Starting phenix.real_space_refine on Thu Mar 5 17:54:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hh1_34748/03_2026/8hh1_34748.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hh1_34748/03_2026/8hh1_34748.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hh1_34748/03_2026/8hh1_34748.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hh1_34748/03_2026/8hh1_34748.map" model { file = "/net/cci-nas-00/data/ceres_data/8hh1_34748/03_2026/8hh1_34748.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hh1_34748/03_2026/8hh1_34748.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 19 5.49 5 Mg 5 5.21 5 S 77 5.16 5 C 15287 2.51 5 N 4219 2.21 5 O 4673 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24280 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3661 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 23, 'TRANS': 454} Chain: "B" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3661 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 23, 'TRANS': 454} Chain: "C" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3661 Classifications: {'peptide': 478} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 454} Chain: "D" Number of atoms: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3630 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 447} Chain: "E" Number of atoms: 3623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3623 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 446} Chain: "F" Number of atoms: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3630 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 23, 'TRANS': 447} Chain: "G" Number of atoms: 2218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2218 Classifications: {'peptide': 283} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 272} Chain: "A" Number of atoms: 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: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'ATP': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.74, per 1000 atoms: 0.24 Number of scatterers: 24280 At special positions: 0 Unit cell: (124.96, 127.6, 155.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 77 16.00 P 19 15.00 Mg 5 11.99 O 4673 8.00 N 4219 7.00 C 15287 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 - 3.00 Amino acid : True - 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: 2.05 Conformation dependent library (CDL) restraints added in 901.7 milliseconds 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5712 Finding SS restraints... Secondary structure from input PDB file: 133 helices and 19 sheets defined 48.9% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 100 through 104 Processing helix chain 'A' and resid 135 through 139 removed outlier: 3.566A pdb=" N ARG A 139 " --> pdb=" O VAL A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 157 Processing helix chain 'A' and resid 174 through 186 removed outlier: 3.603A pdb=" N GLN A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 189 No H-bonds generated for 'chain 'A' and resid 187 through 189' Processing helix chain 'A' and resid 201 through 216 Processing helix chain 'A' and resid 217 through 219 No H-bonds generated for 'chain 'A' and resid 217 through 219' Processing helix chain 'A' and resid 231 through 253 removed outlier: 3.556A pdb=" N LEU A 235 " --> pdb=" O PRO A 231 " (cutoff:3.500A) Proline residue: A 239 - end of helix removed outlier: 3.807A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 277 removed outlier: 4.047A pdb=" N GLN A 266 " --> pdb=" O ASP A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 289 through 299 Processing helix chain 'A' and resid 305 through 309 Processing helix chain 'A' and resid 328 through 338 Processing helix chain 'A' and resid 345 through 351 Processing helix chain 'A' and resid 372 through 391 removed outlier: 3.827A pdb=" N VAL A 378 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N THR A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 400 Processing helix chain 'A' and resid 406 through 421 removed outlier: 3.586A pdb=" N LYS A 421 " --> pdb=" O VAL A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 442 Processing helix chain 'A' and resid 449 through 451 No H-bonds generated for 'chain 'A' and resid 449 through 451' Processing helix chain 'A' and resid 452 through 468 removed outlier: 3.634A pdb=" N LEU A 462 " --> pdb=" O LYS A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 479 Processing helix chain 'A' and resid 483 through 498 removed outlier: 3.647A pdb=" N THR A 497 " --> pdb=" O ALA A 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 104 Processing helix chain 'B' and resid 150 through 157 Processing helix chain 'B' and resid 174 through 186 removed outlier: 3.674A pdb=" N GLN B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 189 No H-bonds generated for 'chain 'B' and resid 187 through 189' Processing helix chain 'B' and resid 201 through 216 Processing helix chain 'B' and resid 217 through 219 No H-bonds generated for 'chain 'B' and resid 217 through 219' Processing helix chain 'B' and resid 231 through 251 removed outlier: 3.576A pdb=" N LEU B 235 " --> pdb=" O PRO B 231 " (cutoff:3.500A) Proline residue: B 239 - end of helix removed outlier: 3.855A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 277 removed outlier: 4.026A pdb=" N GLN B 266 " --> pdb=" O ASP B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 286 Processing helix chain 'B' and resid 289 through 299 removed outlier: 3.639A pdb=" N HIS B 294 " --> pdb=" O ILE B 290 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 336 Processing helix chain 'B' and resid 345 through 351 Processing helix chain 'B' and resid 372 through 399 removed outlier: 3.600A pdb=" N LYS B 377 " --> pdb=" O LYS B 373 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N VAL B 378 " --> pdb=" O ALA B 374 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY B 380 " --> pdb=" O LYS B 376 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N THR B 381 " --> pdb=" O LYS B 377 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU B 382 " --> pdb=" O VAL B 378 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU B 391 " --> pdb=" O ALA B 387 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALA B 394 " --> pdb=" O ARG B 390 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE B 395 " --> pdb=" O GLU B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 420 Processing helix chain 'B' and resid 429 through 442 Processing helix chain 'B' and resid 449 through 451 No H-bonds generated for 'chain 'B' and resid 449 through 451' Processing helix chain 'B' and resid 452 through 468 Processing helix chain 'B' and resid 468 through 479 Processing helix chain 'B' and resid 483 through 498 removed outlier: 3.610A pdb=" N LYS B 496 " --> pdb=" O GLU B 492 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR B 497 " --> pdb=" O ALA B 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 104 removed outlier: 3.607A pdb=" N LEU C 103 " --> pdb=" O GLY C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 157 Processing helix chain 'C' and resid 174 through 186 removed outlier: 3.595A pdb=" N GLN C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 215 Processing helix chain 'C' and resid 216 through 219 removed outlier: 3.746A pdb=" N ASP C 219 " --> pdb=" O GLY C 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 216 through 219' Processing helix chain 'C' and resid 231 through 251 removed outlier: 3.646A pdb=" N LEU C 235 " --> pdb=" O PRO C 231 " (cutoff:3.500A) Proline residue: C 239 - end of helix removed outlier: 3.562A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 277 removed outlier: 3.954A pdb=" N GLN C 266 " --> pdb=" O ASP C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 286 Processing helix chain 'C' and resid 287 through 288 No H-bonds generated for 'chain 'C' and resid 287 through 288' Processing helix chain 'C' and resid 289 through 299 removed outlier: 3.687A pdb=" N HIS C 294 " --> pdb=" O ILE C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 309 Processing helix chain 'C' and resid 328 through 336 Processing helix chain 'C' and resid 345 through 351 Processing helix chain 'C' and resid 372 through 379 Processing helix chain 'C' and resid 381 through 395 Processing helix chain 'C' and resid 403 through 420 removed outlier: 3.702A pdb=" N ALA C 411 " --> pdb=" O GLN C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 442 Processing helix chain 'C' and resid 449 through 451 No H-bonds generated for 'chain 'C' and resid 449 through 451' Processing helix chain 'C' and resid 452 through 468 removed outlier: 3.630A pdb=" N LEU C 462 " --> pdb=" O LYS C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 478 Processing helix chain 'C' and resid 483 through 498 Processing helix chain 'D' and resid 88 through 92 Processing helix chain 'D' and resid 139 through 146 Processing helix chain 'D' and resid 163 through 176 Processing helix chain 'D' and resid 191 through 206 Processing helix chain 'D' and resid 207 through 209 No H-bonds generated for 'chain 'D' and resid 207 through 209' Processing helix chain 'D' and resid 221 through 243 removed outlier: 4.785A pdb=" N ALA D 229 " --> pdb=" O ARG D 225 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N LEU D 230 " --> pdb=" O MET D 226 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N PHE D 239 " --> pdb=" O MET D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 264 removed outlier: 3.840A pdb=" N THR D 258 " --> pdb=" O ILE D 254 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL D 264 " --> pdb=" O ALA D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 269 Processing helix chain 'D' and resid 280 through 290 Processing helix chain 'D' and resid 309 through 312 Processing helix chain 'D' and resid 315 through 322 Processing helix chain 'D' and resid 323 through 325 No H-bonds generated for 'chain 'D' and resid 323 through 325' Processing helix chain 'D' and resid 332 through 338 removed outlier: 3.619A pdb=" N ALA D 336 " --> pdb=" O GLU D 332 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N MET D 338 " --> pdb=" O LYS D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 360 Processing helix chain 'D' and resid 360 through 388 removed outlier: 3.596A pdb=" N GLU D 379 " --> pdb=" O GLN D 375 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU D 380 " --> pdb=" O ARG D 376 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN D 381 " --> pdb=" O TYR D 377 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ASP D 382 " --> pdb=" O LYS D 378 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ILE D 383 " --> pdb=" O GLU D 379 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE D 386 " --> pdb=" O ASP D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 392 Processing helix chain 'D' and resid 393 through 410 removed outlier: 3.658A pdb=" N ARG D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 416 No H-bonds generated for 'chain 'D' and resid 414 through 416' Processing helix chain 'D' and resid 417 through 422 Processing helix chain 'D' and resid 429 through 443 Processing helix chain 'D' and resid 449 through 454 Processing helix chain 'D' and resid 458 through 469 removed outlier: 3.600A pdb=" N LYS D 467 " --> pdb=" O VAL D 463 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA D 468 " --> pdb=" O GLU D 464 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N MET D 469 " --> pdb=" O LYS D 465 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 92 Processing helix chain 'E' and resid 124 through 128 removed outlier: 3.544A pdb=" N LEU E 128 " --> pdb=" O PHE E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 146 Processing helix chain 'E' and resid 163 through 179 Processing helix chain 'E' and resid 191 through 206 Processing helix chain 'E' and resid 207 through 209 No H-bonds generated for 'chain 'E' and resid 207 through 209' Processing helix chain 'E' and resid 221 through 242 removed outlier: 5.022A 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) removed outlier: 4.018A pdb=" N PHE E 239 " --> pdb=" O MET E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 269 removed outlier: 3.673A pdb=" N PHE E 257 " --> pdb=" O ASN E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 290 Processing helix chain 'E' and resid 308 through 312 Processing helix chain 'E' and resid 315 through 323 removed outlier: 3.631A pdb=" N SER E 323 " --> pdb=" O ALA E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 339 Processing helix chain 'E' and resid 355 through 360 removed outlier: 3.538A pdb=" N GLY E 360 " --> pdb=" O PRO E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 360 through 380 Processing helix chain 'E' and resid 380 through 387 Processing helix chain 'E' and resid 388 through 392 Processing helix chain 'E' and resid 393 through 410 removed outlier: 3.646A pdb=" N ARG E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 422 Processing helix chain 'E' and resid 429 through 442 Processing helix chain 'E' and resid 449 through 454 removed outlier: 3.572A pdb=" N PHE E 453 " --> pdb=" O GLU E 450 " (cutoff:3.500A) Processing helix chain 'E' and resid 458 through 470 removed outlier: 3.972A pdb=" N VAL E 462 " --> pdb=" O ARG E 458 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL E 463 " --> pdb=" O ILE E 459 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 92 Processing helix chain 'F' and resid 124 through 128 removed outlier: 3.590A pdb=" N LEU F 128 " --> pdb=" O PHE F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 146 Processing helix chain 'F' and resid 163 through 180 removed outlier: 4.595A pdb=" N GLN F 177 " --> pdb=" O HIS F 173 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N GLU F 178 " --> pdb=" O ASN F 174 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N GLY F 180 " --> pdb=" O ALA F 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 206 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 221 through 243 removed outlier: 4.906A pdb=" N ALA F 229 " --> pdb=" O ARG F 225 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N LEU F 230 " --> pdb=" O MET F 226 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N PHE F 239 " --> pdb=" O MET F 235 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN F 243 " --> pdb=" O PHE F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 269 removed outlier: 3.935A pdb=" N THR F 258 " --> pdb=" O ILE F 254 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALA F 266 " --> pdb=" O SER F 262 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N LEU F 267 " --> pdb=" O GLU F 263 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY F 269 " --> pdb=" O SER F 265 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 290 Processing helix chain 'F' and resid 309 through 312 Processing helix chain 'F' and resid 315 through 321 removed outlier: 3.635A pdb=" N THR F 321 " --> pdb=" O ALA F 317 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 325 Processing helix chain 'F' and resid 332 through 338 Processing helix chain 'F' and resid 355 through 360 Processing helix chain 'F' and resid 360 through 388 removed outlier: 4.450A pdb=" N ASP F 382 " --> pdb=" O LYS F 378 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N ILE F 383 " --> pdb=" O GLU F 379 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE F 386 " --> pdb=" O ASP F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 410 removed outlier: 3.669A pdb=" N ARG F 405 " --> pdb=" O HIS F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 420 Processing helix chain 'F' and resid 429 through 443 Processing helix chain 'F' and resid 449 through 454 removed outlier: 3.800A pdb=" N ARG F 454 " --> pdb=" O ASP F 451 " (cutoff:3.500A) Processing helix chain 'F' and resid 458 through 469 removed outlier: 4.030A pdb=" N VAL F 462 " --> pdb=" O ARG F 458 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL F 463 " --> pdb=" O ILE F 459 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 42 Processing helix chain 'G' and resid 42 through 57 removed outlier: 3.550A pdb=" N MET G 46 " --> pdb=" O PHE G 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 107 removed outlier: 3.954A pdb=" N VAL G 95 " --> pdb=" O TYR G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 111 No H-bonds generated for 'chain 'G' and resid 109 through 111' Processing helix chain 'G' and resid 119 through 129 removed outlier: 3.551A pdb=" N LEU G 123 " --> pdb=" O GLY G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 162 removed outlier: 4.167A pdb=" N ILE G 149 " --> pdb=" O SER G 145 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N GLU G 151 " --> pdb=" O ALA G 147 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ILE G 152 " --> pdb=" O ASP G 148 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS G 155 " --> pdb=" O GLU G 151 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE G 160 " --> pdb=" O THR G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 200 through 205 removed outlier: 3.943A pdb=" N GLU G 204 " --> pdb=" O THR G 201 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N PHE G 205 " --> pdb=" O VAL G 202 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 283 removed outlier: 4.012A pdb=" N VAL G 215 " --> pdb=" O GLU G 211 " (cutoff:3.500A) Proline residue: G 218 - end of helix removed outlier: 3.530A pdb=" N ASP G 231 " --> pdb=" O GLY G 227 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 66 removed outlier: 4.004A pdb=" N GLU A 51 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N LEU A 52 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ARG A 40 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N VAL A 34 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ILE A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL A 74 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N ALA A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N GLU E 75 " --> pdb=" O GLN E 33 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N GLN E 33 " --> pdb=" O GLU E 75 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ALA E 29 " --> pdb=" O THR E 79 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ASN E 28 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ARG E 60 " --> pdb=" O ALA E 51 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N HIS E 53 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N THR E 58 " --> pdb=" O HIS E 53 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N LYS E 17 " --> pdb=" O VAL E 6 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N VAL E 6 " --> pdb=" O LYS E 17 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 98 Processing sheet with id=AA3, first strand: chain 'A' and resid 107 through 108 removed outlier: 6.408A pdb=" N ILE A 192 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N VAL A 259 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ILE A 194 " --> pdb=" O VAL A 259 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 60 through 66 removed outlier: 4.170A pdb=" N GLU B 51 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N ARG B 93 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N GLU B 54 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N THR B 91 " --> pdb=" O GLU B 54 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ARG B 40 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N VAL B 34 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ILE B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL B 74 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N ALA B 63 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N GLU F 75 " --> pdb=" O GLN F 33 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N GLN F 33 " --> pdb=" O GLU F 75 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ARG F 60 " --> pdb=" O ALA F 51 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N HIS F 53 " --> pdb=" O THR F 58 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N THR F 58 " --> pdb=" O HIS F 53 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL F 13 " --> pdb=" O VAL F 9 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N VAL F 9 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ASP F 15 " --> pdb=" O ILE F 7 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 96 through 99 removed outlier: 4.098A pdb=" N GLU B 125 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 107 through 108 removed outlier: 6.641A pdb=" N SER B 193 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N VAL B 224 " --> pdb=" O SER B 193 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N TYR B 195 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N ALA B 226 " --> pdb=" O TYR B 195 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ALA B 197 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE B 192 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N VAL B 259 " --> pdb=" O ILE B 192 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE B 194 " --> pdb=" O VAL B 259 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU B 166 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N LEU B 344 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE B 168 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 60 through 66 removed outlier: 4.222A pdb=" N GLU C 51 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N ARG C 93 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N GLU C 54 " --> pdb=" O THR C 91 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N THR C 91 " --> pdb=" O GLU C 54 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ARG C 40 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N VAL C 34 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ILE C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ASN C 70 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N LEU C 66 " --> pdb=" O ASN C 70 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N GLY C 72 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ALA D 29 " --> pdb=" O THR D 79 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ASN D 28 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ARG D 60 " --> pdb=" O ALA D 51 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N HIS D 53 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N THR D 58 " --> pdb=" O HIS D 53 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN D 8 " --> pdb=" O ASP D 15 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LYS D 17 " --> pdb=" O VAL D 6 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N VAL D 6 " --> pdb=" O LYS D 17 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 96 through 99 removed outlier: 3.968A pdb=" N GLU C 125 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 107 through 108 removed outlier: 6.327A pdb=" N VAL C 108 " --> pdb=" O THR C 225 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 84 through 86 Processing sheet with id=AB2, first strand: chain 'D' and resid 95 through 96 removed outlier: 6.289A pdb=" N VAL D 247 " --> pdb=" O THR D 301 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N ILE D 303 " --> pdb=" O VAL D 247 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LEU D 249 " --> pdb=" O ILE D 303 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N ALA D 305 " --> pdb=" O LEU D 249 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE D 251 " --> pdb=" O ALA D 305 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N TYR D 307 " --> pdb=" O ILE D 251 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ILE D 154 " --> pdb=" O GLN D 304 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N ILE D 306 " --> pdb=" O ILE D 154 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N LEU D 156 " --> pdb=" O ILE D 306 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 134 through 135 removed outlier: 4.155A pdb=" N TYR D 148 " --> pdb=" O LEU D 135 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 84 through 86 Processing sheet with id=AB5, first strand: chain 'E' and resid 95 through 96 removed outlier: 6.427A pdb=" N PHE E 96 " --> pdb=" O PHE E 215 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N GLN E 217 " --> pdb=" O PHE E 96 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL E 247 " --> pdb=" O THR E 301 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ILE E 303 " --> pdb=" O VAL E 247 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU E 249 " --> pdb=" O ILE E 303 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N ALA E 305 " --> pdb=" O LEU E 249 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ILE E 251 " --> pdb=" O ALA E 305 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ILE E 154 " --> pdb=" O GLN E 304 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 134 through 135 removed outlier: 4.406A pdb=" N TYR E 148 " --> pdb=" O LEU E 135 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 84 through 86 Processing sheet with id=AB8, first strand: chain 'F' and resid 95 through 96 removed outlier: 6.685A pdb=" N PHE F 96 " --> pdb=" O PHE F 215 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY F 216 " --> pdb=" O GLY F 187 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N VAL F 247 " --> pdb=" O THR F 301 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ILE F 303 " --> pdb=" O VAL F 247 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU F 249 " --> pdb=" O ILE F 303 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N ALA F 305 " --> pdb=" O LEU F 249 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ILE F 251 " --> pdb=" O ALA F 305 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N TYR F 307 " --> pdb=" O ILE F 251 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE F 154 " --> pdb=" O GLN F 304 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ILE F 306 " --> pdb=" O ILE F 154 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N LEU F 156 " --> pdb=" O ILE F 306 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 134 through 135 removed outlier: 4.196A pdb=" N TYR F 148 " --> pdb=" O LEU F 135 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 133 through 137 removed outlier: 6.584A pdb=" N VAL G 133 " --> pdb=" O TYR G 113 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ILE G 115 " --> pdb=" O VAL G 133 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU G 135 " --> pdb=" O ILE G 115 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N THR G 76 " --> pdb=" O ALA G 114 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ILE G 116 " --> pdb=" O THR G 76 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N TYR G 78 " --> pdb=" O ILE G 116 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N ILE G 118 " --> pdb=" O TYR G 78 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL G 80 " --> pdb=" O ILE G 118 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ASN G 173 " --> pdb=" O ILE G 81 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU G 168 " --> pdb=" O LEU G 188 " (cutoff:3.500A) 1186 hydrogen bonds defined for protein. 3372 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: 4.33 Time building geometry restraints manager: 2.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4187 1.32 - 1.44: 5900 1.44 - 1.56: 14416 1.56 - 1.68: 31 1.68 - 1.81: 154 Bond restraints: 24688 Sorted by residual: bond pdb=" C LYS B 377 " pdb=" O LYS B 377 " ideal model delta sigma weight residual 1.235 1.406 -0.171 1.26e-02 6.30e+03 1.84e+02 bond pdb=" C ARG B 383 " pdb=" O ARG B 383 " ideal model delta sigma weight residual 1.236 1.321 -0.084 1.15e-02 7.56e+03 5.35e+01 bond pdb=" C GLY B 380 " pdb=" O GLY B 380 " ideal model delta sigma weight residual 1.234 1.319 -0.086 1.20e-02 6.94e+03 5.11e+01 bond pdb=" CA TYR F 341 " pdb=" C TYR F 341 " ideal model delta sigma weight residual 1.524 1.465 0.059 1.26e-02 6.30e+03 2.17e+01 bond pdb=" C LEU G 224 " pdb=" O LEU G 224 " ideal model delta sigma weight residual 1.236 1.289 -0.053 1.15e-02 7.56e+03 2.11e+01 ... (remaining 24683 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.94: 33203 2.94 - 5.88: 248 5.88 - 8.82: 30 8.82 - 11.76: 4 11.76 - 14.70: 1 Bond angle restraints: 33486 Sorted by residual: angle pdb=" C TYR F 341 " pdb=" N PRO F 342 " pdb=" CA PRO F 342 " ideal model delta sigma weight residual 119.56 109.44 10.12 1.01e+00 9.80e-01 1.00e+02 angle pdb=" N ALA A 369 " pdb=" CA ALA A 369 " pdb=" C ALA A 369 " ideal model delta sigma weight residual 113.23 102.47 10.76 1.24e+00 6.50e-01 7.53e+01 angle pdb=" N ALA B 379 " pdb=" CA ALA B 379 " pdb=" C ALA B 379 " ideal model delta sigma weight residual 111.36 119.34 -7.98 1.09e+00 8.42e-01 5.36e+01 angle pdb=" N PRO F 342 " pdb=" CA PRO F 342 " pdb=" C PRO F 342 " ideal model delta sigma weight residual 113.86 104.73 9.13 1.25e+00 6.40e-01 5.34e+01 angle pdb=" N TYR F 341 " pdb=" CA TYR F 341 " pdb=" C TYR F 341 " ideal model delta sigma weight residual 109.81 124.51 -14.70 2.21e+00 2.05e-01 4.43e+01 ... (remaining 33481 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 13833 17.66 - 35.31: 901 35.31 - 52.97: 270 52.97 - 70.63: 77 70.63 - 88.28: 35 Dihedral angle restraints: 15116 sinusoidal: 6191 harmonic: 8925 Sorted by residual: dihedral pdb=" N TYR F 341 " pdb=" C TYR F 341 " pdb=" CA TYR F 341 " pdb=" CB TYR F 341 " ideal model delta harmonic sigma weight residual 122.80 142.36 -19.56 0 2.50e+00 1.60e-01 6.12e+01 dihedral pdb=" C TYR F 341 " pdb=" N TYR F 341 " pdb=" CA TYR F 341 " pdb=" CB TYR F 341 " ideal model delta harmonic sigma weight residual -122.60 -141.45 18.85 0 2.50e+00 1.60e-01 5.69e+01 dihedral pdb=" C GLN F 217 " pdb=" N GLN F 217 " pdb=" CA GLN F 217 " pdb=" CB GLN F 217 " ideal model delta harmonic sigma weight residual -122.60 -133.19 10.59 0 2.50e+00 1.60e-01 1.79e+01 ... (remaining 15113 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.197: 3838 0.197 - 0.394: 17 0.394 - 0.591: 0 0.591 - 0.788: 0 0.788 - 0.985: 1 Chirality restraints: 3856 Sorted by residual: chirality pdb=" CA TYR F 341 " pdb=" N TYR F 341 " pdb=" C TYR F 341 " pdb=" CB TYR F 341 " both_signs ideal model delta sigma weight residual False 2.51 1.53 0.98 2.00e-01 2.50e+01 2.43e+01 chirality pdb=" CA ALA B 379 " pdb=" N ALA B 379 " pdb=" C ALA B 379 " pdb=" CB ALA B 379 " both_signs ideal model delta sigma weight residual False 2.48 2.10 0.38 2.00e-01 2.50e+01 3.70e+00 chirality pdb=" CA LYS B 377 " pdb=" N LYS B 377 " pdb=" C LYS B 377 " pdb=" CB LYS B 377 " both_signs ideal model delta sigma weight residual False 2.51 2.89 -0.38 2.00e-01 2.50e+01 3.63e+00 ... (remaining 3853 not shown) Planarity restraints: 4363 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 376 " 0.033 2.00e-02 2.50e+03 6.21e-02 3.86e+01 pdb=" C LYS B 376 " -0.108 2.00e-02 2.50e+03 pdb=" O LYS B 376 " 0.038 2.00e-02 2.50e+03 pdb=" N LYS B 377 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 378 " -0.033 2.00e-02 2.50e+03 6.08e-02 3.70e+01 pdb=" C VAL B 378 " 0.105 2.00e-02 2.50e+03 pdb=" O VAL B 378 " -0.036 2.00e-02 2.50e+03 pdb=" N ALA B 379 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 381 " -0.025 2.00e-02 2.50e+03 5.04e-02 2.54e+01 pdb=" C THR B 381 " 0.087 2.00e-02 2.50e+03 pdb=" O THR B 381 " -0.032 2.00e-02 2.50e+03 pdb=" N LEU B 382 " -0.031 2.00e-02 2.50e+03 ... (remaining 4360 not shown) Histogram of nonbonded interaction distances: 1.08 - 1.84: 4 1.84 - 2.61: 173 2.61 - 3.37: 31398 3.37 - 4.14: 57872 4.14 - 4.90: 110025 Nonbonded interactions: 199472 Sorted by model distance: nonbonded pdb=" CB ASN G 55 " pdb=" CG2 VAL G 202 " model vdw 1.081 3.860 nonbonded pdb=" CG ASN G 55 " pdb=" CG2 VAL G 202 " model vdw 1.567 3.690 nonbonded pdb=" OG1 THR D 165 " pdb="MG MG D 601 " model vdw 1.708 2.170 nonbonded pdb="MG MG D 601 " pdb=" O1G ATP D 602 " model vdw 1.767 2.170 nonbonded pdb=" OG1 THR A 176 " pdb="MG MG A 601 " model vdw 2.016 2.170 ... (remaining 199467 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = (chain 'D' and resid 1 through 470) selection = (chain 'E' and resid 1 through 470) selection = (chain 'F' and resid 1 through 470) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.160 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: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 22.130 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.040 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:6.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.171 24688 Z= 0.255 Angle : 0.655 14.704 33486 Z= 0.423 Chirality : 0.051 0.985 3856 Planarity : 0.005 0.116 4363 Dihedral : 14.404 88.283 9404 Min Nonbonded Distance : 1.081 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.01 % Allowed : 0.90 % Favored : 98.09 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.15), residues: 3115 helix: 1.70 (0.15), residues: 1249 sheet: 1.23 (0.23), residues: 522 loop : 0.07 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 240 TYR 0.036 0.001 TYR F 341 PHE 0.023 0.001 PHE F 322 HIS 0.007 0.001 HIS F 363 Details of bonding type rmsd covalent geometry : bond 0.00379 (24688) covalent geometry : angle 0.65530 (33486) hydrogen bonds : bond 0.15240 ( 1186) hydrogen bonds : angle 6.11261 ( 3372) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 275 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 278 ARG cc_start: 0.8656 (mtp85) cc_final: 0.8396 (mtt90) REVERT: B 60 MET cc_start: 0.9269 (mmp) cc_final: 0.9051 (mmp) REVERT: C 466 GLN cc_start: 0.8588 (tp40) cc_final: 0.8374 (mm-40) REVERT: D 386 ILE cc_start: 0.8423 (mm) cc_final: 0.8173 (mt) REVERT: G 58 LEU cc_start: 0.4792 (OUTLIER) cc_final: 0.4551 (tp) REVERT: G 198 LYS cc_start: 0.7706 (OUTLIER) cc_final: 0.7265 (ptmm) REVERT: G 200 ARG cc_start: 0.6537 (OUTLIER) cc_final: 0.5568 (mmp-170) REVERT: G 206 GLU cc_start: 0.6993 (OUTLIER) cc_final: 0.6685 (tp30) REVERT: G 207 PRO cc_start: 0.6134 (Cg_endo) cc_final: 0.5452 (Cg_exo) outliers start: 26 outliers final: 9 residues processed: 295 average time/residue: 0.8063 time to fit residues: 265.8786 Evaluate side-chains 160 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 147 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain C residue 398 PHE Chi-restraints excluded: chain F residue 218 MET Chi-restraints excluded: chain F residue 341 TYR Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 197 ASN Chi-restraints excluded: chain G residue 198 LYS Chi-restraints excluded: chain G residue 200 ARG Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 206 GLU Chi-restraints excluded: chain G residue 219 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 0.0570 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 8.9990 overall best weight: 2.7904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 397 GLN D 177 GLN E 372 GLN F 219 ASN G 267 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.088820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.068364 restraints weight = 43126.006| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 2.06 r_work: 0.2706 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2580 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9029 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 24688 Z= 0.204 Angle : 0.573 9.457 33486 Z= 0.306 Chirality : 0.047 0.343 3856 Planarity : 0.005 0.045 4363 Dihedral : 9.405 89.965 3634 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.79 % Allowed : 8.10 % Favored : 90.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.15), residues: 3115 helix: 1.56 (0.15), residues: 1249 sheet: 0.96 (0.23), residues: 527 loop : 0.10 (0.17), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 240 TYR 0.037 0.001 TYR F 341 PHE 0.019 0.002 PHE C 456 HIS 0.010 0.001 HIS F 363 Details of bonding type rmsd covalent geometry : bond 0.00500 (24688) covalent geometry : angle 0.57339 (33486) hydrogen bonds : bond 0.05469 ( 1186) hydrogen bonds : angle 5.07599 ( 3372) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 156 time to evaluate : 0.942 Fit side-chains revert: symmetry clash REVERT: A 278 ARG cc_start: 0.9129 (mtp85) cc_final: 0.8861 (mtt90) REVERT: A 404 LYS cc_start: 0.7987 (tttt) cc_final: 0.7645 (ttmt) REVERT: B 451 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.8147 (pt0) REVERT: D 177 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.7886 (mp-120) REVERT: D 352 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.7963 (mpt90) REVERT: D 386 ILE cc_start: 0.8399 (mm) cc_final: 0.8094 (mt) REVERT: G 49 ILE cc_start: 0.7457 (tt) cc_final: 0.7137 (tt) REVERT: G 58 LEU cc_start: 0.4960 (OUTLIER) cc_final: 0.4603 (tp) REVERT: G 67 MET cc_start: 0.7380 (tpp) cc_final: 0.7140 (mmt) REVERT: G 200 ARG cc_start: 0.6503 (mmm160) cc_final: 0.5377 (mmp-170) REVERT: G 219 GLN cc_start: 0.7858 (OUTLIER) cc_final: 0.7542 (mt0) outliers start: 46 outliers final: 17 residues processed: 191 average time/residue: 0.7416 time to fit residues: 160.3092 Evaluate side-chains 159 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 137 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 451 GLU Chi-restraints excluded: chain B residue 465 ASP Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain D residue 177 GLN Chi-restraints excluded: chain D residue 352 ARG Chi-restraints excluded: chain D residue 419 GLN Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain F residue 10 MET Chi-restraints excluded: chain F residue 341 TYR Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 197 ASN Chi-restraints excluded: chain G residue 219 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 176 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 284 optimal weight: 0.9990 chunk 41 optimal weight: 6.9990 chunk 228 optimal weight: 6.9990 chunk 149 optimal weight: 0.0980 chunk 133 optimal weight: 5.9990 chunk 216 optimal weight: 5.9990 chunk 305 optimal weight: 9.9990 chunk 99 optimal weight: 4.9990 chunk 85 optimal weight: 7.9990 overall best weight: 3.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.087461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.067057 restraints weight = 43171.042| |-----------------------------------------------------------------------------| r_work (start): 0.2798 rms_B_bonded: 2.05 r_work: 0.2679 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2554 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9052 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 24688 Z= 0.237 Angle : 0.581 9.546 33486 Z= 0.310 Chirality : 0.048 0.347 3856 Planarity : 0.005 0.050 4363 Dihedral : 9.099 89.652 3617 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.95 % Allowed : 10.20 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.15), residues: 3115 helix: 1.44 (0.15), residues: 1245 sheet: 0.83 (0.23), residues: 529 loop : -0.01 (0.17), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 240 TYR 0.030 0.001 TYR F 341 PHE 0.017 0.002 PHE F 257 HIS 0.010 0.001 HIS F 363 Details of bonding type rmsd covalent geometry : bond 0.00586 (24688) covalent geometry : angle 0.58097 (33486) hydrogen bonds : bond 0.05762 ( 1186) hydrogen bonds : angle 5.03391 ( 3372) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 136 time to evaluate : 0.953 Fit side-chains revert: symmetry clash REVERT: B 451 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8145 (pt0) REVERT: C 89 ARG cc_start: 0.8404 (ttp80) cc_final: 0.8148 (ttp80) REVERT: C 409 LYS cc_start: 0.8332 (mmtt) cc_final: 0.7748 (tmtt) REVERT: D 352 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.8055 (mpt90) REVERT: D 386 ILE cc_start: 0.8407 (mm) cc_final: 0.8078 (mt) REVERT: G 58 LEU cc_start: 0.5049 (OUTLIER) cc_final: 0.4561 (tp) REVERT: G 200 ARG cc_start: 0.6407 (mmm160) cc_final: 0.5618 (mmp-170) outliers start: 50 outliers final: 18 residues processed: 171 average time/residue: 0.7010 time to fit residues: 136.6067 Evaluate side-chains 151 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 451 GLU Chi-restraints excluded: chain B residue 465 ASP Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 352 ARG Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 419 GLN Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain F residue 10 MET Chi-restraints excluded: chain F residue 382 ASP Chi-restraints excluded: chain F residue 383 ILE Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 197 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 181 optimal weight: 5.9990 chunk 235 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 107 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 144 optimal weight: 6.9990 chunk 300 optimal weight: 10.0000 chunk 203 optimal weight: 6.9990 chunk 241 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 177 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.089724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.069409 restraints weight = 42878.399| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 2.06 r_work: 0.2726 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2601 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9013 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24688 Z= 0.120 Angle : 0.495 10.450 33486 Z= 0.264 Chirality : 0.044 0.232 3856 Planarity : 0.004 0.050 4363 Dihedral : 8.260 87.216 3608 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.06 % Allowed : 11.21 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.15), residues: 3115 helix: 1.67 (0.15), residues: 1249 sheet: 0.86 (0.23), residues: 527 loop : 0.08 (0.17), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 164 TYR 0.018 0.001 TYR F 341 PHE 0.014 0.001 PHE A 398 HIS 0.005 0.001 HIS F 363 Details of bonding type rmsd covalent geometry : bond 0.00271 (24688) covalent geometry : angle 0.49457 (33486) hydrogen bonds : bond 0.04566 ( 1186) hydrogen bonds : angle 4.77569 ( 3372) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 138 time to evaluate : 1.015 Fit side-chains REVERT: A 95 MET cc_start: 0.8841 (tpt) cc_final: 0.8117 (tpt) REVERT: A 404 LYS cc_start: 0.8099 (tttt) cc_final: 0.7765 (ttmt) REVERT: B 451 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.8124 (pt0) REVERT: C 89 ARG cc_start: 0.8372 (ttp80) cc_final: 0.8124 (ttp80) REVERT: D 201 GLU cc_start: 0.8663 (tp30) cc_final: 0.8250 (tp30) REVERT: D 352 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.8019 (mpt90) REVERT: D 386 ILE cc_start: 0.8383 (mm) cc_final: 0.8036 (mt) REVERT: D 469 MET cc_start: 0.7696 (mtm) cc_final: 0.7291 (mmt) REVERT: G 58 LEU cc_start: 0.5153 (OUTLIER) cc_final: 0.4581 (tp) REVERT: G 67 MET cc_start: 0.6425 (OUTLIER) cc_final: 0.5974 (OUTLIER) REVERT: G 182 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8180 (mm-30) REVERT: G 191 LEU cc_start: 0.8136 (tm) cc_final: 0.7813 (mt) REVERT: G 200 ARG cc_start: 0.6476 (mmm160) cc_final: 0.5634 (mmp-170) outliers start: 53 outliers final: 17 residues processed: 177 average time/residue: 0.6407 time to fit residues: 130.8797 Evaluate side-chains 151 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 451 GLU Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 352 ARG Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain F residue 10 MET Chi-restraints excluded: chain F residue 382 ASP Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 67 MET Chi-restraints excluded: chain G residue 197 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 119 optimal weight: 6.9990 chunk 118 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 190 optimal weight: 2.9990 chunk 200 optimal weight: 0.1980 chunk 156 optimal weight: 4.9990 chunk 284 optimal weight: 6.9990 chunk 137 optimal weight: 6.9990 chunk 101 optimal weight: 6.9990 chunk 209 optimal weight: 1.9990 chunk 232 optimal weight: 0.9990 overall best weight: 1.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 363 HIS G 267 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.090369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.070058 restraints weight = 42691.582| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 2.05 r_work: 0.2739 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2615 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9005 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24688 Z= 0.117 Angle : 0.481 10.403 33486 Z= 0.256 Chirality : 0.044 0.195 3856 Planarity : 0.004 0.050 4363 Dihedral : 7.817 89.881 3608 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.95 % Allowed : 11.72 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.15), residues: 3115 helix: 1.74 (0.15), residues: 1261 sheet: 0.87 (0.23), residues: 527 loop : 0.15 (0.17), residues: 1327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 200 TYR 0.039 0.001 TYR G 203 PHE 0.015 0.001 PHE A 398 HIS 0.004 0.001 HIS F 363 Details of bonding type rmsd covalent geometry : bond 0.00268 (24688) covalent geometry : angle 0.48078 (33486) hydrogen bonds : bond 0.04315 ( 1186) hydrogen bonds : angle 4.63214 ( 3372) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 141 time to evaluate : 0.885 Fit side-chains REVERT: A 95 MET cc_start: 0.8826 (tpt) cc_final: 0.8078 (tpt) REVERT: A 404 LYS cc_start: 0.7961 (tttt) cc_final: 0.7611 (ttmt) REVERT: B 451 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8135 (pt0) REVERT: C 89 ARG cc_start: 0.8390 (ttp80) cc_final: 0.8160 (ttp80) REVERT: D 201 GLU cc_start: 0.8655 (tp30) cc_final: 0.8359 (tp30) REVERT: D 352 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.7966 (mpt90) REVERT: D 386 ILE cc_start: 0.8386 (mm) cc_final: 0.8035 (mt) REVERT: D 469 MET cc_start: 0.7703 (mtm) cc_final: 0.7289 (mmt) REVERT: G 49 ILE cc_start: 0.7556 (tt) cc_final: 0.7246 (tt) REVERT: G 58 LEU cc_start: 0.5029 (OUTLIER) cc_final: 0.4454 (tp) REVERT: G 67 MET cc_start: 0.6422 (OUTLIER) cc_final: 0.6002 (OUTLIER) REVERT: G 182 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8164 (mm-30) REVERT: G 191 LEU cc_start: 0.8082 (tm) cc_final: 0.7811 (mt) REVERT: G 200 ARG cc_start: 0.6495 (mmm160) cc_final: 0.5649 (mmp-170) outliers start: 50 outliers final: 18 residues processed: 182 average time/residue: 0.6375 time to fit residues: 133.5964 Evaluate side-chains 152 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 451 GLU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 352 ARG Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain F residue 10 MET Chi-restraints excluded: chain F residue 382 ASP Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 67 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 279 optimal weight: 0.6980 chunk 152 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 229 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 237 optimal weight: 0.1980 chunk 5 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 182 optimal weight: 4.9990 chunk 236 optimal weight: 1.9990 chunk 123 optimal weight: 4.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 324 HIS E 304 GLN G 209 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.090655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.070367 restraints weight = 42809.573| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 2.05 r_work: 0.2745 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2620 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8998 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24688 Z= 0.113 Angle : 0.476 10.436 33486 Z= 0.253 Chirality : 0.043 0.178 3856 Planarity : 0.004 0.048 4363 Dihedral : 7.602 86.728 3606 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.75 % Allowed : 12.23 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.15), residues: 3115 helix: 1.78 (0.15), residues: 1262 sheet: 0.86 (0.23), residues: 531 loop : 0.18 (0.17), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 455 TYR 0.037 0.001 TYR G 203 PHE 0.013 0.001 PHE C 494 HIS 0.003 0.001 HIS E 363 Details of bonding type rmsd covalent geometry : bond 0.00257 (24688) covalent geometry : angle 0.47620 (33486) hydrogen bonds : bond 0.04179 ( 1186) hydrogen bonds : angle 4.57228 ( 3372) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 138 time to evaluate : 0.980 Fit side-chains REVERT: A 404 LYS cc_start: 0.8012 (tttt) cc_final: 0.7657 (ttmt) REVERT: B 384 LEU cc_start: 0.7558 (OUTLIER) cc_final: 0.7322 (tp) REVERT: B 451 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.8163 (pt0) REVERT: C 89 ARG cc_start: 0.8379 (ttp80) cc_final: 0.8162 (ttp80) REVERT: D 201 GLU cc_start: 0.8642 (tp30) cc_final: 0.8375 (tp30) REVERT: D 352 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.7967 (mpt90) REVERT: D 386 ILE cc_start: 0.8412 (mm) cc_final: 0.8055 (mt) REVERT: D 469 MET cc_start: 0.7682 (mtm) cc_final: 0.7170 (mmt) REVERT: F 383 ILE cc_start: 0.8756 (mt) cc_final: 0.8419 (tp) REVERT: G 58 LEU cc_start: 0.4927 (OUTLIER) cc_final: 0.4411 (tp) REVERT: G 67 MET cc_start: 0.6467 (mmt) cc_final: 0.6050 (OUTLIER) REVERT: G 131 MET cc_start: 0.5916 (mmt) cc_final: 0.5330 (mmt) REVERT: G 182 GLU cc_start: 0.8524 (mt-10) cc_final: 0.8182 (mm-30) REVERT: G 191 LEU cc_start: 0.8085 (tm) cc_final: 0.7875 (mt) REVERT: G 200 ARG cc_start: 0.6460 (mmm160) cc_final: 0.5669 (mmp-170) outliers start: 45 outliers final: 18 residues processed: 172 average time/residue: 0.6681 time to fit residues: 131.8975 Evaluate side-chains 151 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 451 GLU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 352 ARG Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain F residue 382 ASP Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain G residue 58 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 194 optimal weight: 4.9990 chunk 6 optimal weight: 7.9990 chunk 230 optimal weight: 0.0060 chunk 76 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 chunk 95 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 304 optimal weight: 10.0000 chunk 253 optimal weight: 9.9990 chunk 161 optimal weight: 0.9990 overall best weight: 2.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 304 GLN G 209 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.088586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.068190 restraints weight = 42985.144| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 2.06 r_work: 0.2703 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2577 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9032 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 24688 Z= 0.172 Angle : 0.520 10.544 33486 Z= 0.276 Chirality : 0.045 0.225 3856 Planarity : 0.004 0.048 4363 Dihedral : 7.894 88.795 3606 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.95 % Allowed : 12.27 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.15), residues: 3115 helix: 1.64 (0.15), residues: 1262 sheet: 0.79 (0.23), residues: 527 loop : 0.15 (0.17), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 37 TYR 0.038 0.001 TYR G 203 PHE 0.016 0.001 PHE F 257 HIS 0.003 0.001 HIS A 215 Details of bonding type rmsd covalent geometry : bond 0.00416 (24688) covalent geometry : angle 0.51996 (33486) hydrogen bonds : bond 0.04918 ( 1186) hydrogen bonds : angle 4.71100 ( 3372) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 131 time to evaluate : 0.931 Fit side-chains REVERT: A 95 MET cc_start: 0.8678 (tpp) cc_final: 0.7929 (tpt) REVERT: B 384 LEU cc_start: 0.7497 (OUTLIER) cc_final: 0.7245 (tp) REVERT: B 451 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8176 (pt0) REVERT: D 201 GLU cc_start: 0.8691 (tp30) cc_final: 0.8429 (tp30) REVERT: D 352 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.8020 (mpt90) REVERT: D 386 ILE cc_start: 0.8391 (mm) cc_final: 0.8033 (mt) REVERT: D 469 MET cc_start: 0.7685 (mtm) cc_final: 0.7187 (mmt) REVERT: E 59 VAL cc_start: 0.9196 (OUTLIER) cc_final: 0.8981 (m) REVERT: F 383 ILE cc_start: 0.8830 (mt) cc_final: 0.8508 (tp) REVERT: G 67 MET cc_start: 0.6499 (OUTLIER) cc_final: 0.6162 (tpp) REVERT: G 182 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8188 (mm-30) REVERT: G 191 LEU cc_start: 0.8155 (tm) cc_final: 0.7941 (mt) REVERT: G 200 ARG cc_start: 0.6344 (mmm160) cc_final: 0.5611 (mmp-170) outliers start: 50 outliers final: 25 residues processed: 170 average time/residue: 0.6441 time to fit residues: 126.2352 Evaluate side-chains 156 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 451 GLU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 352 ARG Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain F residue 10 MET Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 382 ASP Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 67 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 308 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 254 optimal weight: 8.9990 chunk 136 optimal weight: 2.9990 chunk 187 optimal weight: 0.0870 chunk 120 optimal weight: 0.8980 chunk 154 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 245 optimal weight: 0.0020 overall best weight: 1.3970 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 304 GLN G 209 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.089900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.069607 restraints weight = 42689.808| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 2.05 r_work: 0.2731 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2607 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9010 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24688 Z= 0.122 Angle : 0.486 10.859 33486 Z= 0.259 Chirality : 0.043 0.190 3856 Planarity : 0.004 0.050 4363 Dihedral : 7.664 88.762 3606 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.52 % Allowed : 13.16 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.15), residues: 3115 helix: 1.75 (0.15), residues: 1261 sheet: 0.83 (0.23), residues: 526 loop : 0.18 (0.17), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 37 TYR 0.036 0.001 TYR G 203 PHE 0.013 0.001 PHE C 494 HIS 0.003 0.001 HIS E 363 Details of bonding type rmsd covalent geometry : bond 0.00283 (24688) covalent geometry : angle 0.48640 (33486) hydrogen bonds : bond 0.04335 ( 1186) hydrogen bonds : angle 4.59751 ( 3372) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 131 time to evaluate : 0.657 Fit side-chains REVERT: A 95 MET cc_start: 0.8631 (tpp) cc_final: 0.7870 (tpt) REVERT: A 404 LYS cc_start: 0.7955 (tttt) cc_final: 0.7639 (tppt) REVERT: B 384 LEU cc_start: 0.7518 (OUTLIER) cc_final: 0.7288 (tp) REVERT: B 451 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8186 (pt0) REVERT: D 201 GLU cc_start: 0.8677 (tp30) cc_final: 0.8429 (tp30) REVERT: D 352 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.8002 (mpt90) REVERT: D 386 ILE cc_start: 0.8393 (mm) cc_final: 0.8036 (mt) REVERT: D 469 MET cc_start: 0.7684 (mtm) cc_final: 0.7189 (mmt) REVERT: F 383 ILE cc_start: 0.8782 (mt) cc_final: 0.8492 (tp) REVERT: G 67 MET cc_start: 0.6487 (OUTLIER) cc_final: 0.6080 (tpp) REVERT: G 131 MET cc_start: 0.5937 (mmt) cc_final: 0.5304 (mmt) REVERT: G 182 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8210 (mm-30) REVERT: G 200 ARG cc_start: 0.6309 (mmm160) cc_final: 0.5674 (mmp-170) outliers start: 39 outliers final: 24 residues processed: 164 average time/residue: 0.6535 time to fit residues: 123.3028 Evaluate side-chains 155 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 127 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 451 GLU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 352 ARG Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain F residue 10 MET Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 382 ASP Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 67 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 244 optimal weight: 3.9990 chunk 177 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 269 optimal weight: 4.9990 chunk 200 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 102 optimal weight: 0.5980 chunk 218 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 103 optimal weight: 0.0970 chunk 150 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 GLN E 304 GLN G 209 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.091018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.070788 restraints weight = 42850.939| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 2.05 r_work: 0.2753 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8991 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 24688 Z= 0.104 Angle : 0.471 10.878 33486 Z= 0.250 Chirality : 0.043 0.160 3856 Planarity : 0.004 0.051 4363 Dihedral : 7.423 84.317 3605 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.48 % Allowed : 13.24 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.15), residues: 3115 helix: 1.87 (0.15), residues: 1262 sheet: 0.81 (0.23), residues: 531 loop : 0.22 (0.17), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 455 TYR 0.036 0.001 TYR G 203 PHE 0.012 0.001 PHE C 494 HIS 0.003 0.001 HIS E 363 Details of bonding type rmsd covalent geometry : bond 0.00230 (24688) covalent geometry : angle 0.47125 (33486) hydrogen bonds : bond 0.03980 ( 1186) hydrogen bonds : angle 4.50846 ( 3372) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 138 time to evaluate : 0.950 Fit side-chains REVERT: A 404 LYS cc_start: 0.7935 (tttt) cc_final: 0.7501 (tppt) REVERT: B 451 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8187 (pt0) REVERT: D 201 GLU cc_start: 0.8662 (tp30) cc_final: 0.8425 (tp30) REVERT: D 352 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.7947 (mpt90) REVERT: D 386 ILE cc_start: 0.8375 (mm) cc_final: 0.8010 (mt) REVERT: D 469 MET cc_start: 0.7729 (mtm) cc_final: 0.7176 (mmt) REVERT: F 383 ILE cc_start: 0.8724 (mt) cc_final: 0.8467 (tp) REVERT: G 67 MET cc_start: 0.6463 (OUTLIER) cc_final: 0.6062 (tpp) REVERT: G 131 MET cc_start: 0.5848 (mmt) cc_final: 0.5227 (mmt) REVERT: G 182 GLU cc_start: 0.8539 (mt-10) cc_final: 0.8197 (mm-30) REVERT: G 200 ARG cc_start: 0.6325 (mmm160) cc_final: 0.5583 (mmp-170) outliers start: 38 outliers final: 21 residues processed: 168 average time/residue: 0.6633 time to fit residues: 128.3356 Evaluate side-chains 155 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 451 GLU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 352 ARG Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain F residue 10 MET Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 382 ASP Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 67 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 197 optimal weight: 6.9990 chunk 149 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 37 optimal weight: 0.0670 chunk 101 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 46 optimal weight: 7.9990 chunk 138 optimal weight: 6.9990 chunk 74 optimal weight: 6.9990 chunk 190 optimal weight: 0.5980 overall best weight: 1.2922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 304 GLN G 209 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.090606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.070363 restraints weight = 42936.996| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 2.05 r_work: 0.2745 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2620 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8999 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24688 Z= 0.117 Angle : 0.482 10.420 33486 Z= 0.255 Chirality : 0.043 0.170 3856 Planarity : 0.004 0.053 4363 Dihedral : 7.437 83.391 3605 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.25 % Allowed : 13.63 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.15), residues: 3115 helix: 1.86 (0.15), residues: 1262 sheet: 0.83 (0.23), residues: 531 loop : 0.21 (0.17), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 5 TYR 0.028 0.001 TYR G 203 PHE 0.013 0.001 PHE C 494 HIS 0.003 0.001 HIS E 363 Details of bonding type rmsd covalent geometry : bond 0.00270 (24688) covalent geometry : angle 0.48158 (33486) hydrogen bonds : bond 0.04148 ( 1186) hydrogen bonds : angle 4.52074 ( 3372) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 128 time to evaluate : 0.944 Fit side-chains REVERT: A 404 LYS cc_start: 0.8057 (tttt) cc_final: 0.7693 (tppt) REVERT: B 451 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.8192 (pt0) REVERT: D 201 GLU cc_start: 0.8663 (tp30) cc_final: 0.8429 (tp30) REVERT: D 352 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.7944 (mpt90) REVERT: D 386 ILE cc_start: 0.8339 (mm) cc_final: 0.7969 (mt) REVERT: D 469 MET cc_start: 0.7743 (mtm) cc_final: 0.7188 (mmt) REVERT: F 383 ILE cc_start: 0.8747 (mt) cc_final: 0.8494 (tp) REVERT: G 67 MET cc_start: 0.6459 (OUTLIER) cc_final: 0.6115 (tpp) REVERT: G 131 MET cc_start: 0.5856 (mmt) cc_final: 0.5243 (mmt) REVERT: G 182 GLU cc_start: 0.8536 (mt-10) cc_final: 0.8194 (mm-30) REVERT: G 200 ARG cc_start: 0.6361 (mmm160) cc_final: 0.5599 (mmp-170) outliers start: 32 outliers final: 22 residues processed: 154 average time/residue: 0.6799 time to fit residues: 120.5486 Evaluate side-chains 150 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 451 GLU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 352 ARG Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain F residue 10 MET Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 382 ASP Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 67 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 216 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 278 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 215 optimal weight: 0.5980 chunk 101 optimal weight: 5.9990 chunk 290 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 212 optimal weight: 6.9990 chunk 271 optimal weight: 6.9990 chunk 280 optimal weight: 0.5980 overall best weight: 3.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 304 GLN G 209 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.087386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.066949 restraints weight = 43166.073| |-----------------------------------------------------------------------------| r_work (start): 0.2795 rms_B_bonded: 2.06 r_work: 0.2676 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2551 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9055 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 24688 Z= 0.227 Angle : 0.575 10.510 33486 Z= 0.304 Chirality : 0.047 0.260 3856 Planarity : 0.005 0.054 4363 Dihedral : 8.110 89.591 3605 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.32 % Allowed : 13.67 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.15), residues: 3115 helix: 1.54 (0.15), residues: 1258 sheet: 0.69 (0.23), residues: 529 loop : 0.07 (0.17), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 193 TYR 0.029 0.001 TYR G 203 PHE 0.018 0.002 PHE F 125 HIS 0.005 0.001 HIS A 215 Details of bonding type rmsd covalent geometry : bond 0.00558 (24688) covalent geometry : angle 0.57501 (33486) hydrogen bonds : bond 0.05546 ( 1186) hydrogen bonds : angle 4.82498 ( 3372) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6502.30 seconds wall clock time: 111 minutes 28.14 seconds (6688.14 seconds total)