Starting phenix.real_space_refine on Thu Apr 11 07:57:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8spw_40688/04_2024/8spw_40688_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8spw_40688/04_2024/8spw_40688.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8spw_40688/04_2024/8spw_40688.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8spw_40688/04_2024/8spw_40688.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8spw_40688/04_2024/8spw_40688_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8spw_40688/04_2024/8spw_40688_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 15 5.49 5 Mg 5 5.21 5 S 67 5.16 5 C 13830 2.51 5 N 3820 2.21 5 O 4223 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 498": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 21960 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 3636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3636 Classifications: {'peptide': 474} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 451} Chain: "B" Number of atoms: 3644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3644 Classifications: {'peptide': 475} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 452} Chain: "C" Number of atoms: 3650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3650 Classifications: {'peptide': 476} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 453} Chain: "D" Number of atoms: 3623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3623 Classifications: {'peptide': 470} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 446} Chain: "E" Number of atoms: 3623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3623 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 446} Chain: "F" Number of atoms: 3623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3623 Classifications: {'peptide': 470} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 446} 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: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 11.77, per 1000 atoms: 0.54 Number of scatterers: 21960 At special positions: 0 Unit cell: (112.56, 120.12, 126.84, 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 67 16.00 P 15 15.00 Mg 5 11.99 O 4223 8.00 N 3820 7.00 C 13830 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: 9.65 Conformation dependent library (CDL) restraints added in 4.4 seconds 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5148 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 102 helices and 22 sheets defined 39.7% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.63 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 187 removed outlier: 3.953A pdb=" N LYS A 187 " --> pdb=" O ILE A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 214 Processing helix chain 'A' and resid 217 through 220 Processing helix chain 'A' and resid 232 through 252 Proline residue: A 239 - end of helix removed outlier: 3.989A pdb=" N MET A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY A 246 " --> pdb=" O GLY A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 276 Processing helix chain 'A' and resid 290 through 300 removed outlier: 4.301A pdb=" N ARG A 300 " --> pdb=" O ARG A 296 " (cutoff:3.500A) 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 Processing helix chain 'A' and resid 346 through 350 Processing helix chain 'A' and resid 373 through 396 removed outlier: 4.185A pdb=" N THR A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA A 394 " --> pdb=" O ARG A 390 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N PHE A 395 " --> pdb=" O GLU A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 420 removed outlier: 3.570A pdb=" N LEU A 420 " --> pdb=" O THR A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 441 Processing helix chain 'A' and resid 450 through 466 removed outlier: 3.816A pdb=" N ARG A 454 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU A 459 " --> pdb=" O PHE A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 478 Processing helix chain 'A' and resid 484 through 497 removed outlier: 3.748A pdb=" N THR A 497 " --> pdb=" O ALA A 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 156 Processing helix chain 'B' and resid 175 through 187 removed outlier: 4.100A pdb=" N LYS B 187 " --> pdb=" O ILE B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 219 removed outlier: 4.688A pdb=" N HIS B 215 " --> pdb=" O THR B 211 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLY B 216 " --> pdb=" O LEU B 212 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ALA B 217 " --> pdb=" O ARG B 213 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N LEU B 218 " --> pdb=" O LYS B 214 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ASP B 219 " --> pdb=" O HIS B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 252 Proline residue: B 239 - end of helix removed outlier: 3.697A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 276 Processing helix chain 'B' and resid 288 through 300 removed outlier: 4.184A pdb=" N PHE B 291 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HIS B 294 " --> pdb=" O PHE B 291 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG B 296 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU B 299 " --> pdb=" O ARG B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 329 through 335 Processing helix chain 'B' and resid 346 through 351 Processing helix chain 'B' and resid 373 through 378 Processing helix chain 'B' and resid 381 through 398 Processing helix chain 'B' and resid 404 through 420 Processing helix chain 'B' and resid 430 through 442 Processing helix chain 'B' and resid 445 through 447 No H-bonds generated for 'chain 'B' and resid 445 through 447' Processing helix chain 'B' and resid 451 through 466 removed outlier: 3.670A pdb=" N ARG B 454 " --> pdb=" O GLU B 451 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU B 459 " --> pdb=" O PHE B 456 " (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 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 185 Processing helix chain 'C' and resid 202 through 214 Processing helix chain 'C' and resid 232 through 251 Proline residue: C 239 - end of helix removed outlier: 3.671A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 277 Processing helix chain 'C' and resid 288 through 300 removed outlier: 4.092A pdb=" N PHE C 291 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER C 295 " --> pdb=" O TYR C 292 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG C 296 " --> pdb=" O LEU C 293 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU C 299 " --> pdb=" O ARG C 296 " (cutoff:3.500A) removed outlier: 3.711A 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 335 Processing helix chain 'C' and resid 346 through 351 Processing helix chain 'C' and resid 373 through 398 removed outlier: 4.040A pdb=" N GLY C 380 " --> pdb=" O LYS C 376 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N THR C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LEU C 382 " --> pdb=" O VAL C 378 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG C 383 " --> pdb=" O ALA C 379 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LEU C 384 " --> pdb=" O GLY C 380 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA C 394 " --> pdb=" O ARG C 390 " (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 444 through 446 No H-bonds generated for 'chain 'C' and resid 444 through 446' Processing helix chain 'C' and resid 450 through 466 removed outlier: 4.243A pdb=" N ARG C 454 " --> pdb=" O VAL C 450 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ARG C 455 " --> pdb=" O GLU C 451 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS C 458 " --> pdb=" O ARG C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 478 Processing helix chain 'C' and resid 484 through 497 Processing helix chain 'D' and resid 89 through 91 No H-bonds generated for 'chain 'D' and resid 89 through 91' Processing helix chain 'D' and resid 125 through 127 No H-bonds generated for 'chain 'D' and resid 125 through 127' Processing helix chain 'D' and resid 140 through 145 Processing helix chain 'D' and resid 164 through 178 removed outlier: 3.700A pdb=" N GLU D 178 " --> pdb=" O ASN D 174 " (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 241 removed outlier: 4.676A pdb=" N ALA D 229 " --> pdb=" O ARG D 225 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N LEU D 230 " --> pdb=" O MET D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 268 removed outlier: 3.747A pdb=" N ALA D 266 " --> pdb=" O GLU D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 291 Processing helix chain 'D' and resid 316 through 324 removed outlier: 3.993A pdb=" N SER D 323 " --> pdb=" O ALA D 319 " (cutoff:3.500A) removed outlier: 4.255A 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: 4.289A pdb=" N ASP D 382 " --> pdb=" O LYS D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 409 removed outlier: 3.692A pdb=" N ARG D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 420 Processing helix chain 'D' and resid 430 through 441 Processing helix chain 'D' and resid 451 through 453 No H-bonds generated for 'chain 'D' and resid 451 through 453' Processing helix chain 'D' and resid 459 through 469 Processing helix chain 'E' and resid 89 through 91 No H-bonds generated for 'chain 'E' and resid 89 through 91' Processing helix chain 'E' and resid 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: 4.823A pdb=" N ALA E 229 " --> pdb=" O ARG E 225 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LEU E 230 " --> pdb=" O MET E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 268 Processing helix chain 'E' and resid 282 through 290 Processing helix chain 'E' and resid 316 through 324 removed outlier: 3.892A pdb=" N HIS E 324 " --> pdb=" O THR E 320 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 337 Processing helix chain 'E' and resid 356 through 359 No H-bonds generated for 'chain 'E' and resid 356 through 359' Processing helix chain 'E' and resid 361 through 387 removed outlier: 4.365A pdb=" N ASP E 382 " --> pdb=" O LYS E 378 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ILE E 383 " --> pdb=" O GLU E 379 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE E 386 " --> pdb=" O ASP E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 394 through 409 removed outlier: 3.758A pdb=" N ARG E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 415 through 421 removed outlier: 4.054A pdb=" N THR E 421 " --> pdb=" O GLU E 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 430 through 442 Processing helix chain 'E' and resid 450 through 453 Processing helix chain 'E' and resid 459 through 469 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 144 Processing helix chain 'F' and resid 164 through 177 Processing helix chain 'F' and resid 193 through 205 removed outlier: 3.644A pdb=" N LEU F 198 " --> pdb=" O GLY F 195 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N MET F 202 " --> pdb=" O TYR F 199 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS F 203 " --> pdb=" O HIS F 200 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER F 205 " --> pdb=" O MET F 202 " (cutoff:3.500A) Processing helix chain 'F' and resid 207 through 209 No H-bonds generated for 'chain 'F' and resid 207 through 209' Processing helix chain 'F' and resid 222 through 242 removed outlier: 5.140A pdb=" N ALA F 229 " --> pdb=" O ARG F 225 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LEU F 230 " --> pdb=" O MET F 226 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA F 236 " --> pdb=" O GLY F 232 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE F 239 " --> pdb=" O MET F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 268 removed outlier: 3.923A pdb=" N GLU F 263 " --> pdb=" O GLN F 259 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA F 266 " --> pdb=" O SER F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 291 removed outlier: 3.709A pdb=" N LEU F 288 " --> pdb=" O GLU F 284 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ARG F 291 " --> pdb=" O GLN F 287 " (cutoff:3.500A) Processing helix chain 'F' and resid 316 through 324 removed outlier: 3.908A pdb=" N HIS F 324 " --> pdb=" O THR F 320 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 338 removed outlier: 3.647A pdb=" N MET F 338 " --> pdb=" O LYS F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 361 through 386 removed outlier: 3.554A pdb=" N ILE F 386 " --> pdb=" O ASP F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 through 410 removed outlier: 3.719A pdb=" N VAL F 399 " --> pdb=" O GLU F 395 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL F 400 " --> pdb=" O ASP F 396 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG F 405 " --> pdb=" O HIS F 401 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU F 410 " --> pdb=" O ILE F 406 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 419 removed outlier: 3.715A pdb=" N GLN F 419 " --> pdb=" O VAL F 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 416 through 419' Processing helix chain 'F' and resid 430 through 442 removed outlier: 3.942A pdb=" N GLU F 439 " --> pdb=" O ARG F 435 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE F 440 " --> pdb=" O GLY F 436 " (cutoff:3.500A) Processing helix chain 'F' and resid 450 through 452 No H-bonds generated for 'chain 'F' and resid 450 through 452' Processing helix chain 'F' and resid 459 through 468 Processing sheet with id= A, first strand: chain 'A' and resid 31 through 35 removed outlier: 6.230A pdb=" N ARG A 40 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N VAL A 34 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL A 74 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N ALA A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 96 through 99 Processing sheet with id= C, first strand: chain 'A' and resid 341 through 344 removed outlier: 7.054A pdb=" N LEU A 166 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N LEU A 344 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ILE A 168 " --> pdb=" O LEU A 344 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 312 through 315 removed outlier: 3.952A pdb=" N ILE A 222 " --> pdb=" O SER A 193 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 28 through 30 removed outlier: 3.784A pdb=" N MET B 60 " --> pdb=" O LEU B 76 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N GLY B 72 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N LEU B 66 " --> pdb=" O ASN B 70 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ASN B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N HIS B 42 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N VAL B 31 " --> pdb=" O HIS B 42 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 96 through 99 Processing sheet with id= G, first strand: chain 'B' and resid 341 through 344 removed outlier: 6.770A pdb=" N LEU B 166 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N LEU B 344 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ILE B 168 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLY B 169 " --> pdb=" O VAL B 319 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 222 through 226 removed outlier: 6.334A pdb=" N SER B 312 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N VAL B 258 " --> pdb=" O SER B 312 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N THR B 314 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N TYR B 260 " --> pdb=" O THR B 314 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 28 through 30 removed outlier: 6.893A pdb=" N GLY C 72 " --> pdb=" O LEU C 64 " (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 341 through 344 removed outlier: 6.682A pdb=" N LEU C 166 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N LEU C 344 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ILE C 168 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY C 169 " --> pdb=" O VAL C 319 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 221 through 227 removed outlier: 6.651A pdb=" N SER C 193 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N VAL C 224 " --> pdb=" O SER C 193 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N TYR C 195 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N ALA C 226 " --> pdb=" O TYR C 195 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ALA C 197 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR C 260 " --> pdb=" O LEU C 316 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 75 through 77 removed outlier: 6.723A pdb=" N ASP D 15 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N VAL D 9 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL D 13 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N ILE D 62 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N VAL D 50 " --> pdb=" O ILE D 62 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE D 44 " --> pdb=" O HIS D 34 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 84 through 86 Processing sheet with id= O, first strand: chain 'D' and resid 327 through 330 removed outlier: 7.039A pdb=" N VAL D 247 " --> pdb=" O THR D 301 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N ILE D 303 " --> pdb=" O VAL D 247 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU D 249 " --> pdb=" O ILE D 303 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N ALA D 305 " --> pdb=" O LEU D 249 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N ILE D 251 " --> pdb=" O ALA D 305 " (cutoff:3.500A) removed outlier: 8.777A pdb=" N TYR D 307 " --> pdb=" O ILE D 251 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE D 182 " --> pdb=" O LEU D 248 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N PHE D 250 " --> pdb=" O ILE D 182 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL D 184 " --> pdb=" O PHE D 250 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N ASP D 252 " --> pdb=" O VAL D 184 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ALA D 186 " --> pdb=" O ASP D 252 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY D 187 " --> pdb=" O VAL D 214 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 5 through 10 removed outlier: 3.539A pdb=" N ARG E 5 " --> pdb=" O LYS E 17 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ASP E 15 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N VAL E 9 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N VAL E 13 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ILE E 62 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 5.403A 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 87 removed outlier: 3.704A pdb=" N ARG E 114 " --> pdb=" O VAL E 87 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 327 through 331 removed outlier: 3.581A pdb=" N ALA E 327 " --> pdb=" O LYS E 153 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N SER E 302 " --> pdb=" O ILE E 154 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N LEU E 156 " --> pdb=" O SER E 302 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLN E 304 " --> pdb=" O LEU E 156 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N GLY E 158 " --> pdb=" O GLN E 304 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ILE E 306 " --> pdb=" O GLY E 158 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA E 305 " --> pdb=" O ILE E 251 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 3 through 5 Processing sheet with id= T, first strand: chain 'F' and resid 29 through 33 removed outlier: 6.911A pdb=" N ARG F 60 " --> pdb=" O ALA F 51 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 84 through 86 Processing sheet with id= V, first strand: chain 'F' and resid 304 through 306 removed outlier: 6.517A pdb=" N ALA F 327 " --> pdb=" O GLY F 155 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N PHE F 157 " --> pdb=" O ALA F 327 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N THR F 329 " --> pdb=" O PHE F 157 " (cutoff:3.500A) 818 hydrogen bonds defined for protein. 2256 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: 6.66 Time building geometry restraints manager: 10.36 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: 7465 1.34 - 1.46: 2997 1.46 - 1.58: 11713 1.58 - 1.69: 21 1.69 - 1.81: 134 Bond restraints: 22330 Sorted by residual: bond pdb=" O2 PO4 E 501 " pdb=" P PO4 E 501 " ideal model delta sigma weight residual 1.567 1.500 0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" O3 PO4 E 501 " pdb=" P PO4 E 501 " ideal model delta sigma weight residual 1.569 1.505 0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" O4 PO4 E 501 " pdb=" P PO4 E 501 " ideal model delta sigma weight residual 1.568 1.505 0.063 2.00e-02 2.50e+03 9.94e+00 bond pdb=" O1 PO4 E 501 " pdb=" P PO4 E 501 " ideal model delta sigma weight residual 1.565 1.505 0.060 2.00e-02 2.50e+03 9.02e+00 bond pdb=" CA PRO B 280 " pdb=" C PRO B 280 " ideal model delta sigma weight residual 1.517 1.528 -0.011 6.70e-03 2.23e+04 2.54e+00 ... (remaining 22325 not shown) Histogram of bond angle deviations from ideal: 98.59 - 106.82: 726 106.82 - 115.05: 13567 115.05 - 123.28: 15189 123.28 - 131.51: 779 131.51 - 139.74: 22 Bond angle restraints: 30283 Sorted by residual: angle pdb=" C LYS C 377 " pdb=" N VAL C 378 " pdb=" CA VAL C 378 " ideal model delta sigma weight residual 123.08 119.52 3.56 1.01e+00 9.80e-01 1.24e+01 angle pdb=" N VAL F 132 " pdb=" CA VAL F 132 " pdb=" C VAL F 132 " ideal model delta sigma weight residual 113.71 110.78 2.93 9.50e-01 1.11e+00 9.54e+00 angle pdb=" N ASP A 262 " pdb=" CA ASP A 262 " pdb=" C ASP A 262 " ideal model delta sigma weight residual 107.49 112.85 -5.36 1.74e+00 3.30e-01 9.50e+00 angle pdb=" CA ILE F 7 " pdb=" C ILE F 7 " pdb=" N GLN F 8 " ideal model delta sigma weight residual 116.60 120.76 -4.16 1.45e+00 4.76e-01 8.23e+00 angle pdb=" N GLY D 223 " pdb=" CA GLY D 223 " pdb=" C GLY D 223 " ideal model delta sigma weight residual 112.83 116.19 -3.36 1.22e+00 6.72e-01 7.57e+00 ... (remaining 30278 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.84: 13164 28.84 - 57.68: 409 57.68 - 86.52: 42 86.52 - 115.36: 4 115.36 - 144.20: 1 Dihedral angle restraints: 13620 sinusoidal: 5565 harmonic: 8055 Sorted by residual: dihedral pdb=" O2A ADP E 500 " pdb=" O3A ADP E 500 " pdb=" PA ADP E 500 " pdb=" PB ADP E 500 " ideal model delta sinusoidal sigma weight residual -60.00 84.20 -144.20 1 2.00e+01 2.50e-03 4.35e+01 dihedral pdb=" O1B ADP E 500 " pdb=" O3A ADP E 500 " pdb=" PB ADP E 500 " pdb=" PA ADP E 500 " ideal model delta sinusoidal sigma weight residual -60.00 -167.52 107.51 1 2.00e+01 2.50e-03 3.12e+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 180.00 158.15 21.85 0 5.00e+00 4.00e-02 1.91e+01 ... (remaining 13617 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1942 0.029 - 0.058: 968 0.058 - 0.087: 296 0.087 - 0.117: 207 0.117 - 0.146: 67 Chirality restraints: 3480 Sorted by residual: chirality pdb=" CA ILE A 38 " pdb=" N ILE A 38 " pdb=" C ILE A 38 " pdb=" CB ILE A 38 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.31e-01 chirality pdb=" CA PRO D 309 " pdb=" N PRO D 309 " pdb=" C PRO D 309 " pdb=" CB PRO D 309 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.14 2.00e-01 2.50e+01 5.20e-01 chirality pdb=" CA ILE A 342 " pdb=" N ILE A 342 " pdb=" C ILE A 342 " pdb=" CB ILE A 342 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.14e-01 ... (remaining 3477 not shown) Planarity restraints: 3960 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR F 199 " 0.011 2.00e-02 2.50e+03 2.27e-02 5.13e+00 pdb=" C TYR F 199 " -0.039 2.00e-02 2.50e+03 pdb=" O TYR F 199 " 0.015 2.00e-02 2.50e+03 pdb=" N HIS F 200 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS D 173 " 0.009 2.00e-02 2.50e+03 1.80e-02 3.25e+00 pdb=" C HIS D 173 " -0.031 2.00e-02 2.50e+03 pdb=" O HIS D 173 " 0.012 2.00e-02 2.50e+03 pdb=" N ASN D 174 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG D 120 " -0.029 5.00e-02 4.00e+02 4.40e-02 3.09e+00 pdb=" N PRO D 121 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO D 121 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 121 " -0.024 5.00e-02 4.00e+02 ... (remaining 3957 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 73 2.46 - 3.07: 14951 3.07 - 3.68: 32347 3.68 - 4.29: 47350 4.29 - 4.90: 78587 Nonbonded interactions: 173308 Sorted by model distance: nonbonded pdb=" O3 PO4 E 501 " pdb="MG MG E 502 " model vdw 1.846 2.170 nonbonded pdb=" O3B ADP E 500 " pdb="MG MG E 502 " model vdw 1.888 2.170 nonbonded pdb=" O2G ATP B 600 " pdb="MG MG B 601 " model vdw 1.909 2.170 nonbonded pdb=" O2B ATP D 500 " pdb="MG MG D 501 " model vdw 1.926 2.170 nonbonded pdb=" OG1 THR C 176 " pdb="MG MG C 601 " model vdw 2.011 2.170 ... (remaining 173303 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) selection = (chain 'E' and resid 2 through 470) selection = (chain 'F' and resid 2 through 470) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 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: 0.010 Extract box with map and model: 4.950 Check model and map are aligned: 0.330 Set scattering table: 0.210 Process input model: 60.960 Find NCS groups from input model: 1.810 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6530 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 22330 Z= 0.219 Angle : 0.611 7.113 30283 Z= 0.346 Chirality : 0.045 0.146 3480 Planarity : 0.005 0.044 3960 Dihedral : 13.740 144.202 8472 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.11 % Allowed : 7.72 % Favored : 90.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % 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: -0.04 (0.15), residues: 2823 helix: 0.68 (0.15), residues: 1110 sheet: 0.17 (0.24), residues: 427 loop : -0.64 (0.17), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 200 PHE 0.026 0.002 PHE C 494 TYR 0.015 0.002 TYR F 238 ARG 0.003 0.000 ARG F 240 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 2319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 572 time to evaluate : 2.439 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: A 444 PHE cc_start: 0.6239 (m-80) cc_final: 0.6007 (m-80) REVERT: A 471 LEU cc_start: 0.7510 (mt) cc_final: 0.7198 (mp) REVERT: B 191 MET cc_start: 0.6369 (mmt) cc_final: 0.5695 (mmt) REVERT: B 236 PHE cc_start: 0.6486 (OUTLIER) cc_final: 0.6244 (p90) REVERT: B 318 PHE cc_start: 0.4423 (m-80) cc_final: 0.4030 (m-80) REVERT: C 95 MET cc_start: 0.5219 (tpp) cc_final: 0.4984 (mmm) REVERT: C 361 LEU cc_start: 0.7258 (tp) cc_final: 0.6991 (mp) REVERT: E 202 MET cc_start: 0.5628 (mmt) cc_final: 0.5411 (ttm) REVERT: E 285 MET cc_start: 0.8383 (tpp) cc_final: 0.7959 (tpp) REVERT: F 49 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7150 (pt0) REVERT: F 256 ARG cc_start: 0.4814 (OUTLIER) cc_final: 0.4292 (mtm-85) REVERT: F 264 VAL cc_start: 0.2961 (t) cc_final: 0.2732 (t) outliers start: 49 outliers final: 12 residues processed: 610 average time/residue: 0.4208 time to fit residues: 376.2041 Evaluate side-chains 340 residues out of total 2319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 325 time to evaluate : 2.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 236 PHE Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 196 ASN Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 256 ARG Chi-restraints excluded: chain F residue 359 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 238 optimal weight: 0.8980 chunk 213 optimal weight: 0.9980 chunk 118 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 144 optimal weight: 10.0000 chunk 114 optimal weight: 0.9980 chunk 221 optimal weight: 10.0000 chunk 85 optimal weight: 30.0000 chunk 134 optimal weight: 9.9990 chunk 164 optimal weight: 7.9990 chunk 256 optimal weight: 5.9990 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 ASN A 186 GLN A 345 GLN A 422 GLN A 474 HIS ** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 143 HIS ** C 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 330 ASN ** E 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 119 HIS ** E 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 259 GLN E 289 GLN E 304 GLN F 53 HIS F 253 ASN ** F 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6761 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 22330 Z= 0.239 Angle : 0.612 7.700 30283 Z= 0.323 Chirality : 0.046 0.293 3480 Planarity : 0.005 0.051 3960 Dihedral : 9.027 121.344 3254 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.28 % Allowed : 15.22 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % 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: 2823 helix: 0.77 (0.15), residues: 1111 sheet: 0.13 (0.24), residues: 427 loop : -0.78 (0.17), residues: 1285 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 173 PHE 0.039 0.002 PHE E 414 TYR 0.019 0.002 TYR C 195 ARG 0.008 0.001 ARG D 5 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 343 time to evaluate : 2.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 64 MET cc_start: 0.5622 (mmm) cc_final: 0.5377 (mmp) REVERT: D 235 MET cc_start: 0.6545 (mtt) cc_final: 0.6179 (mtp) REVERT: D 271 MET cc_start: 0.6687 (mtt) cc_final: 0.6333 (mtt) REVERT: E 202 MET cc_start: 0.5819 (mmt) cc_final: 0.3880 (mtp) REVERT: E 268 LEU cc_start: 0.6429 (OUTLIER) cc_final: 0.6026 (mm) REVERT: E 285 MET cc_start: 0.8240 (tpp) cc_final: 0.7927 (tpp) REVERT: E 469 MET cc_start: 0.5886 (ttm) cc_final: 0.5685 (mtt) REVERT: F 49 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.7036 (pt0) REVERT: F 235 MET cc_start: 0.6312 (mmt) cc_final: 0.6100 (mmt) REVERT: F 253 ASN cc_start: 0.4930 (OUTLIER) cc_final: 0.4635 (p0) REVERT: F 285 MET cc_start: 0.7837 (OUTLIER) cc_final: 0.7383 (ttm) REVERT: F 404 ARG cc_start: 0.7839 (mmm-85) cc_final: 0.7438 (tpp80) outliers start: 76 outliers final: 47 residues processed: 402 average time/residue: 0.3466 time to fit residues: 215.9358 Evaluate side-chains 339 residues out of total 2319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 288 time to evaluate : 2.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 200 GLN Chi-restraints excluded: chain C residue 236 PHE Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 34 HIS Chi-restraints excluded: chain D residue 101 GLU Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain D residue 419 GLN Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 196 ASN Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 411 SER Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 251 ILE Chi-restraints excluded: chain F residue 253 ASN Chi-restraints excluded: chain F residue 285 MET Chi-restraints excluded: chain F residue 321 THR Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 397 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 142 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 213 optimal weight: 8.9990 chunk 174 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 chunk 256 optimal weight: 7.9990 chunk 277 optimal weight: 9.9990 chunk 228 optimal weight: 20.0000 chunk 254 optimal weight: 7.9990 chunk 87 optimal weight: 9.9990 chunk 205 optimal weight: 7.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 ASN A 422 GLN A 474 HIS B 185 ASN B 294 HIS ** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 ASN C 425 HIS ** C 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 HIS D 330 ASN ** E 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 169 GLN ** F 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 324 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.3988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.064 22330 Z= 0.501 Angle : 0.814 8.765 30283 Z= 0.433 Chirality : 0.054 0.263 3480 Planarity : 0.007 0.064 3960 Dihedral : 9.336 116.231 3247 Min Nonbonded Distance : 1.696 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 6.38 % Allowed : 17.46 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % 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: -1.17 (0.15), residues: 2823 helix: -0.03 (0.15), residues: 1076 sheet: -0.39 (0.23), residues: 447 loop : -1.52 (0.16), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS A 470 PHE 0.059 0.003 PHE E 414 TYR 0.033 0.003 TYR F 199 ARG 0.009 0.001 ARG C 296 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 2319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 331 time to evaluate : 2.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 THR cc_start: 0.7532 (OUTLIER) cc_final: 0.7289 (t) REVERT: B 32 ILE cc_start: 0.8086 (OUTLIER) cc_final: 0.7871 (mm) REVERT: B 295 SER cc_start: 0.7111 (t) cc_final: 0.6843 (p) REVERT: D 77 ILE cc_start: 0.6286 (OUTLIER) cc_final: 0.6051 (mm) REVERT: D 167 LEU cc_start: 0.7494 (OUTLIER) cc_final: 0.7174 (mp) REVERT: E 259 GLN cc_start: 0.7452 (OUTLIER) cc_final: 0.6570 (mp-120) REVERT: E 268 LEU cc_start: 0.6643 (OUTLIER) cc_final: 0.6140 (mm) REVERT: E 285 MET cc_start: 0.8384 (tpp) cc_final: 0.8090 (tpp) REVERT: E 328 THR cc_start: 0.8075 (OUTLIER) cc_final: 0.7873 (p) REVERT: E 469 MET cc_start: 0.6037 (ttm) cc_final: 0.5778 (mtt) REVERT: F 49 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.7128 (tt0) REVERT: F 191 ARG cc_start: 0.5306 (OUTLIER) cc_final: 0.2750 (mmp80) REVERT: F 285 MET cc_start: 0.7901 (OUTLIER) cc_final: 0.7265 (ttm) outliers start: 148 outliers final: 95 residues processed: 441 average time/residue: 0.3617 time to fit residues: 243.0609 Evaluate side-chains 385 residues out of total 2319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 280 time to evaluate : 2.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 483 ASN Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 200 GLN Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 236 PHE Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 406 THR Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 34 HIS Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 101 GLU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 322 PHE Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 368 ARG Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 419 GLN Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 259 GLN Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 328 THR Chi-restraints excluded: chain E residue 411 SER Chi-restraints excluded: chain E residue 423 GLN Chi-restraints excluded: chain E residue 447 HIS Chi-restraints excluded: chain F residue 18 PHE Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 191 ARG Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 251 ILE Chi-restraints excluded: chain F residue 285 MET Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain F residue 321 THR Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 394 ASP Chi-restraints excluded: chain F residue 437 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 253 optimal weight: 0.8980 chunk 192 optimal weight: 1.9990 chunk 133 optimal weight: 9.9990 chunk 28 optimal weight: 0.0870 chunk 122 optimal weight: 1.9990 chunk 172 optimal weight: 9.9990 chunk 257 optimal weight: 1.9990 chunk 272 optimal weight: 5.9990 chunk 134 optimal weight: 6.9990 chunk 244 optimal weight: 0.0770 chunk 73 optimal weight: 0.9980 overall best weight: 0.8118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 HIS ** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 294 HIS ** C 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 HIS D 330 ASN E 169 GLN ** F 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 253 ASN ** F 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6884 moved from start: 0.4105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 22330 Z= 0.169 Angle : 0.581 13.550 30283 Z= 0.300 Chirality : 0.045 0.317 3480 Planarity : 0.005 0.049 3960 Dihedral : 8.379 87.931 3244 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.67 % Allowed : 21.35 % Favored : 74.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % 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: -0.55 (0.15), residues: 2823 helix: 0.57 (0.16), residues: 1090 sheet: -0.14 (0.24), residues: 428 loop : -1.21 (0.16), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 474 PHE 0.034 0.002 PHE E 414 TYR 0.020 0.001 TYR F 199 ARG 0.007 0.000 ARG C 127 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 316 time to evaluate : 2.509 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 93 ARG cc_start: 0.6545 (ptt-90) cc_final: 0.6342 (ptt-90) REVERT: C 198 ILE cc_start: 0.5670 (OUTLIER) cc_final: 0.5319 (mt) REVERT: C 448 ILE cc_start: 0.8335 (OUTLIER) cc_final: 0.8080 (mm) REVERT: D 64 MET cc_start: 0.5821 (mmm) cc_final: 0.5456 (mmp) REVERT: D 235 MET cc_start: 0.6561 (mtt) cc_final: 0.6302 (mtp) REVERT: D 288 LEU cc_start: 0.8061 (tp) cc_final: 0.7567 (tp) REVERT: E 196 ASN cc_start: 0.6220 (OUTLIER) cc_final: 0.5365 (t0) REVERT: E 285 MET cc_start: 0.8058 (tpp) cc_final: 0.7751 (tpp) REVERT: E 328 THR cc_start: 0.7982 (OUTLIER) cc_final: 0.7770 (p) REVERT: E 469 MET cc_start: 0.5987 (ttm) cc_final: 0.5731 (mtt) REVERT: F 49 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.7025 (tt0) REVERT: F 404 ARG cc_start: 0.7797 (mmm-85) cc_final: 0.7373 (tpp80) outliers start: 85 outliers final: 49 residues processed: 386 average time/residue: 0.3175 time to fit residues: 192.3264 Evaluate side-chains 324 residues out of total 2319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 270 time to evaluate : 2.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 260 TYR Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 483 ASN Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 200 GLN Chi-restraints excluded: chain C residue 236 PHE Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 294 HIS Chi-restraints excluded: chain C residue 448 ILE Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 34 HIS Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 74 MET Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 196 ASN Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 328 THR Chi-restraints excluded: chain E residue 423 GLN Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 251 ILE Chi-restraints excluded: chain F residue 306 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 227 optimal weight: 9.9990 chunk 154 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 202 optimal weight: 0.8980 chunk 112 optimal weight: 7.9990 chunk 232 optimal weight: 6.9990 chunk 188 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 139 optimal weight: 10.0000 chunk 244 optimal weight: 8.9990 chunk 68 optimal weight: 4.9990 overall best weight: 3.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 HIS ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 HIS ** C 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 330 ASN ** E 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 173 HIS F 253 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 0.4522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 22330 Z= 0.329 Angle : 0.659 9.606 30283 Z= 0.344 Chirality : 0.047 0.216 3480 Planarity : 0.005 0.048 3960 Dihedral : 8.422 86.766 3242 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 6.30 % Allowed : 19.71 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % 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: -0.93 (0.15), residues: 2823 helix: 0.34 (0.15), residues: 1075 sheet: -0.42 (0.24), residues: 420 loop : -1.47 (0.16), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.027 0.001 HIS C 294 PHE 0.034 0.002 PHE C 460 TYR 0.019 0.002 TYR B 240 ARG 0.006 0.001 ARG A 278 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 2319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 294 time to evaluate : 2.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 THR cc_start: 0.7629 (OUTLIER) cc_final: 0.7413 (t) REVERT: B 295 SER cc_start: 0.6953 (t) cc_final: 0.6726 (p) REVERT: D 235 MET cc_start: 0.6668 (mtt) cc_final: 0.6329 (mtp) REVERT: D 268 LEU cc_start: 0.7081 (OUTLIER) cc_final: 0.6872 (mm) REVERT: E 196 ASN cc_start: 0.6522 (OUTLIER) cc_final: 0.5658 (t0) REVERT: E 268 LEU cc_start: 0.6773 (OUTLIER) cc_final: 0.6298 (mm) REVERT: E 285 MET cc_start: 0.8240 (tpp) cc_final: 0.7947 (tpp) REVERT: E 328 THR cc_start: 0.7943 (OUTLIER) cc_final: 0.7742 (p) REVERT: E 369 LYS cc_start: 0.6718 (pttm) cc_final: 0.6356 (tttp) REVERT: E 469 MET cc_start: 0.5960 (ttm) cc_final: 0.5721 (mtt) REVERT: F 49 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.7057 (tt0) REVERT: F 191 ARG cc_start: 0.5293 (OUTLIER) cc_final: 0.3013 (tpp-160) REVERT: F 201 GLU cc_start: 0.6655 (OUTLIER) cc_final: 0.6095 (mm-30) REVERT: F 253 ASN cc_start: 0.5028 (OUTLIER) cc_final: 0.4554 (p0) REVERT: F 304 GLN cc_start: 0.6990 (OUTLIER) cc_final: 0.6763 (pt0) REVERT: F 404 ARG cc_start: 0.7819 (mmm-85) cc_final: 0.7305 (mmm-85) outliers start: 146 outliers final: 91 residues processed: 409 average time/residue: 0.3301 time to fit residues: 211.7906 Evaluate side-chains 372 residues out of total 2319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 271 time to evaluate : 2.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 260 TYR Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 433 GLN Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 236 PHE Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 406 THR Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 34 HIS Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 101 GLU Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 368 ARG Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain D residue 419 GLN Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 196 ASN Chi-restraints excluded: chain E residue 197 ASP Chi-restraints excluded: chain E residue 202 MET Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 278 GLN Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 328 THR Chi-restraints excluded: chain E residue 411 SER Chi-restraints excluded: chain E residue 413 ASN Chi-restraints excluded: chain E residue 423 GLN Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 191 ARG Chi-restraints excluded: chain F residue 193 ARG Chi-restraints excluded: chain F residue 201 GLU Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 251 ILE Chi-restraints excluded: chain F residue 253 ASN Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 304 GLN Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain F residue 437 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 91 optimal weight: 20.0000 chunk 245 optimal weight: 9.9990 chunk 53 optimal weight: 8.9990 chunk 160 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 272 optimal weight: 10.0000 chunk 226 optimal weight: 20.0000 chunk 126 optimal weight: 20.0000 chunk 22 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 143 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 GLN D 173 HIS ** E 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 412 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.4895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 22330 Z= 0.395 Angle : 0.702 9.178 30283 Z= 0.367 Chirality : 0.049 0.181 3480 Planarity : 0.006 0.049 3960 Dihedral : 8.560 85.687 3242 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 6.21 % Allowed : 21.26 % Favored : 72.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % 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: -1.22 (0.15), residues: 2823 helix: 0.13 (0.15), residues: 1066 sheet: -0.57 (0.25), residues: 412 loop : -1.65 (0.16), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS C 294 PHE 0.023 0.002 PHE F 437 TYR 0.022 0.002 TYR B 240 ARG 0.004 0.001 ARG C 296 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 287 time to evaluate : 2.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 THR cc_start: 0.7583 (OUTLIER) cc_final: 0.7374 (t) REVERT: B 295 SER cc_start: 0.6988 (t) cc_final: 0.6698 (p) REVERT: B 452 ASP cc_start: 0.6540 (t0) cc_final: 0.6270 (t0) REVERT: C 93 ARG cc_start: 0.6772 (ptt-90) cc_final: 0.6451 (ptt-90) REVERT: D 235 MET cc_start: 0.6579 (mtt) cc_final: 0.6243 (mtp) REVERT: E 196 ASN cc_start: 0.6728 (OUTLIER) cc_final: 0.5891 (t0) REVERT: E 268 LEU cc_start: 0.6767 (OUTLIER) cc_final: 0.6263 (mm) REVERT: E 285 MET cc_start: 0.8245 (tpp) cc_final: 0.7933 (tpp) REVERT: E 369 LYS cc_start: 0.6902 (pttm) cc_final: 0.6501 (tptm) REVERT: E 469 MET cc_start: 0.5965 (ttm) cc_final: 0.5729 (mtt) REVERT: F 49 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.7073 (tt0) REVERT: F 191 ARG cc_start: 0.5240 (OUTLIER) cc_final: 0.3089 (tpp-160) REVERT: F 201 GLU cc_start: 0.6484 (OUTLIER) cc_final: 0.6033 (mm-30) REVERT: F 404 ARG cc_start: 0.7837 (mmm-85) cc_final: 0.7348 (mmm-85) outliers start: 144 outliers final: 106 residues processed: 399 average time/residue: 0.3404 time to fit residues: 212.0938 Evaluate side-chains 382 residues out of total 2319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 270 time to evaluate : 2.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 260 TYR Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 433 GLN Chi-restraints excluded: chain B residue 483 ASN Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 236 PHE Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 406 THR Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 34 HIS Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 368 ARG Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain D residue 419 GLN Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 74 MET Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 177 GLN Chi-restraints excluded: chain E residue 196 ASN Chi-restraints excluded: chain E residue 197 ASP Chi-restraints excluded: chain E residue 202 MET Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 278 GLN Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 328 THR Chi-restraints excluded: chain E residue 411 SER Chi-restraints excluded: chain E residue 413 ASN Chi-restraints excluded: chain E residue 423 GLN Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 18 PHE Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 191 ARG Chi-restraints excluded: chain F residue 193 ARG Chi-restraints excluded: chain F residue 201 GLU Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 251 ILE Chi-restraints excluded: chain F residue 253 ASN Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 304 GLN Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain F residue 400 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 263 optimal weight: 3.9990 chunk 30 optimal weight: 0.1980 chunk 155 optimal weight: 1.9990 chunk 199 optimal weight: 4.9990 chunk 154 optimal weight: 0.9990 chunk 229 optimal weight: 0.9990 chunk 152 optimal weight: 9.9990 chunk 271 optimal weight: 0.8980 chunk 170 optimal weight: 3.9990 chunk 165 optimal weight: 8.9990 chunk 125 optimal weight: 5.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 470 HIS ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 GLN ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 ASN E 372 GLN F 253 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.4915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 22330 Z= 0.172 Angle : 0.571 9.718 30283 Z= 0.293 Chirality : 0.044 0.170 3480 Planarity : 0.005 0.051 3960 Dihedral : 7.893 75.179 3240 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.92 % Allowed : 23.98 % Favored : 72.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % 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: -0.79 (0.15), residues: 2823 helix: 0.53 (0.16), residues: 1073 sheet: -0.48 (0.24), residues: 432 loop : -1.41 (0.16), residues: 1318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 474 PHE 0.028 0.001 PHE C 460 TYR 0.042 0.001 TYR C 461 ARG 0.007 0.000 ARG A 278 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 282 time to evaluate : 2.470 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 176 THR cc_start: 0.8107 (m) cc_final: 0.7807 (p) REVERT: C 101 GLU cc_start: 0.6686 (OUTLIER) cc_final: 0.6441 (mp0) REVERT: C 198 ILE cc_start: 0.5573 (OUTLIER) cc_final: 0.5264 (mt) REVERT: C 415 ARG cc_start: 0.7995 (mtt90) cc_final: 0.7771 (mpt-90) REVERT: D 64 MET cc_start: 0.5413 (mmm) cc_final: 0.4868 (mmp) REVERT: D 235 MET cc_start: 0.6558 (mtt) cc_final: 0.6289 (mtp) REVERT: E 196 ASN cc_start: 0.6424 (OUTLIER) cc_final: 0.5545 (t0) REVERT: E 285 MET cc_start: 0.8058 (tpp) cc_final: 0.7724 (tpp) REVERT: E 328 THR cc_start: 0.7734 (OUTLIER) cc_final: 0.7500 (p) REVERT: E 369 LYS cc_start: 0.6637 (pttm) cc_final: 0.6237 (tttp) REVERT: E 469 MET cc_start: 0.5995 (ttm) cc_final: 0.5756 (mtt) REVERT: F 49 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6853 (tt0) REVERT: F 64 MET cc_start: 0.7479 (mmt) cc_final: 0.7061 (mmm) REVERT: F 191 ARG cc_start: 0.5115 (OUTLIER) cc_final: 0.3091 (tpp-160) REVERT: F 253 ASN cc_start: 0.5039 (OUTLIER) cc_final: 0.4635 (p0) REVERT: F 404 ARG cc_start: 0.7765 (mmm-85) cc_final: 0.7431 (tpp-160) outliers start: 91 outliers final: 67 residues processed: 350 average time/residue: 0.3515 time to fit residues: 190.3899 Evaluate side-chains 334 residues out of total 2319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 260 time to evaluate : 2.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 260 TYR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 433 GLN Chi-restraints excluded: chain B residue 483 ASN Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 200 GLN Chi-restraints excluded: chain C residue 236 PHE Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 34 HIS Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 368 ARG Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 35 LYS Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 74 MET Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 174 ASN Chi-restraints excluded: chain E residue 196 ASN Chi-restraints excluded: chain E residue 197 ASP Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 259 GLN Chi-restraints excluded: chain E residue 262 SER Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 328 THR Chi-restraints excluded: chain E residue 423 GLN Chi-restraints excluded: chain F residue 18 PHE Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 191 ARG Chi-restraints excluded: chain F residue 193 ARG Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 253 ASN Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain F residue 408 PHE Chi-restraints excluded: chain F residue 428 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 168 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 162 optimal weight: 6.9990 chunk 81 optimal weight: 20.0000 chunk 53 optimal weight: 6.9990 chunk 52 optimal weight: 9.9990 chunk 172 optimal weight: 0.0670 chunk 185 optimal weight: 6.9990 chunk 134 optimal weight: 8.9990 chunk 25 optimal weight: 0.9990 chunk 213 optimal weight: 1.9990 overall best weight: 1.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.5001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22330 Z= 0.202 Angle : 0.585 9.272 30283 Z= 0.300 Chirality : 0.045 0.292 3480 Planarity : 0.005 0.048 3960 Dihedral : 7.762 73.715 3240 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.03 % Favored : 94.93 % Rotamer: Outliers : 4.01 % Allowed : 24.49 % Favored : 71.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % 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: -0.74 (0.15), residues: 2823 helix: 0.57 (0.16), residues: 1073 sheet: -0.43 (0.24), residues: 437 loop : -1.40 (0.16), residues: 1313 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS A 470 PHE 0.027 0.001 PHE E 414 TYR 0.027 0.001 TYR C 461 ARG 0.007 0.000 ARG A 278 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 272 time to evaluate : 2.397 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 176 THR cc_start: 0.8125 (m) cc_final: 0.7818 (p) REVERT: C 101 GLU cc_start: 0.6690 (OUTLIER) cc_final: 0.6414 (mp0) REVERT: C 198 ILE cc_start: 0.5447 (OUTLIER) cc_final: 0.5174 (mt) REVERT: D 64 MET cc_start: 0.5875 (mmm) cc_final: 0.5649 (mmt) REVERT: D 235 MET cc_start: 0.6550 (mtt) cc_final: 0.6253 (mtp) REVERT: E 196 ASN cc_start: 0.6470 (OUTLIER) cc_final: 0.5634 (t0) REVERT: E 285 MET cc_start: 0.8067 (tpp) cc_final: 0.7658 (tpp) REVERT: E 328 THR cc_start: 0.7740 (OUTLIER) cc_final: 0.7520 (p) REVERT: E 369 LYS cc_start: 0.6654 (pttm) cc_final: 0.6241 (tttp) REVERT: E 469 MET cc_start: 0.5991 (ttm) cc_final: 0.5737 (mtt) REVERT: F 49 GLU cc_start: 0.7140 (OUTLIER) cc_final: 0.6922 (tt0) REVERT: F 191 ARG cc_start: 0.5181 (OUTLIER) cc_final: 0.3122 (tpp-160) REVERT: F 404 ARG cc_start: 0.7826 (mmm-85) cc_final: 0.7445 (tpp-160) outliers start: 93 outliers final: 73 residues processed: 349 average time/residue: 0.3354 time to fit residues: 183.6662 Evaluate side-chains 341 residues out of total 2319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 262 time to evaluate : 2.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 260 TYR Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 433 GLN Chi-restraints excluded: chain B residue 483 ASN Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 236 PHE Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 406 THR Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 34 HIS Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 368 ARG Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 447 HIS Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 74 MET Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 196 ASN Chi-restraints excluded: chain E residue 197 ASP Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 259 GLN Chi-restraints excluded: chain E residue 262 SER Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 328 THR Chi-restraints excluded: chain E residue 423 GLN Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 191 ARG Chi-restraints excluded: chain F residue 193 ARG Chi-restraints excluded: chain F residue 201 GLU Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 304 GLN Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 428 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 247 optimal weight: 5.9990 chunk 260 optimal weight: 0.8980 chunk 237 optimal weight: 8.9990 chunk 253 optimal weight: 9.9990 chunk 152 optimal weight: 0.2980 chunk 110 optimal weight: 6.9990 chunk 198 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 228 optimal weight: 10.0000 chunk 239 optimal weight: 2.9990 chunk 252 optimal weight: 4.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 365 GLN ** F 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.5170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 22330 Z= 0.246 Angle : 0.613 11.168 30283 Z= 0.315 Chirality : 0.045 0.161 3480 Planarity : 0.005 0.048 3960 Dihedral : 7.800 72.593 3240 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.53 % Favored : 94.44 % Rotamer: Outliers : 4.10 % Allowed : 24.32 % Favored : 71.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % 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: 2823 helix: 0.51 (0.16), residues: 1068 sheet: -0.47 (0.24), residues: 431 loop : -1.40 (0.16), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS A 470 PHE 0.034 0.002 PHE C 460 TYR 0.021 0.002 TYR C 461 ARG 0.008 0.000 ARG A 278 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 270 time to evaluate : 2.836 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 ILE cc_start: 0.5988 (OUTLIER) cc_final: 0.5734 (tp) REVERT: A 245 MET cc_start: 0.6127 (mmm) cc_final: 0.5413 (ptt) REVERT: B 176 THR cc_start: 0.8155 (m) cc_final: 0.7855 (p) REVERT: C 198 ILE cc_start: 0.5515 (OUTLIER) cc_final: 0.5230 (mt) REVERT: D 64 MET cc_start: 0.5946 (mmm) cc_final: 0.5435 (mmp) REVERT: D 235 MET cc_start: 0.6588 (mtt) cc_final: 0.6276 (mtp) REVERT: E 196 ASN cc_start: 0.6547 (OUTLIER) cc_final: 0.5714 (t0) REVERT: E 285 MET cc_start: 0.8127 (tpp) cc_final: 0.7767 (tpp) REVERT: E 328 THR cc_start: 0.7718 (OUTLIER) cc_final: 0.7504 (p) REVERT: E 369 LYS cc_start: 0.6809 (pttm) cc_final: 0.6341 (tttp) REVERT: F 49 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6932 (tt0) REVERT: F 191 ARG cc_start: 0.5184 (OUTLIER) cc_final: 0.2878 (mmp80) REVERT: F 404 ARG cc_start: 0.7827 (mmm-85) cc_final: 0.7537 (mmm-85) outliers start: 95 outliers final: 73 residues processed: 345 average time/residue: 0.3372 time to fit residues: 182.6542 Evaluate side-chains 337 residues out of total 2319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 258 time to evaluate : 2.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 260 TYR Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 433 GLN Chi-restraints excluded: chain B residue 483 ASN Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 236 PHE Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 406 THR Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 34 HIS Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 368 ARG Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 19 GLU Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 74 MET Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 196 ASN Chi-restraints excluded: chain E residue 197 ASP Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 259 GLN Chi-restraints excluded: chain E residue 262 SER Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 328 THR Chi-restraints excluded: chain E residue 411 SER Chi-restraints excluded: chain E residue 423 GLN Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 18 PHE Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 191 ARG Chi-restraints excluded: chain F residue 193 ARG Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 306 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 166 optimal weight: 2.9990 chunk 267 optimal weight: 9.9990 chunk 163 optimal weight: 4.9990 chunk 127 optimal weight: 8.9990 chunk 186 optimal weight: 8.9990 chunk 280 optimal weight: 10.0000 chunk 258 optimal weight: 3.9990 chunk 223 optimal weight: 0.4980 chunk 23 optimal weight: 0.9980 chunk 172 optimal weight: 0.9980 chunk 137 optimal weight: 6.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 GLN ** D 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 moved from start: 0.5263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22330 Z= 0.203 Angle : 0.608 14.167 30283 Z= 0.306 Chirality : 0.044 0.159 3480 Planarity : 0.005 0.047 3960 Dihedral : 7.615 71.899 3239 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.82 % Favored : 95.15 % Rotamer: Outliers : 3.75 % Allowed : 24.92 % Favored : 71.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.15), residues: 2823 helix: 0.59 (0.16), residues: 1071 sheet: -0.40 (0.25), residues: 431 loop : -1.37 (0.16), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS A 470 PHE 0.016 0.001 PHE E 414 TYR 0.020 0.001 TYR C 461 ARG 0.008 0.000 ARG A 278 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 264 time to evaluate : 2.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 GLU cc_start: 0.6685 (mp0) cc_final: 0.6455 (mp0) REVERT: B 176 THR cc_start: 0.8134 (m) cc_final: 0.7847 (p) REVERT: C 198 ILE cc_start: 0.5531 (OUTLIER) cc_final: 0.5220 (mt) REVERT: D 235 MET cc_start: 0.6527 (mtt) cc_final: 0.6224 (mtp) REVERT: D 337 GLU cc_start: 0.6837 (OUTLIER) cc_final: 0.6392 (mp0) REVERT: E 196 ASN cc_start: 0.6473 (OUTLIER) cc_final: 0.5656 (t0) REVERT: E 268 LEU cc_start: 0.6573 (OUTLIER) cc_final: 0.6255 (mm) REVERT: E 285 MET cc_start: 0.8053 (tpp) cc_final: 0.7663 (tpp) REVERT: E 328 THR cc_start: 0.7681 (OUTLIER) cc_final: 0.7466 (p) REVERT: E 369 LYS cc_start: 0.6730 (pttm) cc_final: 0.6267 (tttp) REVERT: F 191 ARG cc_start: 0.4963 (OUTLIER) cc_final: 0.2848 (mmp80) REVERT: F 404 ARG cc_start: 0.7830 (mmm-85) cc_final: 0.7522 (mmm-85) outliers start: 87 outliers final: 74 residues processed: 333 average time/residue: 0.3515 time to fit residues: 182.4887 Evaluate side-chains 338 residues out of total 2319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 258 time to evaluate : 2.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 260 TYR Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 433 GLN Chi-restraints excluded: chain B residue 483 ASN Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 236 PHE Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 406 THR Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 34 HIS Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 337 GLU Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 368 ARG Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 74 MET Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 196 ASN Chi-restraints excluded: chain E residue 197 ASP Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 259 GLN Chi-restraints excluded: chain E residue 262 SER Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 328 THR Chi-restraints excluded: chain E residue 411 SER Chi-restraints excluded: chain E residue 423 GLN Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 18 PHE Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 191 ARG Chi-restraints excluded: chain F residue 193 ARG Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain F residue 338 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 177 optimal weight: 10.0000 chunk 238 optimal weight: 20.0000 chunk 68 optimal weight: 1.9990 chunk 206 optimal weight: 9.9990 chunk 33 optimal weight: 8.9990 chunk 62 optimal weight: 0.8980 chunk 224 optimal weight: 10.0000 chunk 93 optimal weight: 20.0000 chunk 230 optimal weight: 7.9990 chunk 28 optimal weight: 0.8980 chunk 41 optimal weight: 8.9990 overall best weight: 4.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.186799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.151689 restraints weight = 26894.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.153711 restraints weight = 20924.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.155347 restraints weight = 14844.169| |-----------------------------------------------------------------------------| r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.5462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 22330 Z= 0.345 Angle : 0.689 14.185 30283 Z= 0.356 Chirality : 0.047 0.157 3480 Planarity : 0.006 0.049 3960 Dihedral : 7.969 76.890 3236 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.19 % Favored : 92.77 % Rotamer: Outliers : 4.14 % Allowed : 24.84 % Favored : 71.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % 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: -1.16 (0.15), residues: 2823 helix: 0.26 (0.16), residues: 1060 sheet: -0.75 (0.25), residues: 407 loop : -1.61 (0.16), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS A 470 PHE 0.034 0.002 PHE C 460 TYR 0.019 0.002 TYR C 461 ARG 0.007 0.001 ARG A 278 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4722.46 seconds wall clock time: 86 minutes 48.19 seconds (5208.19 seconds total)