Starting phenix.real_space_refine on Mon Aug 25 02:01:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hh9_34756/08_2025/8hh9_34756.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hh9_34756/08_2025/8hh9_34756.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hh9_34756/08_2025/8hh9_34756.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hh9_34756/08_2025/8hh9_34756.map" model { file = "/net/cci-nas-00/data/ceres_data/8hh9_34756/08_2025/8hh9_34756.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hh9_34756/08_2025/8hh9_34756.cif" } resolution = 3.6 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 16 5.49 5 Mg 5 5.21 5 S 77 5.16 5 C 15277 2.51 5 N 4214 2.21 5 O 4661 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 189 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24250 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: {'PTRANS': 23, 'TRANS': 454} Chain: "D" Number of atoms: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3630 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 447} Chain: "E" Number of atoms: 3623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3623 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 446} Chain: "F" Number of atoms: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3630 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 447} Chain: "G" Number of atoms: 2218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2218 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 10, 'TRANS': 272} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 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: 5.23, per 1000 atoms: 0.22 Number of scatterers: 24250 At special positions: 0 Unit cell: (129.36, 122.32, 151.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 77 16.00 P 16 15.00 Mg 5 11.99 O 4661 8.00 N 4214 7.00 C 15277 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 2.09 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 126 helices and 18 sheets defined 48.3% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 78 through 82 removed outlier: 4.197A pdb=" N GLY A 81 " --> pdb=" O PRO A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 104 removed outlier: 3.555A pdb=" N LEU A 103 " --> pdb=" O GLY A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 139 removed outlier: 4.020A 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: 3.653A 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 251 removed outlier: 3.599A pdb=" N LEU A 235 " --> pdb=" O PRO A 231 " (cutoff:3.500A) Proline residue: A 239 - end of helix removed outlier: 3.708A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 277 removed outlier: 3.875A 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 328 through 338 Processing helix chain 'A' and resid 345 through 352 Processing helix chain 'A' and resid 372 through 393 removed outlier: 3.983A pdb=" N VAL A 378 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLY A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N THR A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLU A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A 392 " --> pdb=" O ALA A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 421 removed outlier: 3.529A pdb=" N GLN A 407 " --> pdb=" O ASP A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 442 Processing helix chain 'A' and resid 449 through 468 removed outlier: 4.298A pdb=" N ARG A 454 " --> pdb=" O VAL A 450 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ARG A 455 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS A 458 " --> pdb=" O ARG A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 479 Processing helix chain 'A' and resid 483 through 496 Processing helix chain 'B' and resid 100 through 104 Processing helix chain 'B' and resid 150 through 157 removed outlier: 4.167A pdb=" N LEU B 156 " --> pdb=" O ALA B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 186 removed outlier: 3.507A pdb=" N GLN B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) 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 253 removed outlier: 3.721A pdb=" N LEU B 235 " --> pdb=" O PRO B 231 " (cutoff:3.500A) Proline residue: B 239 - end of helix removed outlier: 3.742A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 277 Processing helix chain 'B' and resid 282 through 286 Processing helix chain 'B' and resid 287 through 288 No H-bonds generated for 'chain 'B' and resid 287 through 288' Processing helix chain 'B' and resid 289 through 300 removed outlier: 3.781A pdb=" N HIS B 294 " --> pdb=" O ILE B 290 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ARG B 300 " --> pdb=" O ARG B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 336 Processing helix chain 'B' and resid 345 through 350 Processing helix chain 'B' and resid 372 through 396 removed outlier: 4.038A pdb=" N GLY B 380 " --> pdb=" O LYS B 376 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N THR B 381 " --> pdb=" O LYS B 377 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LEU B 382 " --> pdb=" O VAL B 378 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU B 384 " --> pdb=" O GLY B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 420 removed outlier: 3.576A pdb=" N GLN B 407 " --> pdb=" O ASP B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 442 removed outlier: 3.905A pdb=" N LEU B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 468 removed outlier: 4.571A pdb=" N ARG B 454 " --> pdb=" O VAL B 450 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ARG B 455 " --> pdb=" O GLU B 451 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR B 461 " --> pdb=" O GLU B 457 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU B 462 " --> pdb=" O LYS B 458 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLN B 466 " --> pdb=" O LEU B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 479 Processing helix chain 'B' and resid 483 through 498 Processing helix chain 'C' and resid 100 through 104 removed outlier: 3.676A 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: 3.582A 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 Processing helix chain 'C' and resid 231 through 251 removed outlier: 3.599A pdb=" N LEU C 235 " --> pdb=" O PRO C 231 " (cutoff:3.500A) Proline residue: C 239 - end of helix removed outlier: 3.798A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 277 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 Processing helix chain 'C' and resid 328 through 336 removed outlier: 3.536A pdb=" N SER C 336 " --> pdb=" O THR C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 352 removed outlier: 3.687A pdb=" N GLY C 352 " --> pdb=" O LEU C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 396 removed outlier: 3.533A pdb=" N LYS C 377 " --> pdb=" O LYS C 373 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL C 378 " --> pdb=" O ALA C 374 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLY C 380 " --> pdb=" O LYS C 376 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N THR C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLU C 391 " --> pdb=" O ALA C 387 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LEU C 392 " --> pdb=" O ALA C 388 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU C 393 " --> pdb=" O TYR C 389 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ALA C 394 " --> pdb=" O ARG C 390 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N PHE C 395 " --> pdb=" O GLU C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 420 removed outlier: 4.036A pdb=" N LYS C 409 " --> pdb=" O ALA C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 442 removed outlier: 3.658A pdb=" N ILE C 436 " --> pdb=" O LYS C 432 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE C 437 " --> pdb=" O GLN C 433 " (cutoff:3.500A) 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 Processing helix chain 'C' and resid 468 through 479 Processing helix chain 'C' and resid 483 through 498 removed outlier: 3.687A pdb=" N ALA C 490 " --> pdb=" O ASP C 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 92 Processing helix chain 'D' and resid 124 through 128 removed outlier: 3.525A pdb=" N LEU D 128 " --> pdb=" O PHE D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 145 Processing helix chain 'D' and resid 163 through 179 Processing helix chain 'D' and resid 191 through 206 removed outlier: 3.508A pdb=" N GLY D 195 " --> pdb=" O ARG D 191 " (cutoff:3.500A) 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: 3.533A pdb=" N ARG D 225 " --> pdb=" O PRO D 221 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N ALA D 229 " --> pdb=" O ARG D 225 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N LEU D 230 " --> pdb=" O MET D 226 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET D 235 " --> pdb=" O THR D 231 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE D 239 " --> pdb=" O MET D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 269 removed outlier: 3.823A pdb=" N THR D 258 " --> pdb=" O ILE D 254 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA D 266 " --> pdb=" O SER D 262 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LEU D 267 " --> pdb=" O GLU D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 290 removed outlier: 3.738A pdb=" N LEU D 288 " --> pdb=" O GLU D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 312 Processing helix chain 'D' and resid 315 through 321 removed outlier: 3.964A pdb=" N THR D 321 " --> pdb=" O ALA D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 325 Processing helix chain 'D' and resid 335 through 339 Processing helix chain 'D' and resid 355 through 360 Processing helix chain 'D' and resid 360 through 387 removed outlier: 3.893A pdb=" N TYR D 377 " --> pdb=" O THR D 373 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS D 378 " --> pdb=" O LEU D 374 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLU D 379 " --> pdb=" O GLN D 375 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU D 380 " --> pdb=" O ARG D 376 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ASP D 382 " --> pdb=" O LYS D 378 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE D 383 " --> pdb=" O GLU D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 410 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 removed outlier: 3.865A pdb=" N PHE D 453 " --> pdb=" O PRO D 449 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG D 454 " --> pdb=" O GLU D 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 449 through 454' Processing helix chain 'D' and resid 458 through 471 Processing helix chain 'E' and resid 88 through 92 Processing helix chain 'E' and resid 124 through 128 Processing helix chain 'E' and resid 139 through 146 Processing helix chain 'E' and resid 159 through 162 Processing helix chain 'E' and resid 163 through 180 removed outlier: 3.657A pdb=" N LEU E 167 " --> pdb=" O GLY E 163 " (cutoff:3.500A) 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: 5.274A pdb=" N ALA E 229 " --> pdb=" O ARG E 225 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU E 230 " --> pdb=" O MET E 226 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TYR E 238 " --> pdb=" O THR E 234 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N PHE E 239 " --> pdb=" O MET E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 269 removed outlier: 4.090A pdb=" N PHE E 257 " --> pdb=" O ASN E 253 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR E 258 " --> pdb=" O ILE E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 290 Processing helix chain 'E' and resid 308 through 312 removed outlier: 3.682A pdb=" N ASP E 311 " --> pdb=" O VAL E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 323 removed outlier: 3.744A pdb=" N SER E 323 " --> pdb=" O ALA E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 338 Processing helix chain 'E' and resid 355 through 360 Processing helix chain 'E' and resid 360 through 387 removed outlier: 3.505A pdb=" N GLU E 379 " --> pdb=" O GLN E 375 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP E 382 " --> pdb=" O LYS E 378 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU E 387 " --> pdb=" O ILE E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 393 through 410 removed outlier: 3.910A 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: 3.624A pdb=" N PHE E 453 " --> pdb=" O GLU E 450 " (cutoff:3.500A) Processing helix chain 'E' and resid 459 through 468 removed outlier: 3.747A pdb=" N VAL E 463 " --> pdb=" O ILE E 459 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA E 468 " --> pdb=" O GLU E 464 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 92 Processing helix chain 'F' and resid 124 through 128 removed outlier: 3.760A pdb=" N GLU F 127 " --> pdb=" O LYS F 124 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU F 128 " --> pdb=" O PHE F 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 124 through 128' Processing helix chain 'F' and resid 139 through 145 Processing helix chain 'F' and resid 163 through 176 Processing helix chain 'F' and resid 177 through 179 No H-bonds generated for 'chain 'F' and resid 177 through 179' 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: 5.316A pdb=" N ALA F 229 " --> pdb=" O ARG F 225 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LEU F 230 " --> pdb=" O MET F 226 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR F 238 " --> pdb=" O THR F 234 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N PHE F 239 " --> pdb=" O MET F 235 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLN F 243 " --> pdb=" O PHE F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 266 removed outlier: 3.974A pdb=" N THR F 258 " --> pdb=" O ILE F 254 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA F 266 " --> pdb=" O SER F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 277 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: 3.748A pdb=" N THR F 321 " --> pdb=" O ALA F 317 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 324 No H-bonds generated for 'chain 'F' and resid 322 through 324' Processing helix chain 'F' and resid 332 through 338 removed outlier: 3.619A pdb=" N MET F 338 " --> pdb=" O LYS F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 360 Processing helix chain 'F' and resid 360 through 388 removed outlier: 4.579A pdb=" N ASP F 382 " --> pdb=" O LYS F 378 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ILE F 383 " --> pdb=" O GLU F 379 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 410 removed outlier: 3.830A pdb=" N ARG F 405 " --> pdb=" O HIS F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 420 removed outlier: 3.606A pdb=" N GLN F 419 " --> pdb=" O VAL F 416 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 442 Processing helix chain 'F' and resid 449 through 454 removed outlier: 3.596A pdb=" N ARG F 454 " --> pdb=" O ASP F 451 " (cutoff:3.500A) Processing helix chain 'F' and resid 458 through 469 removed outlier: 3.973A pdb=" N VAL F 462 " --> pdb=" O ARG F 458 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL F 463 " --> pdb=" O ILE F 459 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 57 removed outlier: 3.521A pdb=" N ARG G 34 " --> pdb=" O SER G 30 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLN G 37 " --> pdb=" O ASN G 33 " (cutoff:3.500A) Proline residue: G 44 - end of helix removed outlier: 4.155A pdb=" N ASN G 55 " --> pdb=" O GLU G 51 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL G 56 " --> pdb=" O VAL G 52 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA G 57 " --> pdb=" O VAL G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 107 removed outlier: 3.619A 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 Processing helix chain 'G' and resid 145 through 162 removed outlier: 3.819A pdb=" N ILE G 149 " --> pdb=" O SER G 145 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLU G 151 " --> pdb=" O ALA G 147 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ILE G 152 " --> pdb=" O ASP G 148 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS G 155 " --> pdb=" O GLU G 151 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE G 160 " --> pdb=" O THR G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 189 through 192 Processing helix chain 'G' and resid 208 through 284 Proline residue: G 218 - end of helix removed outlier: 3.714A pdb=" N ALA G 283 " --> pdb=" O ALA G 279 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LEU G 284 " --> pdb=" O GLY G 280 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 66 removed outlier: 3.928A pdb=" N GLU A 51 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LEU A 52 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ARG A 40 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N VAL A 34 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N ASN A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N LEU A 66 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N GLY A 72 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N GLU E 75 " --> pdb=" O GLN E 33 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N GLN E 33 " --> pdb=" O GLU E 75 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ARG E 60 " --> pdb=" O ALA E 51 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N HIS E 53 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N THR E 58 " --> pdb=" O HIS E 53 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N VAL E 13 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N VAL E 9 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ASP E 15 " --> pdb=" O ILE E 7 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 99 removed outlier: 3.938A pdb=" N GLU A 125 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 107 through 108 removed outlier: 6.551A pdb=" N SER A 193 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N VAL A 224 " --> pdb=" O SER A 193 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N TYR A 195 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N ALA A 226 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ALA A 197 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR A 260 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N PHE A 343 " --> pdb=" O LEU A 361 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU A 361 " --> pdb=" O PHE A 343 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 60 through 66 removed outlier: 4.241A pdb=" N GLU B 51 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ARG B 93 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N GLU B 54 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N THR B 91 " --> pdb=" O GLU B 54 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ARG B 40 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N VAL B 34 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL B 74 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N ALA B 63 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N GLU F 75 " --> pdb=" O GLN F 33 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N GLN F 33 " --> pdb=" O GLU F 75 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ARG F 60 " --> pdb=" O ALA F 51 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N HIS F 53 " --> pdb=" O THR F 58 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N THR F 58 " --> pdb=" O HIS F 53 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN F 8 " --> pdb=" O ASP F 15 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LYS F 17 " --> pdb=" O VAL F 6 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N VAL F 6 " --> pdb=" O LYS F 17 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 96 through 99 removed outlier: 3.517A pdb=" N ARG B 127 " --> pdb=" O VAL B 97 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 107 through 108 removed outlier: 6.412A pdb=" N VAL B 108 " --> pdb=" O THR B 225 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ILE B 192 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N VAL B 259 " --> pdb=" O ILE B 192 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE B 194 " --> pdb=" O VAL B 259 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N ASP B 261 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N VAL B 196 " --> pdb=" O ASP B 261 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR B 260 " --> pdb=" O LEU B 316 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 60 through 66 removed outlier: 4.259A pdb=" N GLU C 51 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ARG C 93 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N GLU C 54 " --> pdb=" O THR C 91 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N THR C 91 " --> pdb=" O GLU C 54 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ARG C 40 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N VAL C 34 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ASN C 70 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N LEU C 66 " --> pdb=" O ASN C 70 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N GLY C 72 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N GLU D 75 " --> pdb=" O GLN D 33 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N GLN D 33 " --> pdb=" O GLU D 75 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ARG D 60 " --> pdb=" O ALA D 51 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N HIS D 53 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N THR D 58 " --> pdb=" O HIS D 53 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N VAL D 13 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N VAL D 9 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ASP D 15 " --> pdb=" O ILE D 7 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 96 through 99 removed outlier: 4.053A 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: 6.159A pdb=" N VAL C 108 " --> pdb=" O THR C 225 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N SER C 193 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N VAL C 224 " --> pdb=" O SER C 193 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N TYR C 195 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ALA C 226 " --> pdb=" O TYR C 195 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ALA C 197 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR C 260 " --> pdb=" O LEU C 316 " (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: 6.872A pdb=" N SER D 183 " --> pdb=" O ALA D 212 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N VAL D 214 " --> pdb=" O SER D 183 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N PHE D 185 " --> pdb=" O VAL D 214 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N GLY D 216 " --> pdb=" O PHE D 185 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N GLY D 187 " --> pdb=" O GLY D 216 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL D 184 " --> pdb=" O PHE D 250 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ASP D 252 " --> pdb=" O VAL D 184 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ALA D 186 " --> pdb=" O ASP D 252 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N VAL D 247 " --> pdb=" O THR D 301 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N ILE D 303 " --> pdb=" O VAL D 247 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N LEU D 249 " --> pdb=" O ILE D 303 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N ALA D 305 " --> pdb=" O LEU D 249 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ILE D 251 " --> pdb=" O ALA D 305 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA D 327 " --> pdb=" O LYS D 153 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 84 through 86 Processing sheet with id=AB4, first strand: chain 'E' and resid 95 through 96 removed outlier: 6.398A pdb=" N PHE E 96 " --> pdb=" O PHE E 215 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N GLN E 217 " --> pdb=" O PHE E 96 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY E 298 " --> pdb=" O THR E 295 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 95 through 96 removed outlier: 6.398A pdb=" N PHE E 96 " --> pdb=" O PHE E 215 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N GLN E 217 " --> pdb=" O PHE E 96 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LYS E 153 " --> pdb=" O ASP E 326 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N THR E 328 " --> pdb=" O LYS E 153 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLY E 155 " --> pdb=" O THR E 328 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N ASN E 330 " --> pdb=" O GLY E 155 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N PHE E 157 " --> pdb=" O ASN E 330 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 134 through 135 removed outlier: 4.042A 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: 6.787A pdb=" N SER F 183 " --> pdb=" O ALA F 212 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N VAL F 214 " --> pdb=" O SER F 183 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N PHE F 185 " --> pdb=" O VAL F 214 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP F 252 " --> pdb=" O ALA F 186 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ILE F 154 " --> pdb=" O GLN F 304 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N ILE F 306 " --> pdb=" O ILE F 154 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N LEU F 156 " --> pdb=" O ILE F 306 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LYS F 153 " --> pdb=" O ALA F 327 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N THR F 329 " --> pdb=" O LYS F 153 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLY F 155 " --> pdb=" O THR F 329 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 133 through 137 removed outlier: 6.923A pdb=" N VAL G 133 " --> pdb=" O TYR G 113 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ILE G 115 " --> pdb=" O VAL G 133 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU G 135 " --> pdb=" O ILE G 115 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N THR G 76 " --> pdb=" O ALA G 114 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N ILE G 116 " --> pdb=" O THR G 76 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N TYR G 78 " --> pdb=" O ILE G 116 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ILE G 118 " --> pdb=" O TYR G 78 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL G 80 " --> pdb=" O ILE G 118 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N GLY G 77 " --> pdb=" O TYR G 169 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N TYR G 171 " --> pdb=" O GLY G 77 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU G 79 " --> pdb=" O TYR G 171 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N ASN G 173 " --> pdb=" O LEU G 79 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N ILE G 81 " --> pdb=" O ASN G 173 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET G 170 " --> pdb=" O ARG G 186 " (cutoff:3.500A) 1163 hydrogen bonds defined for protein. 3318 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: 4.03 Time building geometry restraints manager: 2.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7260 1.33 - 1.45: 3280 1.45 - 1.57: 13939 1.57 - 1.69: 22 1.69 - 1.81: 154 Bond restraints: 24655 Sorted by residual: bond pdb=" N GLY D 159 " pdb=" CA GLY D 159 " ideal model delta sigma weight residual 1.449 1.495 -0.046 1.45e-02 4.76e+03 1.01e+01 bond pdb=" N ALA D 160 " pdb=" CA ALA D 160 " ideal model delta sigma weight residual 1.455 1.495 -0.040 1.33e-02 5.65e+03 8.92e+00 bond pdb=" CZ ARG E 454 " pdb=" NH2 ARG E 454 " ideal model delta sigma weight residual 1.330 1.292 0.038 1.30e-02 5.92e+03 8.62e+00 bond pdb=" CZ ARG E 404 " pdb=" NH2 ARG E 404 " ideal model delta sigma weight residual 1.330 1.293 0.037 1.30e-02 5.92e+03 8.17e+00 bond pdb=" N THR E 192 " pdb=" CA THR E 192 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.33e-02 5.65e+03 6.96e+00 ... (remaining 24650 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 32812 2.15 - 4.30: 548 4.30 - 6.45: 64 6.45 - 8.61: 5 8.61 - 10.76: 4 Bond angle restraints: 33433 Sorted by residual: angle pdb=" O GLY D 158 " pdb=" C GLY D 158 " pdb=" N GLY D 159 " ideal model delta sigma weight residual 122.70 113.47 9.23 1.30e+00 5.92e-01 5.04e+01 angle pdb=" C ASP E 252 " pdb=" CA ASP E 252 " pdb=" CB ASP E 252 " ideal model delta sigma weight residual 110.90 102.86 8.04 1.58e+00 4.01e-01 2.59e+01 angle pdb=" OE1 GLN E 412 " pdb=" CD GLN E 412 " pdb=" NE2 GLN E 412 " ideal model delta sigma weight residual 122.60 118.05 4.55 1.00e+00 1.00e+00 2.07e+01 angle pdb=" CA ASP E 252 " pdb=" C ASP E 252 " pdb=" O ASP E 252 " ideal model delta sigma weight residual 120.70 116.25 4.45 1.03e+00 9.43e-01 1.87e+01 angle pdb=" OD1 ASN E 413 " pdb=" CG ASN E 413 " pdb=" ND2 ASN E 413 " ideal model delta sigma weight residual 122.60 118.32 4.28 1.00e+00 1.00e+00 1.83e+01 ... (remaining 33428 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.71: 14181 22.71 - 45.41: 741 45.41 - 68.11: 100 68.11 - 90.82: 36 90.82 - 113.52: 1 Dihedral angle restraints: 15059 sinusoidal: 6134 harmonic: 8925 Sorted by residual: dihedral pdb=" C5' ADP D 603 " pdb=" O5' ADP D 603 " pdb=" PA ADP D 603 " pdb=" O2A ADP D 603 " ideal model delta sinusoidal sigma weight residual -60.00 53.53 -113.52 1 2.00e+01 2.50e-03 3.36e+01 dihedral pdb=" CA LYS D 334 " pdb=" C LYS D 334 " pdb=" N LEU D 335 " pdb=" CA LEU D 335 " ideal model delta harmonic sigma weight residual 180.00 153.87 26.13 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" CA TYR E 341 " pdb=" C TYR E 341 " pdb=" N PRO E 342 " pdb=" CA PRO E 342 " ideal model delta harmonic sigma weight residual 0.00 23.60 -23.60 0 5.00e+00 4.00e-02 2.23e+01 ... (remaining 15056 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 3284 0.064 - 0.128: 543 0.128 - 0.193: 21 0.193 - 0.257: 3 0.257 - 0.321: 1 Chirality restraints: 3852 Sorted by residual: chirality pdb=" CA ALA E 343 " pdb=" N ALA E 343 " pdb=" C ALA E 343 " pdb=" CB ALA E 343 " both_signs ideal model delta sigma weight residual False 2.48 2.16 0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" CA PRO E 342 " pdb=" N PRO E 342 " pdb=" C PRO E 342 " pdb=" CB PRO E 342 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CB VAL D 162 " pdb=" CA VAL D 162 " pdb=" CG1 VAL D 162 " pdb=" CG2 VAL D 162 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 3849 not shown) Planarity restraints: 4362 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 341 " -0.088 2.00e-02 2.50e+03 5.16e-02 5.32e+01 pdb=" CG TYR E 341 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR E 341 " 0.042 2.00e-02 2.50e+03 pdb=" CD2 TYR E 341 " 0.034 2.00e-02 2.50e+03 pdb=" CE1 TYR E 341 " 0.031 2.00e-02 2.50e+03 pdb=" CE2 TYR E 341 " 0.039 2.00e-02 2.50e+03 pdb=" CZ TYR E 341 " 0.011 2.00e-02 2.50e+03 pdb=" OH TYR E 341 " -0.088 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 414 " 0.079 2.00e-02 2.50e+03 5.12e-02 4.58e+01 pdb=" CG PHE E 414 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE E 414 " -0.041 2.00e-02 2.50e+03 pdb=" CD2 PHE E 414 " -0.063 2.00e-02 2.50e+03 pdb=" CE1 PHE E 414 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE E 414 " 0.011 2.00e-02 2.50e+03 pdb=" CZ PHE E 414 " 0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 377 " 0.078 2.00e-02 2.50e+03 3.96e-02 3.14e+01 pdb=" CG TYR E 377 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR E 377 " -0.037 2.00e-02 2.50e+03 pdb=" CD2 TYR E 377 " -0.037 2.00e-02 2.50e+03 pdb=" CE1 TYR E 377 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR E 377 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR E 377 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR E 377 " 0.044 2.00e-02 2.50e+03 ... (remaining 4359 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 101 2.44 - 3.06: 16003 3.06 - 3.67: 36395 3.67 - 4.29: 53030 4.29 - 4.90: 90561 Nonbonded interactions: 196090 Sorted by model distance: nonbonded pdb=" OE2 GLU E 190 " pdb=" CE1 PHE E 215 " model vdw 1.830 3.340 nonbonded pdb=" CB ALA D 160 " pdb=" O2 PO4 D 602 " model vdw 1.920 3.460 nonbonded pdb=" CA ALA D 160 " pdb=" O2 PO4 D 602 " model vdw 1.929 3.470 nonbonded pdb=" O2G ATP F 501 " pdb="MG MG F 502 " model vdw 1.971 2.170 nonbonded pdb=" OG1 THR F 165 " pdb="MG MG F 502 " model vdw 2.006 2.170 ... (remaining 196085 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' and resid 24 through 501) selection = (chain 'B' and resid 24 through 501) selection = (chain 'C' and resid 24 through 501) } ncs_group { reference = (chain 'D' and resid 1 through 470) selection = (chain 'E' 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.740 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 20.010 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.060 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:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 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 0.048 24655 Z= 0.198 Angle : 0.667 10.757 33433 Z= 0.388 Chirality : 0.046 0.321 3852 Planarity : 0.005 0.052 4362 Dihedral : 13.989 113.525 9347 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.89 % Favored : 97.05 % Rotamer: Outliers : 0.19 % Allowed : 0.43 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % 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 aren not related in a simple way. whole: 0.73 (0.15), residues: 3115 helix: 1.09 (0.15), residues: 1249 sheet: 0.67 (0.24), residues: 505 loop : -0.04 (0.17), residues: 1361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 454 TYR 0.088 0.002 TYR E 341 PHE 0.079 0.002 PHE E 414 HIS 0.007 0.001 HIS B 470 Details of bonding type rmsd covalent geometry : bond 0.00400 (24655) covalent geometry : angle 0.66724 (33433) hydrogen bonds : bond 0.15528 ( 1148) hydrogen bonds : angle 6.56475 ( 3318) *********************** 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 135 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 130 time to evaluate : 0.967 Fit side-chains REVERT: B 62 MET cc_start: 0.8191 (tpt) cc_final: 0.7708 (tpt) REVERT: B 455 ARG cc_start: 0.8911 (ttp80) cc_final: 0.8545 (ttp80) REVERT: D 164 LYS cc_start: 0.7853 (OUTLIER) cc_final: 0.7561 (mtpt) REVERT: D 378 LYS cc_start: 0.6753 (mmtp) cc_final: 0.6490 (ptmt) REVERT: D 389 MET cc_start: 0.6715 (ttt) cc_final: 0.6020 (tmm) REVERT: D 462 VAL cc_start: 0.4425 (t) cc_final: 0.4219 (t) REVERT: G 67 MET cc_start: 0.7535 (mmm) cc_final: 0.7119 (mmp) outliers start: 5 outliers final: 2 residues processed: 135 average time/residue: 0.1353 time to fit residues: 31.0569 Evaluate side-chains 108 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 105 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 164 LYS Chi-restraints excluded: chain E residue 251 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 0.1980 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.2980 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 8.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 189 GLN D 375 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.073222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.058055 restraints weight = 73399.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.059947 restraints weight = 37767.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.061184 restraints weight = 24091.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.061988 restraints weight = 17709.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.062517 restraints weight = 14369.422| |-----------------------------------------------------------------------------| r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.0756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24655 Z= 0.122 Angle : 0.545 10.996 33433 Z= 0.282 Chirality : 0.044 0.153 3852 Planarity : 0.004 0.045 4362 Dihedral : 8.047 108.330 3553 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.60 % Favored : 97.37 % Rotamer: Outliers : 0.31 % Allowed : 5.30 % Favored : 94.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % 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 aren not related in a simple way. whole: 0.93 (0.15), residues: 3115 helix: 1.37 (0.15), residues: 1243 sheet: 0.71 (0.23), residues: 520 loop : -0.03 (0.17), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 376 TYR 0.017 0.001 TYR D 377 PHE 0.014 0.001 PHE B 395 HIS 0.006 0.001 HIS B 470 Details of bonding type rmsd covalent geometry : bond 0.00269 (24655) covalent geometry : angle 0.54519 (33433) hydrogen bonds : bond 0.04444 ( 1148) hydrogen bonds : angle 5.18295 ( 3318) *********************** 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 134 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 126 time to evaluate : 1.014 Fit side-chains revert: symmetry clash REVERT: B 375 MET cc_start: 0.8655 (tpp) cc_final: 0.8264 (tmm) REVERT: B 407 GLN cc_start: 0.8119 (mt0) cc_final: 0.7827 (mp10) REVERT: B 455 ARG cc_start: 0.8959 (ttp80) cc_final: 0.8722 (ttp80) REVERT: D 389 MET cc_start: 0.6447 (ttt) cc_final: 0.6166 (tmm) REVERT: D 462 VAL cc_start: 0.4743 (t) cc_final: 0.4436 (t) REVERT: G 131 MET cc_start: 0.7138 (mmm) cc_final: 0.6666 (mmm) outliers start: 8 outliers final: 5 residues processed: 130 average time/residue: 0.1372 time to fit residues: 29.7141 Evaluate side-chains 114 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 109 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain G residue 191 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 111 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 283 optimal weight: 6.9990 chunk 140 optimal weight: 1.9990 chunk 161 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 11 optimal weight: 0.3980 chunk 167 optimal weight: 4.9990 chunk 215 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 375 GLN D 381 GLN G 107 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.072568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.057308 restraints weight = 73488.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.059181 restraints weight = 38129.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.060389 restraints weight = 24446.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.061213 restraints weight = 18067.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.061731 restraints weight = 14652.210| |-----------------------------------------------------------------------------| r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.0970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24655 Z= 0.142 Angle : 0.534 10.766 33433 Z= 0.276 Chirality : 0.044 0.156 3852 Planarity : 0.004 0.054 4362 Dihedral : 7.691 110.405 3547 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.66 % Favored : 97.30 % Rotamer: Outliers : 0.55 % Allowed : 8.22 % Favored : 91.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % 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 aren not related in a simple way. whole: 0.89 (0.15), residues: 3115 helix: 1.35 (0.15), residues: 1249 sheet: 0.67 (0.23), residues: 519 loop : -0.06 (0.17), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 283 TYR 0.013 0.001 TYR D 377 PHE 0.017 0.001 PHE B 395 HIS 0.006 0.001 HIS B 470 Details of bonding type rmsd covalent geometry : bond 0.00330 (24655) covalent geometry : angle 0.53379 (33433) hydrogen bonds : bond 0.04247 ( 1148) hydrogen bonds : angle 4.92972 ( 3318) *********************** 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 132 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 0.910 Fit side-chains revert: symmetry clash REVERT: B 62 MET cc_start: 0.8471 (tpp) cc_final: 0.7974 (ttt) REVERT: B 375 MET cc_start: 0.8627 (tpp) cc_final: 0.8214 (tmm) REVERT: B 407 GLN cc_start: 0.8160 (mt0) cc_final: 0.7821 (mp10) REVERT: B 455 ARG cc_start: 0.8961 (ttp80) cc_final: 0.8743 (ttp80) REVERT: D 376 ARG cc_start: 0.8085 (tpt90) cc_final: 0.7806 (tpt90) REVERT: D 389 MET cc_start: 0.6539 (ttt) cc_final: 0.6118 (tmm) REVERT: D 462 VAL cc_start: 0.4725 (t) cc_final: 0.4401 (t) REVERT: E 407 GLN cc_start: 0.8952 (tm-30) cc_final: 0.8702 (tm-30) REVERT: F 64 MET cc_start: 0.9258 (mmt) cc_final: 0.9006 (mmt) REVERT: G 67 MET cc_start: 0.7464 (mmm) cc_final: 0.7135 (mmp) REVERT: G 102 THR cc_start: 0.6106 (t) cc_final: 0.5869 (t) REVERT: G 131 MET cc_start: 0.7211 (mmm) cc_final: 0.6842 (mmm) outliers start: 14 outliers final: 10 residues processed: 126 average time/residue: 0.1429 time to fit residues: 30.1009 Evaluate side-chains 123 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 113 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 338 MET Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain G residue 191 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 201 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 282 optimal weight: 3.9990 chunk 43 optimal weight: 8.9990 chunk 86 optimal weight: 8.9990 chunk 102 optimal weight: 7.9990 chunk 249 optimal weight: 4.9990 chunk 245 optimal weight: 6.9990 chunk 303 optimal weight: 9.9990 chunk 110 optimal weight: 4.9990 chunk 123 optimal weight: 0.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 375 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.073301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.057963 restraints weight = 72513.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.059960 restraints weight = 35266.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.061247 restraints weight = 21948.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.062089 restraints weight = 15974.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.062652 restraints weight = 12879.700| |-----------------------------------------------------------------------------| r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 24655 Z= 0.209 Angle : 0.583 10.471 33433 Z= 0.302 Chirality : 0.046 0.153 3852 Planarity : 0.005 0.060 4362 Dihedral : 7.716 117.500 3547 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.99 % Favored : 96.98 % Rotamer: Outliers : 1.21 % Allowed : 9.85 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % 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 aren not related in a simple way. whole: 0.69 (0.15), residues: 3115 helix: 1.25 (0.15), residues: 1227 sheet: 0.52 (0.23), residues: 518 loop : -0.20 (0.17), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 283 TYR 0.014 0.001 TYR B 248 PHE 0.018 0.001 PHE B 395 HIS 0.006 0.001 HIS E 363 Details of bonding type rmsd covalent geometry : bond 0.00495 (24655) covalent geometry : angle 0.58260 (33433) hydrogen bonds : bond 0.04686 ( 1148) hydrogen bonds : angle 4.99256 ( 3318) *********************** 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 147 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 116 time to evaluate : 0.871 Fit side-chains revert: symmetry clash REVERT: A 157 VAL cc_start: 0.8780 (OUTLIER) cc_final: 0.8501 (m) REVERT: B 455 ARG cc_start: 0.8966 (ttp80) cc_final: 0.8750 (ttp80) REVERT: D 389 MET cc_start: 0.6569 (ttt) cc_final: 0.6073 (tmm) REVERT: D 462 VAL cc_start: 0.4639 (t) cc_final: 0.4298 (t) REVERT: E 407 GLN cc_start: 0.9004 (tm-30) cc_final: 0.8783 (tm-30) REVERT: F 64 MET cc_start: 0.9317 (mmt) cc_final: 0.9030 (mmt) REVERT: G 102 THR cc_start: 0.6044 (t) cc_final: 0.5786 (t) REVERT: G 131 MET cc_start: 0.7090 (mmm) cc_final: 0.6878 (mmm) outliers start: 31 outliers final: 20 residues processed: 138 average time/residue: 0.1346 time to fit residues: 31.5116 Evaluate side-chains 130 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 202 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 185 optimal weight: 7.9990 chunk 124 optimal weight: 0.9980 chunk 275 optimal weight: 1.9990 chunk 242 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 186 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 chunk 127 optimal weight: 9.9990 chunk 50 optimal weight: 8.9990 chunk 75 optimal weight: 10.0000 chunk 108 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 107 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.074438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.059407 restraints weight = 72004.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.061342 restraints weight = 35863.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.062590 restraints weight = 22589.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.063411 restraints weight = 16525.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.063932 restraints weight = 13355.609| |-----------------------------------------------------------------------------| r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24655 Z= 0.129 Angle : 0.518 10.687 33433 Z= 0.267 Chirality : 0.043 0.149 3852 Planarity : 0.004 0.063 4362 Dihedral : 7.326 115.148 3547 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.25 % Allowed : 10.09 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % 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 aren not related in a simple way. whole: 0.85 (0.15), residues: 3115 helix: 1.40 (0.15), residues: 1240 sheet: 0.59 (0.23), residues: 507 loop : -0.13 (0.17), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 283 TYR 0.012 0.001 TYR B 248 PHE 0.016 0.001 PHE B 395 HIS 0.005 0.001 HIS E 363 Details of bonding type rmsd covalent geometry : bond 0.00298 (24655) covalent geometry : angle 0.51809 (33433) hydrogen bonds : bond 0.04019 ( 1148) hydrogen bonds : angle 4.76028 ( 3318) *********************** 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 150 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 118 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 157 VAL cc_start: 0.8697 (OUTLIER) cc_final: 0.8422 (m) REVERT: B 455 ARG cc_start: 0.8954 (ttp80) cc_final: 0.8590 (ttp80) REVERT: D 389 MET cc_start: 0.6406 (ttt) cc_final: 0.6023 (tmm) REVERT: D 462 VAL cc_start: 0.4723 (t) cc_final: 0.4408 (t) REVERT: F 64 MET cc_start: 0.9323 (mmt) cc_final: 0.9066 (mmt) REVERT: G 25 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7433 (tt0) REVERT: G 67 MET cc_start: 0.7465 (mmm) cc_final: 0.7129 (mmp) REVERT: G 241 MET cc_start: 0.8318 (ptt) cc_final: 0.8101 (tmm) outliers start: 32 outliers final: 23 residues processed: 143 average time/residue: 0.1342 time to fit residues: 31.9341 Evaluate side-chains 137 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 404 ARG Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 338 MET Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain G residue 25 GLU Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 202 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 5 optimal weight: 0.9990 chunk 17 optimal weight: 7.9990 chunk 291 optimal weight: 9.9990 chunk 103 optimal weight: 2.9990 chunk 66 optimal weight: 8.9990 chunk 238 optimal weight: 7.9990 chunk 32 optimal weight: 7.9990 chunk 252 optimal weight: 7.9990 chunk 83 optimal weight: 10.0000 chunk 240 optimal weight: 9.9990 chunk 207 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN A 425 HIS D 53 HIS D 375 GLN ** G 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.071843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.056492 restraints weight = 73404.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.058459 restraints weight = 35851.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.059741 restraints weight = 22378.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.060556 restraints weight = 16298.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.061104 restraints weight = 13210.402| |-----------------------------------------------------------------------------| r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 24655 Z= 0.297 Angle : 0.662 10.339 33433 Z= 0.343 Chirality : 0.048 0.161 3852 Planarity : 0.005 0.064 4362 Dihedral : 7.610 125.511 3547 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.91 % Allowed : 10.83 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % 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 aren not related in a simple way. whole: 0.36 (0.15), residues: 3115 helix: 0.95 (0.15), residues: 1232 sheet: 0.37 (0.23), residues: 522 loop : -0.37 (0.17), residues: 1361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 3 TYR 0.017 0.002 TYR B 438 PHE 0.020 0.002 PHE G 125 HIS 0.007 0.001 HIS C 470 Details of bonding type rmsd covalent geometry : bond 0.00708 (24655) covalent geometry : angle 0.66164 (33433) hydrogen bonds : bond 0.05164 ( 1148) hydrogen bonds : angle 5.13146 ( 3318) *********************** 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 159 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 110 time to evaluate : 0.699 Fit side-chains revert: symmetry clash REVERT: A 157 VAL cc_start: 0.8912 (OUTLIER) cc_final: 0.8648 (m) REVERT: B 407 GLN cc_start: 0.8097 (mt0) cc_final: 0.7747 (mp10) REVERT: D 462 VAL cc_start: 0.4618 (t) cc_final: 0.4399 (t) REVERT: G 25 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7578 (tt0) REVERT: G 67 MET cc_start: 0.7649 (mmm) cc_final: 0.7177 (mmp) outliers start: 49 outliers final: 35 residues processed: 151 average time/residue: 0.1270 time to fit residues: 32.8363 Evaluate side-chains 144 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 107 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 338 MET Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain G residue 25 GLU Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 191 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 30 optimal weight: 0.5980 chunk 294 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 169 optimal weight: 8.9990 chunk 162 optimal weight: 9.9990 chunk 134 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 chunk 180 optimal weight: 7.9990 chunk 291 optimal weight: 4.9990 chunk 201 optimal weight: 10.0000 chunk 207 optimal weight: 2.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN G 107 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.072843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.057849 restraints weight = 72642.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.059743 restraints weight = 36241.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.060976 restraints weight = 22937.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.061771 restraints weight = 16823.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.062204 restraints weight = 13653.106| |-----------------------------------------------------------------------------| r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 24655 Z= 0.187 Angle : 0.571 10.644 33433 Z= 0.295 Chirality : 0.045 0.152 3852 Planarity : 0.004 0.066 4362 Dihedral : 7.335 126.067 3547 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.67 % Allowed : 11.21 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % 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 aren not related in a simple way. whole: 0.47 (0.15), residues: 3115 helix: 1.07 (0.15), residues: 1245 sheet: 0.39 (0.23), residues: 518 loop : -0.33 (0.17), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 283 TYR 0.015 0.001 TYR B 248 PHE 0.017 0.001 PHE B 395 HIS 0.006 0.001 HIS E 363 Details of bonding type rmsd covalent geometry : bond 0.00442 (24655) covalent geometry : angle 0.57101 (33433) hydrogen bonds : bond 0.04522 ( 1148) hydrogen bonds : angle 4.92865 ( 3318) *********************** 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 157 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 114 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 157 VAL cc_start: 0.8833 (OUTLIER) cc_final: 0.8557 (m) REVERT: D 462 VAL cc_start: 0.4677 (t) cc_final: 0.4349 (t) REVERT: G 25 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7575 (tt0) outliers start: 43 outliers final: 35 residues processed: 151 average time/residue: 0.1337 time to fit residues: 34.0599 Evaluate side-chains 144 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 107 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 404 ARG Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain G residue 25 GLU Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 202 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 102 optimal weight: 0.5980 chunk 308 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 162 optimal weight: 9.9990 chunk 157 optimal weight: 10.0000 chunk 139 optimal weight: 6.9990 chunk 205 optimal weight: 7.9990 chunk 202 optimal weight: 2.9990 chunk 101 optimal weight: 10.0000 chunk 171 optimal weight: 3.9990 chunk 190 optimal weight: 10.0000 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 375 GLN ** G 107 HIS ** 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 = 0.3266 r_free = 0.3266 target = 0.072769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.057551 restraints weight = 72235.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.059529 restraints weight = 35229.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.060812 restraints weight = 21888.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.061639 restraints weight = 15854.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.062185 restraints weight = 12777.573| |-----------------------------------------------------------------------------| r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 24655 Z= 0.196 Angle : 0.578 10.738 33433 Z= 0.298 Chirality : 0.045 0.152 3852 Planarity : 0.004 0.064 4362 Dihedral : 7.210 125.952 3547 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.06 % Allowed : 11.37 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % 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 aren not related in a simple way. whole: 0.46 (0.15), residues: 3115 helix: 1.07 (0.15), residues: 1246 sheet: 0.37 (0.23), residues: 522 loop : -0.35 (0.17), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 283 TYR 0.014 0.001 TYR B 248 PHE 0.016 0.001 PHE B 395 HIS 0.010 0.001 HIS G 107 Details of bonding type rmsd covalent geometry : bond 0.00466 (24655) covalent geometry : angle 0.57760 (33433) hydrogen bonds : bond 0.04531 ( 1148) hydrogen bonds : angle 4.90835 ( 3318) *********************** 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 163 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 110 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 157 VAL cc_start: 0.8845 (OUTLIER) cc_final: 0.8580 (m) REVERT: B 407 GLN cc_start: 0.8000 (mt0) cc_final: 0.7682 (mp10) REVERT: B 412 ARG cc_start: 0.7743 (OUTLIER) cc_final: 0.7211 (tpt170) REVERT: D 462 VAL cc_start: 0.4664 (t) cc_final: 0.4329 (t) REVERT: F 136 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.8046 (pt0) REVERT: G 25 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7533 (tt0) REVERT: G 67 MET cc_start: 0.7551 (mmm) cc_final: 0.7138 (mmp) outliers start: 53 outliers final: 42 residues processed: 158 average time/residue: 0.1290 time to fit residues: 34.5120 Evaluate side-chains 151 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 105 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain B residue 412 ARG Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 404 ARG Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain G residue 25 GLU Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 202 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 263 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 183 optimal weight: 9.9990 chunk 239 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 chunk 47 optimal weight: 10.0000 chunk 154 optimal weight: 8.9990 chunk 57 optimal weight: 5.9990 chunk 110 optimal weight: 6.9990 chunk 269 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN A 294 HIS ** G 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.071873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.056566 restraints weight = 73197.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.058535 restraints weight = 35657.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.059808 restraints weight = 22267.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.060634 restraints weight = 16237.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.061177 restraints weight = 13121.609| |-----------------------------------------------------------------------------| r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 24655 Z= 0.263 Angle : 0.633 10.573 33433 Z= 0.327 Chirality : 0.047 0.155 3852 Planarity : 0.005 0.062 4362 Dihedral : 7.232 130.163 3547 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.99 % Allowed : 11.64 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % 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 aren not related in a simple way. whole: 0.24 (0.15), residues: 3115 helix: 0.88 (0.14), residues: 1241 sheet: 0.28 (0.23), residues: 525 loop : -0.47 (0.17), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 376 TYR 0.015 0.002 TYR B 248 PHE 0.017 0.002 PHE B 395 HIS 0.007 0.001 HIS E 363 Details of bonding type rmsd covalent geometry : bond 0.00625 (24655) covalent geometry : angle 0.63334 (33433) hydrogen bonds : bond 0.04965 ( 1148) hydrogen bonds : angle 5.07160 ( 3318) *********************** 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 160 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 109 time to evaluate : 0.774 Fit side-chains revert: symmetry clash REVERT: A 157 VAL cc_start: 0.8917 (OUTLIER) cc_final: 0.8654 (m) REVERT: B 412 ARG cc_start: 0.7806 (OUTLIER) cc_final: 0.7319 (tpt170) REVERT: D 381 GLN cc_start: 0.6371 (mm110) cc_final: 0.5980 (mm110) REVERT: D 462 VAL cc_start: 0.4623 (t) cc_final: 0.4416 (t) REVERT: F 136 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8029 (pt0) REVERT: G 25 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7586 (tt0) REVERT: G 67 MET cc_start: 0.7622 (mmm) cc_final: 0.7129 (mmp) outliers start: 51 outliers final: 43 residues processed: 155 average time/residue: 0.1249 time to fit residues: 32.6350 Evaluate side-chains 152 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 105 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain B residue 412 ARG Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 404 ARG Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain G residue 25 GLU Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 202 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 134 optimal weight: 0.5980 chunk 180 optimal weight: 20.0000 chunk 229 optimal weight: 10.0000 chunk 168 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 104 optimal weight: 0.5980 chunk 210 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 147 optimal weight: 0.7980 chunk 41 optimal weight: 9.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN D 375 GLN G 107 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.072755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.057622 restraints weight = 72986.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.059499 restraints weight = 37560.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.060729 restraints weight = 23911.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.061529 restraints weight = 17581.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.062057 restraints weight = 14280.525| |-----------------------------------------------------------------------------| r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 24655 Z= 0.098 Angle : 0.517 11.214 33433 Z= 0.265 Chirality : 0.043 0.150 3852 Planarity : 0.004 0.064 4362 Dihedral : 6.586 119.475 3547 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.44 % Allowed : 12.31 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % 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 aren not related in a simple way. whole: 0.82 (0.15), residues: 3115 helix: 1.43 (0.15), residues: 1237 sheet: 0.47 (0.23), residues: 522 loop : -0.17 (0.17), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 283 TYR 0.012 0.001 TYR B 248 PHE 0.012 0.001 PHE B 395 HIS 0.004 0.001 HIS B 470 Details of bonding type rmsd covalent geometry : bond 0.00204 (24655) covalent geometry : angle 0.51697 (33433) hydrogen bonds : bond 0.03699 ( 1148) hydrogen bonds : angle 4.65113 ( 3318) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 118 time to evaluate : 0.630 Fit side-chains revert: symmetry clash REVERT: A 157 VAL cc_start: 0.8711 (OUTLIER) cc_final: 0.8419 (m) REVERT: B 455 ARG cc_start: 0.8970 (ttp80) cc_final: 0.8628 (ttp80) REVERT: D 37 ARG cc_start: 0.7388 (mtm180) cc_final: 0.7169 (mtm180) REVERT: D 381 GLN cc_start: 0.6320 (mm110) cc_final: 0.5939 (mm110) REVERT: D 462 VAL cc_start: 0.4647 (t) cc_final: 0.4357 (t) REVERT: G 25 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7488 (tt0) REVERT: G 67 MET cc_start: 0.7380 (mmm) cc_final: 0.6990 (mmp) outliers start: 37 outliers final: 28 residues processed: 150 average time/residue: 0.1395 time to fit residues: 34.2819 Evaluate side-chains 142 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 112 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 404 ARG Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain G residue 25 GLU Chi-restraints excluded: chain G residue 107 HIS Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 202 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 232 optimal weight: 0.9980 chunk 178 optimal weight: 10.0000 chunk 127 optimal weight: 9.9990 chunk 253 optimal weight: 9.9990 chunk 116 optimal weight: 0.6980 chunk 176 optimal weight: 6.9990 chunk 6 optimal weight: 0.9980 chunk 284 optimal weight: 7.9990 chunk 275 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 333 ASN G 107 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.072010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.056876 restraints weight = 73118.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.058722 restraints weight = 37916.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.059927 restraints weight = 24298.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.060712 restraints weight = 17945.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.061245 restraints weight = 14612.097| |-----------------------------------------------------------------------------| r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24655 Z= 0.129 Angle : 0.532 10.911 33433 Z= 0.271 Chirality : 0.043 0.149 3852 Planarity : 0.004 0.062 4362 Dihedral : 6.495 116.449 3547 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.44 % Allowed : 12.58 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % 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 aren not related in a simple way. whole: 0.80 (0.15), residues: 3115 helix: 1.40 (0.15), residues: 1242 sheet: 0.49 (0.23), residues: 534 loop : -0.18 (0.17), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 106 TYR 0.011 0.001 TYR B 248 PHE 0.013 0.001 PHE B 395 HIS 0.012 0.001 HIS G 107 Details of bonding type rmsd covalent geometry : bond 0.00298 (24655) covalent geometry : angle 0.53203 (33433) hydrogen bonds : bond 0.03886 ( 1148) hydrogen bonds : angle 4.65753 ( 3318) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2863.14 seconds wall clock time: 50 minutes 30.93 seconds (3030.93 seconds total)