal weight: 2.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN A 474 HIS B 333 ASN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 GLN ** C 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 8 GLN D 119 HIS ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 95 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.4559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.115 24604 Z= 0.282 Angle : 0.626 8.336 33364 Z= 0.326 Chirality : 0.046 0.169 3840 Planarity : 0.006 0.099 4349 Dihedral : 5.858 103.620 3417 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer Outliers : 2.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.83 % 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: 0.20 (0.15), residues: 3104 helix: 1.03 (0.15), residues: 1239 sheet: 0.32 (0.22), residues: 544 loop : -0.76 (0.17), residues: 1321 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1122 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 1067 time to evaluate : 2.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 37 residues processed: 1085 average time/residue: 0.4239 time to fit residues: 679.9472 Evaluate side-chains 1093 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 1056 time to evaluate : 3.064 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.2520 time to fit residues: 20.8940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 289 optimal weight: 8.9990 chunk 33 optimal weight: 4.9990 chunk 170 optimal weight: 9.9990 chunk 219 optimal weight: 5.9990 chunk 169 optimal weight: 3.9990 chunk 252 optimal weight: 6.9990 chunk 167 optimal weight: 6.9990 chunk 298 optimal weight: 6.9990 chunk 186 optimal weight: 4.9990 chunk 182 optimal weight: 5.9990 chunk 137 optimal weight: 2.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 GLN B 467 ASN C 163 GLN C 172 GLN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 358 ASN C 371 GLN C 474 HIS ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 324 HIS ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.4722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.083 24604 Z= 0.526 Angle : 0.763 9.033 33364 Z= 0.405 Chirality : 0.053 0.251 3840 Planarity : 0.007 0.111 4349 Dihedral : 6.410 93.013 3417 Min Nonbonded Distance : 1.680 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer Outliers : 2.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.83 % 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: -0.53 (0.15), residues: 3104 helix: 0.40 (0.14), residues: 1236 sheet: -0.13 (0.22), residues: 520 loop : -1.08 (0.17), residues: 1348 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1170 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 1097 time to evaluate : 2.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 73 outliers final: 51 residues processed: 1121 average time/residue: 0.4576 time to fit residues: 765.4863 Evaluate side-chains 1137 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 1086 time to evaluate : 3.315 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 0 residues processed: 51 average time/residue: 0.2642 time to fit residues: 27.7881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 184 optimal weight: 0.9990 chunk 119 optimal weight: 0.9980 chunk 178 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 189 optimal weight: 1.9990 chunk 203 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 234 optimal weight: 8.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 46 ASN ** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 GLN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 GLN ** C 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 447 HIS ** E 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 95 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.4892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.117 24604 Z= 0.255 Angle : 0.638 8.949 33364 Z= 0.332 Chirality : 0.045 0.172 3840 Planarity : 0.006 0.104 4349 Dihedral : 5.973 92.419 3417 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer Outliers : 1.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.83 % 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: -0.17 (0.15), residues: 3104 helix: 0.74 (0.15), residues: 1238 sheet: 0.09 (0.22), residues: 538 loop : -0.96 (0.17), residues: 1328 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1116 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 1078 time to evaluate : 2.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 23 residues processed: 1089 average time/residue: 0.4211 time to fit residues: 674.7473 Evaluate side-chains 1093 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 1070 time to evaluate : 3.063 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.3040 time to fit residues: 15.4954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 271 optimal weight: 0.5980 chunk 286 optimal weight: 0.4980 chunk 261 optimal weight: 5.9990 chunk 278 optimal weight: 0.8980 chunk 167 optimal weight: 0.5980 chunk 121 optimal weight: 4.9990 chunk 218 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 251 optimal weight: 2.9990 chunk 263 optimal weight: 0.9990 chunk 277 optimal weight: 3.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 GLN ** B 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 ASN C 371 GLN ** C 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 169 GLN F 28 ASN F 217 GLN G 40 GLN G 95 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.5076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.137 24604 Z= 0.202 Angle : 0.608 9.106 33364 Z= 0.316 Chirality : 0.044 0.178 3840 Planarity : 0.006 0.112 4349 Dihedral : 5.527 82.837 3417 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer Outliers : 0.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.83 % 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: 0.12 (0.15), residues: 3104 helix: 0.99 (0.15), residues: 1243 sheet: 0.31 (0.22), residues: 543 loop : -0.85 (0.17), residues: 1318 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1078 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 1053 time to evaluate : 2.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 18 residues processed: 1063 average time/residue: 0.4329 time to fit residues: 677.0273 Evaluate side-chains 1054 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 1036 time to evaluate : 2.993 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2679 time to fit residues: 12.5145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 182 optimal weight: 0.9990 chunk 294 optimal weight: 10.0000 chunk 179 optimal weight: 4.9990 chunk 139 optimal weight: 0.7980 chunk 204 optimal weight: 7.9990 chunk 308 optimal weight: 4.9990 chunk 284 optimal weight: 0.8980 chunk 245 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 189 optimal weight: 4.9990 chunk 150 optimal weight: 5.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN B 358 ASN B 433 GLN C 70 ASN C 371 GLN C 474 HIS D 173 HIS D 289 GLN D 304 GLN E 169 GLN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 217 GLN G 36 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.5077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.067 24604 Z= 0.312 Angle : 0.665 9.168 33364 Z= 0.345 Chirality : 0.047 0.167 3840 Planarity : 0.006 0.125 4349 Dihedral : 5.710 89.936 3417 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer Outliers : 0.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.83 % 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: -0.03 (0.15), residues: 3104 helix: 0.88 (0.15), residues: 1244 sheet: 0.19 (0.23), residues: 534 loop : -0.92 (0.17), residues: 1326 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1083 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 1068 time to evaluate : 2.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 9 residues processed: 1069 average time/residue: 0.4400 time to fit residues: 691.9108 Evaluate side-chains 1065 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 1056 time to evaluate : 2.863 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2445 time to fit residues: 7.9054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 75 optimal weight: 9.9990 chunk 226 optimal weight: 6.9990 chunk 36 optimal weight: 7.9990 chunk 68 optimal weight: 0.9990 chunk 246 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 252 optimal weight: 0.8980 chunk 31 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 371 GLN B 433 GLN C 371 GLN ** C 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 HIS D 289 GLN F 8 GLN ** F 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.127603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.113025 restraints weight = 35199.520| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.16 r_work: 0.3439 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 1.94 restraints_weight: 0.2500 r_work: 0.3413 rms_B_bonded: 1.99 restraints_weight: 0.1250 r_work: 0.3399 rms_B_bonded: 2.08 restraints_weight: 0.0625 r_work: 0.3384 rms_B_bonded: 2.20 restraints_weight: 0.0312 r_work: 0.3368 rms_B_bonded: 2.36 restraints_weight: 0.0156 r_work: 0.3351 rms_B_bonded: 2.56 restraints_weight: 0.0078 r_work: 0.3332 rms_B_bonded: 2.79 restraints_weight: 0.0039 r_work: 0.3312 rms_B_bonded: 3.05 restraints_weight: 0.0020 r_work: 0.3289 rms_B_bonded: 3.36 restraints_weight: 0.0010 r_work: 0.3265 rms_B_bonded: 3.71 restraints_weight: 0.0005 r_work: 0.3238 rms_B_bonded: 4.10 restraints_weight: 0.0002 r_work: 0.3209 rms_B_bonded: 4.55 restraints_weight: 0.0001 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.5137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.135 24604 Z= 0.324 Angle : 0.675 11.929 33364 Z= 0.352 Chirality : 0.047 0.188 3840 Planarity : 0.006 0.129 4349 Dihedral : 5.751 89.676 3417 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer Outliers : 0.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.83 % 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: -0.13 (0.15), residues: 3104 helix: 0.78 (0.15), residues: 1244 sheet: 0.21 (0.23), residues: 519 loop : -0.98 (0.17), residues: 1341 =============================================================================== Job complete usr+sys time: 9552.33 seconds wall clock time: 169 minutes 40.69 seconds (10180.69 seconds total)