Starting phenix.real_space_refine on Sun Jul 5 00:44:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hh9_34756/07_2026/8hh9_34756.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hh9_34756/07_2026/8hh9_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_34756/07_2026/8hh9_34756.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hh9_34756/07_2026/8hh9_34756.map" model { file = "/net/cci-nas-00/data/ceres_data/8hh9_34756/07_2026/8hh9_34756.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hh9_34756/07_2026/8hh9_34756.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8hh9_34756/07_2026/8hh9_34756.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hh9_34756/07_2026/8hh9_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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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: 5.21, per 1000 atoms: 0.21 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: 2.12 Conformation dependent library (CDL) restraints added in 1.1 seconds 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5712 Finding SS restraints... 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: 0.74 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: 4.57 Time building geometry restraints manager: 2.82 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: 14133 22.71 - 45.41: 695 45.41 - 68.11: 75 68.11 - 90.82: 31 90.82 - 113.52: 1 Dihedral angle restraints: 14935 sinusoidal: 6010 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 14932 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: 3.200 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: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 22.470 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.050 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 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 : 13.411 113.525 9223 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 are 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/Z covalent geometry : bond 0.00400 / 0.20 (24655) covalent geometry : angle 0.66724 / 0.39 (33433) hydrogen bonds : bond 0.15528 / 10.29 ( 1148) hydrogen bonds : angle 6.56475 / 4.65 ( 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 : 0.934 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: 0.1570 time to fit residues: 35.5542 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 : 0.968 ------------------------------------------------------------------------------- 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... 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 = 0.3267 r_free = 0.3267 target = 0.073258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.058069 restraints weight = 73345.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.059948 restraints weight = 37759.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.061184 restraints weight = 24164.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.062012 restraints weight = 17744.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.062475 restraints weight = 14379.834| |-----------------------------------------------------------------------------| r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.0769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24655 Z= 0.120 Angle : 0.544 11.034 33433 Z= 0.281 Chirality : 0.044 0.154 3852 Planarity : 0.004 0.045 4362 Dihedral : 5.682 108.194 3429 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.60 % Favored : 97.37 % Rotamer: Outliers : 0.27 % Allowed : 5.30 % Favored : 94.43 % 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 are not related in a simple way. whole: 0.92 (0.15), residues: 3115 helix: 1.37 (0.15), residues: 1243 sheet: 0.68 (0.23), residues: 530 loop : -0.03 (0.17), residues: 1342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 376 TYR 0.016 0.001 TYR E 341 PHE 0.014 0.001 PHE B 395 HIS 0.006 0.001 HIS B 470 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (24655) covalent geometry : angle 0.54409 / 0.28 (33433) hydrogen bonds : bond 0.04378 / 2.95 ( 1148) hydrogen bonds : angle 5.16442 / 3.64 ( 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: 7 poor density : 127 time to evaluate : 1.020 Fit side-chains revert: symmetry clash REVERT: B 375 MET cc_start: 0.8651 (tpp) cc_final: 0.8266 (tmm) REVERT: B 407 GLN cc_start: 0.8132 (mt0) cc_final: 0.7835 (mp10) REVERT: B 455 ARG cc_start: 0.8960 (ttp80) cc_final: 0.8722 (ttp80) REVERT: D 389 MET cc_start: 0.6489 (ttt) cc_final: 0.6153 (tmm) REVERT: D 462 VAL cc_start: 0.4706 (t) cc_final: 0.4400 (t) REVERT: E 407 GLN cc_start: 0.8965 (tm-30) cc_final: 0.8741 (tm-30) REVERT: G 131 MET cc_start: 0.7133 (mmm) cc_final: 0.6662 (mmm) outliers start: 7 outliers final: 4 residues processed: 131 average time/residue: 0.1605 time to fit residues: 35.2460 Evaluate side-chains 115 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 111 time to evaluate : 1.116 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 283 optimal weight: 6.9990 chunk 140 optimal weight: 3.9990 chunk 161 optimal weight: 9.9990 chunk 10 optimal weight: 8.9990 chunk 11 optimal weight: 0.0270 chunk 167 optimal weight: 1.9990 chunk 215 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 overall best weight: 2.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3254 r_free = 0.3254 target = 0.072657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.057392 restraints weight = 73477.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.059258 restraints weight = 38397.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.060492 restraints weight = 24578.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.061304 restraints weight = 18074.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.061820 restraints weight = 14669.308| |-----------------------------------------------------------------------------| r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.0932 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= 0.139 Angle : 0.529 10.796 33433 Z= 0.272 Chirality : 0.044 0.154 3852 Planarity : 0.004 0.055 4362 Dihedral : 5.542 109.998 3423 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.70 % Favored : 97.27 % Rotamer: Outliers : 0.55 % Allowed : 7.79 % Favored : 91.67 % 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 are not related in a simple way. whole: 0.90 (0.15), residues: 3115 helix: 1.37 (0.15), residues: 1249 sheet: 0.65 (0.23), residues: 520 loop : -0.05 (0.17), residues: 1346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 283 TYR 0.012 0.001 TYR D 377 PHE 0.017 0.001 PHE B 395 HIS 0.005 0.001 HIS B 470 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (24655) covalent geometry : angle 0.52938 / 0.27 (33433) hydrogen bonds : bond 0.04243 / 2.86 ( 1148) hydrogen bonds : angle 4.95257 / 3.51 ( 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 : 0.998 Fit side-chains REVERT: B 62 MET cc_start: 0.8463 (tpp) cc_final: 0.7978 (ttt) REVERT: B 375 MET cc_start: 0.8604 (tpp) cc_final: 0.8181 (tmm) REVERT: B 407 GLN cc_start: 0.8163 (mt0) cc_final: 0.7831 (mp10) REVERT: B 455 ARG cc_start: 0.8962 (ttp80) cc_final: 0.8741 (ttp80) REVERT: D 381 GLN cc_start: 0.6301 (mm110) cc_final: 0.5481 (tt0) REVERT: D 389 MET cc_start: 0.6543 (ttt) cc_final: 0.6149 (tmm) REVERT: D 462 VAL cc_start: 0.4731 (t) cc_final: 0.4406 (t) REVERT: E 407 GLN cc_start: 0.8955 (tm-30) cc_final: 0.8676 (tm-30) REVERT: F 64 MET cc_start: 0.9254 (mmt) cc_final: 0.9002 (mmt) REVERT: G 67 MET cc_start: 0.7509 (mmm) cc_final: 0.7168 (mmp) REVERT: G 131 MET cc_start: 0.7206 (mmm) cc_final: 0.6820 (mmm) outliers start: 14 outliers final: 10 residues processed: 126 average time/residue: 0.1529 time to fit residues: 32.7839 Evaluate side-chains 119 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 109 time to evaluate : 0.966 ------------------------------------------------------------------------------- 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: 4.9990 chunk 43 optimal weight: 9.9990 chunk 86 optimal weight: 8.9990 chunk 102 optimal weight: 7.9990 chunk 249 optimal weight: 4.9990 chunk 245 optimal weight: 8.9990 chunk 303 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 172 GLN A 425 HIS D 375 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.072855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.057572 restraints weight = 72801.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.059515 restraints weight = 35329.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.060822 restraints weight = 22117.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.061652 restraints weight = 16059.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.062194 restraints weight = 12978.819| |-----------------------------------------------------------------------------| r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 24655 Z= 0.252 Angle : 0.612 10.695 33433 Z= 0.317 Chirality : 0.047 0.157 3852 Planarity : 0.005 0.060 4362 Dihedral : 5.893 119.550 3423 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.02 % Favored : 96.95 % Rotamer: Outliers : 1.17 % Allowed : 9.74 % Favored : 89.10 % 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 are not related in a simple way. whole: 0.60 (0.15), residues: 3115 helix: 1.16 (0.15), residues: 1228 sheet: 0.50 (0.23), residues: 518 loop : -0.25 (0.17), residues: 1369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 3 TYR 0.014 0.002 TYR B 248 PHE 0.018 0.002 PHE B 395 HIS 0.006 0.001 HIS E 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00600 / 0.25 (24655) covalent geometry : angle 0.61193 / 0.32 (33433) hydrogen bonds : bond 0.04899 / 3.29 ( 1148) hydrogen bonds : angle 5.09519 / 3.61 ( 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 145 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 115 time to evaluate : 1.002 Fit side-chains revert: symmetry clash REVERT: A 157 VAL cc_start: 0.8788 (OUTLIER) cc_final: 0.8524 (m) REVERT: B 62 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.8088 (ttp) REVERT: B 407 GLN cc_start: 0.8125 (mt0) cc_final: 0.7788 (mp10) REVERT: B 455 ARG cc_start: 0.8965 (ttp80) cc_final: 0.8751 (ttp80) REVERT: D 376 ARG cc_start: 0.8087 (tpt90) cc_final: 0.7858 (tpt90) REVERT: D 389 MET cc_start: 0.6533 (ttt) cc_final: 0.6055 (tmm) REVERT: D 462 VAL cc_start: 0.4709 (t) cc_final: 0.4363 (t) REVERT: E 407 GLN cc_start: 0.9009 (tm-30) cc_final: 0.8772 (tm-30) REVERT: F 64 MET cc_start: 0.9316 (mmt) cc_final: 0.9031 (mmt) REVERT: G 131 MET cc_start: 0.7113 (mmm) cc_final: 0.6858 (mmm) outliers start: 30 outliers final: 19 residues processed: 134 average time/residue: 0.1584 time to fit residues: 35.7138 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 : 1.216 ------------------------------------------------------------------------------- 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 416 THR Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 62 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 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 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: 0.9980 chunk 124 optimal weight: 0.8980 chunk 275 optimal weight: 1.9990 chunk 242 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 186 optimal weight: 7.9990 chunk 101 optimal weight: 9.9990 chunk 127 optimal weight: 8.9990 chunk 50 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 chunk 108 optimal weight: 3.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3256 r_free = 0.3256 target = 0.072747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.057580 restraints weight = 72913.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.059445 restraints weight = 37748.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.060677 restraints weight = 24199.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.061479 restraints weight = 17789.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.061966 restraints weight = 14467.156| |-----------------------------------------------------------------------------| r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 24655 Z= 0.108 Angle : 0.505 10.868 33433 Z= 0.260 Chirality : 0.043 0.151 3852 Planarity : 0.004 0.064 4362 Dihedral : 5.531 114.784 3423 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.09 % Allowed : 10.16 % Favored : 88.75 % 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 are not related in a simple way. whole: 0.92 (0.15), residues: 3115 helix: 1.44 (0.15), residues: 1241 sheet: 0.63 (0.24), residues: 496 loop : -0.08 (0.17), residues: 1378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 283 TYR 0.012 0.001 TYR D 377 PHE 0.016 0.001 PHE B 395 HIS 0.004 0.001 HIS E 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (24655) covalent geometry : angle 0.50545 / 0.26 (33433) hydrogen bonds : bond 0.03874 / 2.62 ( 1148) hydrogen bonds : angle 4.73298 / 3.36 ( 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 148 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 120 time to evaluate : 1.000 Fit side-chains revert: symmetry clash REVERT: A 157 VAL cc_start: 0.8667 (OUTLIER) cc_final: 0.8401 (m) REVERT: B 407 GLN cc_start: 0.8147 (mt0) cc_final: 0.7825 (mp10) REVERT: B 455 ARG cc_start: 0.8966 (ttp80) cc_final: 0.8591 (ttp80) REVERT: D 376 ARG cc_start: 0.8071 (tpt90) cc_final: 0.7804 (tpt90) REVERT: D 389 MET cc_start: 0.6520 (ttt) cc_final: 0.6089 (tmm) REVERT: D 462 VAL cc_start: 0.4650 (t) cc_final: 0.4337 (t) REVERT: G 25 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7515 (tt0) REVERT: G 67 MET cc_start: 0.7459 (mmm) cc_final: 0.7111 (mmp) outliers start: 28 outliers final: 17 residues processed: 141 average time/residue: 0.1655 time to fit residues: 38.4382 Evaluate side-chains 132 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.865 ------------------------------------------------------------------------------- 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 372 ILE 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 381 THR Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain F residue 275 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 5 optimal weight: 1.9990 chunk 17 optimal weight: 8.9990 chunk 291 optimal weight: 10.0000 chunk 103 optimal weight: 0.0040 chunk 66 optimal weight: 8.9990 chunk 238 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 252 optimal weight: 0.3980 chunk 83 optimal weight: 9.9990 chunk 240 optimal weight: 9.9990 chunk 207 optimal weight: 9.9990 overall best weight: 2.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3292 r_free = 0.3292 target = 0.073953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.058901 restraints weight = 72584.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.060823 restraints weight = 36158.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.062056 restraints weight = 22798.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.062886 restraints weight = 16735.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.063409 restraints weight = 13514.719| |-----------------------------------------------------------------------------| r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 24655 Z= 0.157 Angle : 0.532 10.645 33433 Z= 0.274 Chirality : 0.044 0.149 3852 Planarity : 0.004 0.065 4362 Dihedral : 5.546 114.973 3423 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.56 % Allowed : 10.48 % Favored : 87.97 % 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 are not related in a simple way. whole: 0.85 (0.15), residues: 3115 helix: 1.42 (0.15), residues: 1235 sheet: 0.54 (0.23), residues: 518 loop : -0.13 (0.17), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 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/Z covalent geometry : bond 0.00371 / 0.16 (24655) covalent geometry : angle 0.53206 / 0.27 (33433) hydrogen bonds : bond 0.04152 / 2.80 ( 1148) hydrogen bonds : angle 4.76161 / 3.38 ( 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 154 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 114 time to evaluate : 0.993 Fit side-chains revert: symmetry clash REVERT: A 157 VAL cc_start: 0.8752 (OUTLIER) cc_final: 0.8459 (m) REVERT: B 407 GLN cc_start: 0.8076 (mt0) cc_final: 0.7772 (mp10) REVERT: B 455 ARG cc_start: 0.8962 (ttp80) cc_final: 0.8605 (ttp80) REVERT: D 376 ARG cc_start: 0.7984 (tpt90) cc_final: 0.7706 (tpt90) REVERT: D 381 GLN cc_start: 0.6351 (mm110) cc_final: 0.6010 (mm110) REVERT: D 389 MET cc_start: 0.6364 (ttt) cc_final: 0.6019 (tmm) REVERT: D 462 VAL cc_start: 0.4742 (t) cc_final: 0.4411 (t) REVERT: F 64 MET cc_start: 0.9302 (mmt) cc_final: 0.9021 (mmt) REVERT: G 25 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7529 (tt0) REVERT: G 67 MET cc_start: 0.7427 (mmm) cc_final: 0.7050 (mmp) REVERT: G 131 MET cc_start: 0.7074 (mmm) cc_final: 0.6865 (mmm) outliers start: 40 outliers final: 26 residues processed: 148 average time/residue: 0.1528 time to fit residues: 37.7289 Evaluate side-chains 139 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 111 time to evaluate : 0.917 ------------------------------------------------------------------------------- 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 475 ILE Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 499 VAL 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 30 optimal weight: 0.6980 chunk 294 optimal weight: 10.0000 chunk 4 optimal weight: 0.7980 chunk 169 optimal weight: 10.0000 chunk 162 optimal weight: 10.0000 chunk 134 optimal weight: 0.7980 chunk 35 optimal weight: 6.9990 chunk 180 optimal weight: 20.0000 chunk 291 optimal weight: 9.9990 chunk 201 optimal weight: 5.9990 chunk 207 optimal weight: 1.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 333 ASN ** 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 = 0.3246 r_free = 0.3246 target = 0.072265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.057113 restraints weight = 73449.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.058944 restraints weight = 37892.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.060156 restraints weight = 24353.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.060969 restraints weight = 17977.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.061499 restraints weight = 14583.296| |-----------------------------------------------------------------------------| r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.1364 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= 0.130 Angle : 0.517 10.622 33433 Z= 0.265 Chirality : 0.043 0.148 3852 Planarity : 0.004 0.066 4362 Dihedral : 5.475 113.643 3423 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.71 % Allowed : 10.75 % Favored : 87.54 % 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 are not related in a simple way. whole: 0.91 (0.15), residues: 3115 helix: 1.45 (0.15), residues: 1242 sheet: 0.55 (0.23), residues: 519 loop : -0.08 (0.17), residues: 1354 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 0.015 0.001 PHE B 395 HIS 0.005 0.001 HIS E 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (24655) covalent geometry : angle 0.51735 / 0.26 (33433) hydrogen bonds : bond 0.03931 / 2.65 ( 1148) hydrogen bonds : angle 4.67864 / 3.32 ( 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 159 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 115 time to evaluate : 1.018 Fit side-chains revert: symmetry clash REVERT: A 157 VAL cc_start: 0.8720 (OUTLIER) cc_final: 0.8458 (m) REVERT: B 407 GLN cc_start: 0.8121 (mt0) cc_final: 0.7810 (mp10) REVERT: B 455 ARG cc_start: 0.8964 (ttp80) cc_final: 0.8599 (ttp80) REVERT: D 381 GLN cc_start: 0.6268 (mm110) cc_final: 0.5924 (mm110) REVERT: D 462 VAL cc_start: 0.4678 (t) cc_final: 0.4361 (t) REVERT: G 25 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7396 (tt0) REVERT: G 131 MET cc_start: 0.7167 (mmm) cc_final: 0.6926 (mmm) REVERT: G 241 MET cc_start: 0.8343 (ptt) cc_final: 0.8126 (tmm) outliers start: 44 outliers final: 35 residues processed: 153 average time/residue: 0.1537 time to fit residues: 39.1164 Evaluate side-chains 149 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 112 time to evaluate : 0.891 ------------------------------------------------------------------------------- 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 146 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 499 VAL 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 333 ASN Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 410 LEU 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 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 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: 0.2980 chunk 308 optimal weight: 7.9990 chunk 22 optimal weight: 5.9990 chunk 162 optimal weight: 9.9990 chunk 157 optimal weight: 9.9990 chunk 139 optimal weight: 8.9990 chunk 205 optimal weight: 6.9990 chunk 202 optimal weight: 7.9990 chunk 101 optimal weight: 0.6980 chunk 171 optimal weight: 3.9990 chunk 190 optimal weight: 5.9990 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 333 ASN D 53 HIS D 375 GLN ** G 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.073352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.058335 restraints weight = 72250.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.060229 restraints weight = 36137.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.061479 restraints weight = 22850.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.062279 restraints weight = 16747.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.062787 restraints weight = 13604.694| |-----------------------------------------------------------------------------| r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 24655 Z= 0.189 Angle : 0.562 10.397 33433 Z= 0.289 Chirality : 0.045 0.150 3852 Planarity : 0.004 0.064 4362 Dihedral : 5.621 117.004 3423 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.79 % Allowed : 10.94 % 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 are not related in a simple way. whole: 0.78 (0.15), residues: 3115 helix: 1.35 (0.15), residues: 1232 sheet: 0.61 (0.24), residues: 494 loop : -0.20 (0.17), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 283 TYR 0.017 0.001 TYR G 171 PHE 0.016 0.001 PHE B 395 HIS 0.006 0.001 HIS E 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.19 (24655) covalent geometry : angle 0.56160 / 0.29 (33433) hydrogen bonds : bond 0.04329 / 2.91 ( 1148) hydrogen bonds : angle 4.78886 / 3.40 ( 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 161 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 115 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 157 VAL cc_start: 0.8828 (OUTLIER) cc_final: 0.8551 (m) REVERT: B 407 GLN cc_start: 0.7973 (mt0) cc_final: 0.7697 (mp10) REVERT: B 455 ARG cc_start: 0.8948 (ttp80) cc_final: 0.8593 (ttp80) REVERT: D 462 VAL cc_start: 0.4767 (t) cc_final: 0.4446 (t) REVERT: F 64 MET cc_start: 0.9309 (mmt) cc_final: 0.9046 (mmt) REVERT: G 25 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7539 (tt0) REVERT: G 67 MET cc_start: 0.7537 (mmm) cc_final: 0.7128 (mmp) REVERT: G 131 MET cc_start: 0.7179 (mmm) cc_final: 0.6945 (mmm) REVERT: G 171 TYR cc_start: 0.7777 (m-80) cc_final: 0.7534 (m-80) outliers start: 46 outliers final: 36 residues processed: 154 average time/residue: 0.1458 time to fit residues: 38.0456 Evaluate side-chains 149 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 111 time to evaluate : 0.827 ------------------------------------------------------------------------------- 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 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 499 VAL 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 333 ASN 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 263 optimal weight: 0.9980 chunk 67 optimal weight: 7.9990 chunk 183 optimal weight: 8.9990 chunk 239 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 47 optimal weight: 10.0000 chunk 154 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 chunk 110 optimal weight: 7.9990 chunk 269 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.072149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.056934 restraints weight = 73583.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.058790 restraints weight = 38158.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.060003 restraints weight = 24450.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.060811 restraints weight = 18071.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.061268 restraints weight = 14656.160| |-----------------------------------------------------------------------------| r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.1453 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= 0.128 Angle : 0.520 10.677 33433 Z= 0.267 Chirality : 0.043 0.149 3852 Planarity : 0.004 0.064 4362 Dihedral : 5.489 115.461 3423 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.48 % Allowed : 11.37 % Favored : 87.15 % 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 are not related in a simple way. whole: 0.90 (0.15), residues: 3115 helix: 1.45 (0.15), residues: 1244 sheet: 0.51 (0.23), residues: 513 loop : -0.08 (0.17), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 283 TYR 0.015 0.001 TYR G 171 PHE 0.014 0.001 PHE B 395 HIS 0.008 0.001 HIS G 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (24655) covalent geometry : angle 0.52010 / 0.27 (33433) hydrogen bonds : bond 0.03930 / 2.65 ( 1148) hydrogen bonds : angle 4.66121 / 3.31 ( 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 154 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 116 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 VAL cc_start: 0.8667 (OUTLIER) cc_final: 0.8439 (m) REVERT: A 157 VAL cc_start: 0.8727 (OUTLIER) cc_final: 0.8433 (m) REVERT: B 407 GLN cc_start: 0.8006 (mt0) cc_final: 0.7732 (mp10) REVERT: B 455 ARG cc_start: 0.8952 (ttp80) cc_final: 0.8581 (ttp80) REVERT: D 462 VAL cc_start: 0.4659 (t) cc_final: 0.4343 (t) REVERT: G 25 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7520 (tt0) REVERT: G 67 MET cc_start: 0.7531 (mmm) cc_final: 0.7094 (mmp) REVERT: G 131 MET cc_start: 0.7246 (mmm) cc_final: 0.6988 (mmm) REVERT: G 171 TYR cc_start: 0.7709 (m-80) cc_final: 0.7474 (m-80) outliers start: 38 outliers final: 31 residues processed: 150 average time/residue: 0.1580 time to fit residues: 39.1470 Evaluate side-chains 146 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 112 time to evaluate : 0.955 ------------------------------------------------------------------------------- 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 225 THR Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain B residue 499 VAL 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 134 optimal weight: 0.0570 chunk 180 optimal weight: 1.9990 chunk 229 optimal weight: 9.9990 chunk 168 optimal weight: 7.9990 chunk 118 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 210 optimal weight: 0.7980 chunk 86 optimal weight: 6.9990 chunk 147 optimal weight: 7.9990 chunk 41 optimal weight: 8.9990 overall best weight: 1.9704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 294 HIS D 375 GLN ** 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 = 0.3247 r_free = 0.3247 target = 0.072357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.057239 restraints weight = 72973.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.059079 restraints weight = 37621.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.060297 restraints weight = 24125.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.061101 restraints weight = 17755.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.061623 restraints weight = 14408.851| |-----------------------------------------------------------------------------| r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.1518 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= 0.127 Angle : 0.517 10.625 33433 Z= 0.264 Chirality : 0.043 0.149 3852 Planarity : 0.004 0.063 4362 Dihedral : 5.380 112.729 3423 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.60 % Allowed : 11.37 % Favored : 87.03 % 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 are not related in a simple way. whole: 0.94 (0.15), residues: 3115 helix: 1.52 (0.15), residues: 1238 sheet: 0.59 (0.23), residues: 508 loop : -0.11 (0.17), residues: 1369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 283 TYR 0.014 0.001 TYR G 171 PHE 0.013 0.001 PHE B 395 HIS 0.005 0.001 HIS E 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (24655) covalent geometry : angle 0.51731 / 0.26 (33433) hydrogen bonds : bond 0.03854 / 2.60 ( 1148) hydrogen bonds : angle 4.60300 / 3.26 ( 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 157 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 116 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 157 VAL cc_start: 0.8748 (OUTLIER) cc_final: 0.8462 (m) REVERT: B 455 ARG cc_start: 0.8977 (ttp80) cc_final: 0.8633 (ttp80) REVERT: D 462 VAL cc_start: 0.4666 (t) cc_final: 0.4361 (t) REVERT: G 25 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7540 (tt0) REVERT: G 67 MET cc_start: 0.7554 (mmm) cc_final: 0.7116 (mmp) REVERT: G 131 MET cc_start: 0.7267 (mmm) cc_final: 0.7033 (mmm) REVERT: G 171 TYR cc_start: 0.7664 (m-80) cc_final: 0.7431 (m-80) outliers start: 41 outliers final: 36 residues processed: 153 average time/residue: 0.1507 time to fit residues: 38.5768 Evaluate side-chains 150 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 112 time to evaluate : 0.913 ------------------------------------------------------------------------------- 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 225 THR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain B residue 499 VAL 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 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 7 ILE 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 188 LEU 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: 1.9990 chunk 178 optimal weight: 9.9990 chunk 127 optimal weight: 9.9990 chunk 253 optimal weight: 8.9990 chunk 116 optimal weight: 0.7980 chunk 176 optimal weight: 6.9990 chunk 6 optimal weight: 9.9990 chunk 284 optimal weight: 9.9990 chunk 275 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.073414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.058425 restraints weight = 72365.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.060316 restraints weight = 36252.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.061576 restraints weight = 22955.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.062377 restraints weight = 16710.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.062814 restraints weight = 13589.602| |-----------------------------------------------------------------------------| r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 24655 Z= 0.177 Angle : 0.551 10.396 33433 Z= 0.283 Chirality : 0.044 0.153 3852 Planarity : 0.004 0.062 4362 Dihedral : 5.522 116.060 3423 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.48 % Allowed : 11.60 % Favored : 86.92 % 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 are not related in a simple way. whole: 0.81 (0.15), residues: 3115 helix: 1.39 (0.15), residues: 1237 sheet: 0.51 (0.23), residues: 516 loop : -0.16 (0.17), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 283 TYR 0.013 0.001 TYR G 171 PHE 0.014 0.001 PHE A 350 HIS 0.005 0.001 HIS E 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 (24655) covalent geometry : angle 0.55114 / 0.28 (33433) hydrogen bonds : bond 0.04226 / 2.84 ( 1148) hydrogen bonds : angle 4.71985 / 3.35 ( 3318) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3272.74 seconds wall clock time: 57 minutes 45.20 seconds (3465.20 seconds total)