Starting phenix.real_space_refine on Sat Jun 21 05:07:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hh9_34756/06_2025/8hh9_34756.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hh9_34756/06_2025/8hh9_34756.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hh9_34756/06_2025/8hh9_34756.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hh9_34756/06_2025/8hh9_34756.map" model { file = "/net/cci-nas-00/data/ceres_data/8hh9_34756/06_2025/8hh9_34756.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hh9_34756/06_2025/8hh9_34756.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 14.23, per 1000 atoms: 0.59 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: 5.74 Conformation dependent library (CDL) restraints added in 2.9 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: 2.96 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: 8.39 Time building geometry restraints manager: 6.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7260 1.33 - 1.45: 3280 1.45 - 1.57: 13939 1.57 - 1.69: 22 1.69 - 1.81: 154 Bond restraints: 24655 Sorted by residual: bond pdb=" N GLY D 159 " pdb=" CA GLY D 159 " ideal model delta sigma weight residual 1.449 1.495 -0.046 1.45e-02 4.76e+03 1.01e+01 bond pdb=" N ALA D 160 " pdb=" CA ALA D 160 " ideal model delta sigma weight residual 1.455 1.495 -0.040 1.33e-02 5.65e+03 8.92e+00 bond pdb=" CZ ARG E 454 " pdb=" NH2 ARG E 454 " ideal model delta sigma weight residual 1.330 1.292 0.038 1.30e-02 5.92e+03 8.62e+00 bond pdb=" CZ ARG E 404 " pdb=" NH2 ARG E 404 " ideal model delta sigma weight residual 1.330 1.293 0.037 1.30e-02 5.92e+03 8.17e+00 bond pdb=" N THR E 192 " pdb=" CA THR E 192 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.33e-02 5.65e+03 6.96e+00 ... (remaining 24650 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 32812 2.15 - 4.30: 548 4.30 - 6.45: 64 6.45 - 8.61: 5 8.61 - 10.76: 4 Bond angle restraints: 33433 Sorted by residual: angle pdb=" O GLY D 158 " pdb=" C GLY D 158 " pdb=" N GLY D 159 " ideal model delta sigma weight residual 122.70 113.47 9.23 1.30e+00 5.92e-01 5.04e+01 angle pdb=" C ASP E 252 " pdb=" CA ASP E 252 " pdb=" CB ASP E 252 " ideal model delta sigma weight residual 110.90 102.86 8.04 1.58e+00 4.01e-01 2.59e+01 angle pdb=" OE1 GLN E 412 " pdb=" CD GLN E 412 " pdb=" NE2 GLN E 412 " ideal model delta sigma weight residual 122.60 118.05 4.55 1.00e+00 1.00e+00 2.07e+01 angle pdb=" CA ASP E 252 " pdb=" C ASP E 252 " pdb=" O ASP E 252 " ideal model delta sigma weight residual 120.70 116.25 4.45 1.03e+00 9.43e-01 1.87e+01 angle pdb=" OD1 ASN E 413 " pdb=" CG ASN E 413 " pdb=" ND2 ASN E 413 " ideal model delta sigma weight residual 122.60 118.32 4.28 1.00e+00 1.00e+00 1.83e+01 ... (remaining 33428 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.71: 14181 22.71 - 45.41: 741 45.41 - 68.11: 100 68.11 - 90.82: 36 90.82 - 113.52: 1 Dihedral angle restraints: 15059 sinusoidal: 6134 harmonic: 8925 Sorted by residual: dihedral pdb=" C5' ADP D 603 " pdb=" O5' ADP D 603 " pdb=" PA ADP D 603 " pdb=" O2A ADP D 603 " ideal model delta sinusoidal sigma weight residual -60.00 53.53 -113.52 1 2.00e+01 2.50e-03 3.36e+01 dihedral pdb=" CA LYS D 334 " pdb=" C LYS D 334 " pdb=" N LEU D 335 " pdb=" CA LEU D 335 " ideal model delta harmonic sigma weight residual 180.00 153.87 26.13 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" CA TYR E 341 " pdb=" C TYR E 341 " pdb=" N PRO E 342 " pdb=" CA PRO E 342 " ideal model delta harmonic sigma weight residual 0.00 23.60 -23.60 0 5.00e+00 4.00e-02 2.23e+01 ... (remaining 15056 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 3284 0.064 - 0.128: 543 0.128 - 0.193: 21 0.193 - 0.257: 3 0.257 - 0.321: 1 Chirality restraints: 3852 Sorted by residual: chirality pdb=" CA ALA E 343 " pdb=" N ALA E 343 " pdb=" C ALA E 343 " pdb=" CB ALA E 343 " both_signs ideal model delta sigma weight residual False 2.48 2.16 0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" CA PRO E 342 " pdb=" N PRO E 342 " pdb=" C PRO E 342 " pdb=" CB PRO E 342 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CB VAL D 162 " pdb=" CA VAL D 162 " pdb=" CG1 VAL D 162 " pdb=" CG2 VAL D 162 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 3849 not shown) Planarity restraints: 4362 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 341 " -0.088 2.00e-02 2.50e+03 5.16e-02 5.32e+01 pdb=" CG TYR E 341 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR E 341 " 0.042 2.00e-02 2.50e+03 pdb=" CD2 TYR E 341 " 0.034 2.00e-02 2.50e+03 pdb=" CE1 TYR E 341 " 0.031 2.00e-02 2.50e+03 pdb=" CE2 TYR E 341 " 0.039 2.00e-02 2.50e+03 pdb=" CZ TYR E 341 " 0.011 2.00e-02 2.50e+03 pdb=" OH TYR E 341 " -0.088 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 414 " 0.079 2.00e-02 2.50e+03 5.12e-02 4.58e+01 pdb=" CG PHE E 414 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE E 414 " -0.041 2.00e-02 2.50e+03 pdb=" CD2 PHE E 414 " -0.063 2.00e-02 2.50e+03 pdb=" CE1 PHE E 414 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE E 414 " 0.011 2.00e-02 2.50e+03 pdb=" CZ PHE E 414 " 0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 377 " 0.078 2.00e-02 2.50e+03 3.96e-02 3.14e+01 pdb=" CG TYR E 377 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR E 377 " -0.037 2.00e-02 2.50e+03 pdb=" CD2 TYR E 377 " -0.037 2.00e-02 2.50e+03 pdb=" CE1 TYR E 377 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR E 377 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR E 377 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR E 377 " 0.044 2.00e-02 2.50e+03 ... (remaining 4359 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 101 2.44 - 3.06: 16003 3.06 - 3.67: 36395 3.67 - 4.29: 53030 4.29 - 4.90: 90561 Nonbonded interactions: 196090 Sorted by model distance: nonbonded pdb=" OE2 GLU E 190 " pdb=" CE1 PHE E 215 " model vdw 1.830 3.340 nonbonded pdb=" CB ALA D 160 " pdb=" O2 PO4 D 602 " model vdw 1.920 3.460 nonbonded pdb=" CA ALA D 160 " pdb=" O2 PO4 D 602 " model vdw 1.929 3.470 nonbonded pdb=" O2G ATP F 501 " pdb="MG MG F 502 " model vdw 1.971 2.170 nonbonded pdb=" OG1 THR F 165 " pdb="MG MG F 502 " model vdw 2.006 2.170 ... (remaining 196085 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 24 through 501) selection = (chain 'B' and resid 24 through 501) selection = (chain 'C' and resid 24 through 501) } ncs_group { reference = (chain 'D' and resid 1 through 470) selection = (chain 'E' and resid 1 through 470) selection = (chain 'F' and resid 1 through 470) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.900 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 52.820 Find NCS groups from input model: 1.530 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 24655 Z= 0.198 Angle : 0.667 10.757 33433 Z= 0.388 Chirality : 0.046 0.321 3852 Planarity : 0.005 0.052 4362 Dihedral : 13.989 113.525 9347 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.89 % Favored : 97.05 % Rotamer: Outliers : 0.19 % Allowed : 0.43 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (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 HIS 0.007 0.001 HIS B 470 PHE 0.079 0.002 PHE E 414 TYR 0.088 0.002 TYR E 341 ARG 0.009 0.000 ARG E 454 Details of bonding type rmsd hydrogen bonds : bond 0.15528 ( 1148) hydrogen bonds : angle 6.56475 ( 3318) covalent geometry : bond 0.00400 (24655) covalent geometry : angle 0.66724 (33433) *********************** 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 : 2.951 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: 0.4221 (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: 0.4273 time to fit residues: 98.6384 Evaluate side-chains 107 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 104 time to evaluate : 3.016 ------------------------------------------------------------------------------- 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 261 optimal weight: 10.0000 chunk 234 optimal weight: 9.9990 chunk 130 optimal weight: 9.9990 chunk 80 optimal weight: 10.0000 chunk 158 optimal weight: 10.0000 chunk 125 optimal weight: 4.9990 chunk 242 optimal weight: 3.9990 chunk 94 optimal weight: 11.9990 chunk 147 optimal weight: 7.9990 chunk 180 optimal weight: 8.9990 chunk 281 optimal weight: 2.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN A 425 HIS C 189 GLN C 470 HIS D 53 HIS D 375 GLN E 179 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.070053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.054855 restraints weight = 74332.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.056666 restraints weight = 38726.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.057863 restraints weight = 24973.120| |-----------------------------------------------------------------------------| r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.0982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 24655 Z= 0.310 Angle : 0.691 11.645 33433 Z= 0.360 Chirality : 0.049 0.159 3852 Planarity : 0.005 0.053 4362 Dihedral : 8.452 121.349 3553 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.40 % Favored : 96.57 % Rotamer: Outliers : 0.62 % Allowed : 6.85 % Favored : 92.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.15), residues: 3115 helix: 0.69 (0.14), residues: 1267 sheet: 0.46 (0.23), residues: 508 loop : -0.37 (0.17), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS B 470 PHE 0.017 0.002 PHE D 125 TYR 0.016 0.002 TYR A 329 ARG 0.008 0.001 ARG D 376 Details of bonding type rmsd hydrogen bonds : bond 0.05537 ( 1148) hydrogen bonds : angle 5.50743 ( 3318) covalent geometry : bond 0.00738 (24655) covalent geometry : angle 0.69086 (33433) *********************** 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 126 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 4.282 Fit side-chains revert: symmetry clash REVERT: B 375 MET cc_start: 0.8694 (tpp) cc_final: 0.8348 (tmm) REVERT: F 64 MET cc_start: 0.9317 (mmt) cc_final: 0.9050 (mmt) REVERT: G 131 MET cc_start: 0.7041 (mmm) cc_final: 0.6649 (mmm) outliers start: 16 outliers final: 9 residues processed: 119 average time/residue: 0.4303 time to fit residues: 90.0945 Evaluate side-chains 114 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 105 time to evaluate : 2.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain B residue 262 ASP 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 252 ASP Chi-restraints excluded: chain F residue 338 MET 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 292 optimal weight: 8.9990 chunk 222 optimal weight: 9.9990 chunk 133 optimal weight: 9.9990 chunk 218 optimal weight: 7.9990 chunk 274 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 183 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 134 optimal weight: 8.9990 chunk 159 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN D 375 GLN G 107 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.074486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.059366 restraints weight = 72027.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.061313 restraints weight = 35508.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.062592 restraints weight = 22247.917| |-----------------------------------------------------------------------------| r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 24655 Z= 0.164 Angle : 0.559 11.131 33433 Z= 0.290 Chirality : 0.045 0.152 3852 Planarity : 0.004 0.056 4362 Dihedral : 8.043 126.150 3547 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.83 % Favored : 97.14 % Rotamer: Outliers : 1.01 % Allowed : 9.07 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.15), residues: 3115 helix: 1.09 (0.15), residues: 1245 sheet: 0.41 (0.23), residues: 518 loop : -0.30 (0.17), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 363 PHE 0.017 0.001 PHE B 395 TYR 0.014 0.001 TYR B 248 ARG 0.003 0.000 ARG A 476 Details of bonding type rmsd hydrogen bonds : bond 0.04609 ( 1148) hydrogen bonds : angle 5.10153 ( 3318) covalent geometry : bond 0.00384 (24655) covalent geometry : angle 0.55903 (33433) *********************** 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 145 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 119 time to evaluate : 3.848 Fit side-chains revert: symmetry clash REVERT: B 62 MET cc_start: 0.8485 (tpp) cc_final: 0.7943 (ttt) REVERT: B 407 GLN cc_start: 0.8139 (mt0) cc_final: 0.7867 (mp10) REVERT: D 389 MET cc_start: 0.6608 (ttt) cc_final: 0.6050 (tmm) REVERT: D 462 VAL cc_start: 0.4655 (t) cc_final: 0.4337 (t) REVERT: E 407 GLN cc_start: 0.9005 (tm-30) cc_final: 0.8778 (tm-30) REVERT: F 64 MET cc_start: 0.9335 (mmt) cc_final: 0.9049 (mmt) REVERT: G 67 MET cc_start: 0.7431 (mmm) cc_final: 0.7082 (mmp) REVERT: G 131 MET cc_start: 0.7104 (mmm) cc_final: 0.6762 (mmm) outliers start: 26 outliers final: 19 residues processed: 137 average time/residue: 0.4268 time to fit residues: 103.6073 Evaluate side-chains 126 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 3.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 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 156 LEU Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain C residue 250 MET Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain G residue 191 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 129 optimal weight: 10.0000 chunk 95 optimal weight: 7.9990 chunk 277 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 238 optimal weight: 6.9990 chunk 30 optimal weight: 9.9990 chunk 245 optimal weight: 8.9990 chunk 137 optimal weight: 9.9990 chunk 158 optimal weight: 6.9990 chunk 163 optimal weight: 4.9990 chunk 86 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 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 = 0.3268 r_free = 0.3268 target = 0.073120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.058028 restraints weight = 73082.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.059949 restraints weight = 36078.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.061202 restraints weight = 22616.449| |-----------------------------------------------------------------------------| r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 24655 Z= 0.247 Angle : 0.619 10.972 33433 Z= 0.321 Chirality : 0.047 0.162 3852 Planarity : 0.005 0.061 4362 Dihedral : 8.027 130.202 3547 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.95 % Allowed : 10.12 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.15), residues: 3115 helix: 0.94 (0.15), residues: 1240 sheet: 0.34 (0.23), residues: 522 loop : -0.43 (0.17), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS E 363 PHE 0.020 0.002 PHE B 395 TYR 0.015 0.001 TYR B 248 ARG 0.004 0.000 ARG D 405 Details of bonding type rmsd hydrogen bonds : bond 0.05008 ( 1148) hydrogen bonds : angle 5.15001 ( 3318) covalent geometry : bond 0.00588 (24655) covalent geometry : angle 0.61868 (33433) *********************** 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 159 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 109 time to evaluate : 2.676 Fit side-chains revert: symmetry clash REVERT: A 157 VAL cc_start: 0.8833 (OUTLIER) cc_final: 0.8576 (m) REVERT: B 62 MET cc_start: 0.8424 (OUTLIER) cc_final: 0.8202 (ttt) REVERT: D 376 ARG cc_start: 0.8138 (tpt90) cc_final: 0.7834 (tpt90) REVERT: D 462 VAL cc_start: 0.4549 (t) cc_final: 0.4228 (t) REVERT: E 407 GLN cc_start: 0.9020 (tm-30) cc_final: 0.8810 (tm-30) REVERT: G 25 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7583 (tt0) REVERT: G 131 MET cc_start: 0.7118 (mmm) cc_final: 0.6833 (mmm) outliers start: 50 outliers final: 33 residues processed: 149 average time/residue: 0.3092 time to fit residues: 78.1930 Evaluate side-chains 142 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 106 time to evaluate : 2.702 ------------------------------------------------------------------------------- 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 B residue 48 MET Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain C residue 250 MET Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 252 ASP 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 1 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 chunk 187 optimal weight: 4.9990 chunk 276 optimal weight: 1.9990 chunk 236 optimal weight: 3.9990 chunk 113 optimal weight: 6.9990 chunk 200 optimal weight: 1.9990 chunk 204 optimal weight: 0.8980 chunk 298 optimal weight: 9.9990 chunk 149 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN G 107 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.073575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.058560 restraints weight = 72618.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.060495 restraints weight = 36175.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.061726 restraints weight = 22712.988| |-----------------------------------------------------------------------------| r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1288 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= 0.138 Angle : 0.533 11.294 33433 Z= 0.275 Chirality : 0.044 0.152 3852 Planarity : 0.004 0.064 4362 Dihedral : 7.545 127.024 3547 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.52 % Allowed : 11.37 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.15), residues: 3115 helix: 1.26 (0.15), residues: 1238 sheet: 0.39 (0.23), residues: 522 loop : -0.28 (0.17), residues: 1355 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS G 107 PHE 0.017 0.001 PHE B 395 TYR 0.013 0.001 TYR B 248 ARG 0.004 0.000 ARG E 3 Details of bonding type rmsd hydrogen bonds : bond 0.04243 ( 1148) hydrogen bonds : angle 4.87502 ( 3318) covalent geometry : bond 0.00319 (24655) covalent geometry : angle 0.53299 (33433) *********************** 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 155 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 116 time to evaluate : 2.690 Fit side-chains REVERT: A 157 VAL cc_start: 0.8746 (OUTLIER) cc_final: 0.8440 (m) REVERT: B 407 GLN cc_start: 0.8105 (mt0) cc_final: 0.7822 (mp10) REVERT: B 455 ARG cc_start: 0.8961 (ttp80) cc_final: 0.8617 (ttp80) REVERT: D 376 ARG cc_start: 0.8098 (tpt90) cc_final: 0.7795 (tpt170) REVERT: D 381 GLN cc_start: 0.6085 (mm-40) cc_final: 0.5822 (mm110) REVERT: D 462 VAL cc_start: 0.4644 (t) cc_final: 0.4329 (t) REVERT: G 25 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7474 (tt0) REVERT: G 67 MET cc_start: 0.7461 (mmm) cc_final: 0.7080 (mmp) REVERT: G 241 MET cc_start: 0.8330 (ptt) cc_final: 0.8115 (tmm) outliers start: 39 outliers final: 28 residues processed: 147 average time/residue: 0.3460 time to fit residues: 85.8200 Evaluate side-chains 139 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 109 time to evaluate : 3.600 ------------------------------------------------------------------------------- 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 A residue 416 THR Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 298 LEU 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 250 MET Chi-restraints excluded: chain D residue 162 VAL 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 335 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 58 optimal weight: 0.0170 chunk 170 optimal weight: 10.0000 chunk 214 optimal weight: 0.9990 chunk 257 optimal weight: 0.7980 chunk 224 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 chunk 43 optimal weight: 10.0000 chunk 95 optimal weight: 8.9990 chunk 287 optimal weight: 7.9990 chunk 282 optimal weight: 4.9990 chunk 182 optimal weight: 10.0000 overall best weight: 2.5624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3295 r_free = 0.3295 target = 0.074447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.059252 restraints weight = 72001.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.061169 restraints weight = 36048.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.062433 restraints weight = 22768.247| |-----------------------------------------------------------------------------| r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 24655 Z= 0.153 Angle : 0.539 11.268 33433 Z= 0.278 Chirality : 0.044 0.151 3852 Planarity : 0.004 0.066 4362 Dihedral : 7.396 125.246 3547 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.26 % Allowed : 11.33 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.15), residues: 3115 helix: 1.28 (0.15), residues: 1242 sheet: 0.41 (0.23), residues: 523 loop : -0.26 (0.17), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 363 PHE 0.017 0.001 PHE B 395 TYR 0.013 0.001 TYR B 248 ARG 0.002 0.000 ARG D 405 Details of bonding type rmsd hydrogen bonds : bond 0.04231 ( 1148) hydrogen bonds : angle 4.83050 ( 3318) covalent geometry : bond 0.00360 (24655) covalent geometry : angle 0.53865 (33433) *********************** 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 169 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 111 time to evaluate : 3.255 Fit side-chains revert: symmetry clash REVERT: A 157 VAL cc_start: 0.8790 (OUTLIER) cc_final: 0.8501 (m) REVERT: B 407 GLN cc_start: 0.8066 (mt0) cc_final: 0.7790 (mp10) REVERT: B 455 ARG cc_start: 0.8962 (ttp80) cc_final: 0.8619 (ttp80) REVERT: D 376 ARG cc_start: 0.8062 (tpt90) cc_final: 0.7731 (tpt90) REVERT: D 381 GLN cc_start: 0.6162 (mm-40) cc_final: 0.5883 (mm110) REVERT: D 462 VAL cc_start: 0.4600 (t) cc_final: 0.4281 (t) REVERT: F 136 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7997 (pt0) REVERT: G 25 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7516 (tt0) REVERT: G 67 MET cc_start: 0.7447 (mmm) cc_final: 0.7032 (mmp) REVERT: G 131 MET cc_start: 0.7052 (mmm) cc_final: 0.6845 (mmm) outliers start: 58 outliers final: 41 residues processed: 160 average time/residue: 0.3565 time to fit residues: 96.9226 Evaluate side-chains 154 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 110 time to evaluate : 2.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 298 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 107 VAL Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 250 MET Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 404 ARG Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain E residue 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 335 LEU Chi-restraints excluded: chain E residue 383 ILE Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain 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 204 optimal weight: 7.9990 chunk 278 optimal weight: 8.9990 chunk 89 optimal weight: 10.0000 chunk 214 optimal weight: 1.9990 chunk 156 optimal weight: 7.9990 chunk 295 optimal weight: 20.0000 chunk 190 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 31 optimal weight: 10.0000 chunk 63 optimal weight: 8.9990 chunk 256 optimal weight: 3.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN G 107 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.071890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.056601 restraints weight = 73156.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.058555 restraints weight = 35747.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.059829 restraints weight = 22294.372| |-----------------------------------------------------------------------------| r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 24655 Z= 0.264 Angle : 0.629 10.939 33433 Z= 0.326 Chirality : 0.047 0.155 3852 Planarity : 0.005 0.064 4362 Dihedral : 7.556 131.785 3547 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.65 % Allowed : 11.84 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.15), residues: 3115 helix: 0.95 (0.15), residues: 1241 sheet: 0.30 (0.23), residues: 521 loop : -0.44 (0.17), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS E 363 PHE 0.025 0.002 PHE G 165 TYR 0.015 0.002 TYR B 248 ARG 0.004 0.000 ARG A 283 Details of bonding type rmsd hydrogen bonds : bond 0.04992 ( 1148) hydrogen bonds : angle 5.07975 ( 3318) covalent geometry : bond 0.00627 (24655) covalent geometry : angle 0.62861 (33433) *********************** 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 178 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 110 time to evaluate : 2.614 Fit side-chains revert: symmetry clash REVERT: A 157 VAL cc_start: 0.8922 (OUTLIER) cc_final: 0.8663 (m) REVERT: B 407 GLN cc_start: 0.8149 (mt0) cc_final: 0.7848 (mp10) REVERT: D 376 ARG cc_start: 0.8118 (tpt90) cc_final: 0.7805 (tpt170) REVERT: D 381 GLN cc_start: 0.6106 (mm-40) cc_final: 0.5818 (mm110) REVERT: D 462 VAL cc_start: 0.4501 (t) cc_final: 0.4173 (t) REVERT: F 64 MET cc_start: 0.9336 (mmp) cc_final: 0.8821 (mmp) REVERT: F 136 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8064 (pt0) REVERT: G 25 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7564 (tt0) REVERT: G 107 HIS cc_start: 0.5931 (m-70) cc_final: 0.5700 (m170) outliers start: 68 outliers final: 50 residues processed: 170 average time/residue: 0.3575 time to fit residues: 103.5979 Evaluate side-chains 159 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 106 time to evaluate : 2.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL 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 445 LEU Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 404 ARG Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 383 ILE Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain G residue 25 GLU Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 202 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 97 optimal weight: 2.9990 chunk 213 optimal weight: 1.9990 chunk 228 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 85 optimal weight: 8.9990 chunk 183 optimal weight: 9.9990 chunk 76 optimal weight: 2.9990 chunk 225 optimal weight: 6.9990 chunk 260 optimal weight: 0.7980 chunk 221 optimal weight: 9.9990 chunk 82 optimal weight: 0.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.071633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.056506 restraints weight = 73196.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.058341 restraints weight = 37925.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.059550 restraints weight = 24354.515| |-----------------------------------------------------------------------------| r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1539 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= 0.123 Angle : 0.527 11.432 33433 Z= 0.271 Chirality : 0.043 0.151 3852 Planarity : 0.004 0.064 4362 Dihedral : 7.131 127.644 3547 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.10 % Allowed : 12.31 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.15), residues: 3115 helix: 1.33 (0.15), residues: 1239 sheet: 0.47 (0.23), residues: 510 loop : -0.32 (0.17), residues: 1366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 363 PHE 0.015 0.001 PHE B 395 TYR 0.013 0.001 TYR B 248 ARG 0.002 0.000 ARG A 296 Details of bonding type rmsd hydrogen bonds : bond 0.04003 ( 1148) hydrogen bonds : angle 4.74558 ( 3318) covalent geometry : bond 0.00283 (24655) covalent geometry : angle 0.52708 (33433) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 116 time to evaluate : 3.015 Fit side-chains revert: symmetry clash REVERT: A 157 VAL cc_start: 0.8784 (OUTLIER) cc_final: 0.8499 (m) REVERT: B 407 GLN cc_start: 0.8061 (mt0) cc_final: 0.7788 (mp10) REVERT: B 455 ARG cc_start: 0.8976 (ttp80) cc_final: 0.8629 (ttp80) REVERT: C 250 MET cc_start: 0.8535 (OUTLIER) cc_final: 0.8263 (tmm) REVERT: D 376 ARG cc_start: 0.8073 (tpt90) cc_final: 0.7867 (tpt90) REVERT: D 381 GLN cc_start: 0.6144 (mm-40) cc_final: 0.5862 (mm110) REVERT: D 462 VAL cc_start: 0.4605 (t) cc_final: 0.4305 (t) REVERT: F 136 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7992 (pt0) REVERT: G 25 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7405 (tt0) REVERT: G 67 MET cc_start: 0.7510 (mmm) cc_final: 0.7105 (mmp) REVERT: G 107 HIS cc_start: 0.5810 (m-70) cc_final: 0.5601 (m170) REVERT: G 171 TYR cc_start: 0.8076 (m-80) cc_final: 0.7696 (m-80) REVERT: G 241 MET cc_start: 0.8368 (ptt) cc_final: 0.8154 (tmm) outliers start: 54 outliers final: 39 residues processed: 163 average time/residue: 0.4589 time to fit residues: 131.8141 Evaluate side-chains 156 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 113 time to evaluate : 3.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 88 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 499 VAL Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 94 ILE 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 250 MET Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 404 ARG Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 383 ILE Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain G residue 25 GLU Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 202 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 139 optimal weight: 0.8980 chunk 166 optimal weight: 7.9990 chunk 200 optimal weight: 0.9990 chunk 225 optimal weight: 7.9990 chunk 117 optimal weight: 0.7980 chunk 303 optimal weight: 7.9990 chunk 251 optimal weight: 0.3980 chunk 246 optimal weight: 9.9990 chunk 238 optimal weight: 6.9990 chunk 110 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 333 ASN D 375 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.073375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.058295 restraints weight = 73492.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.060165 restraints weight = 37659.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.061396 restraints weight = 23950.870| |-----------------------------------------------------------------------------| r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 24655 Z= 0.095 Angle : 0.496 11.378 33433 Z= 0.253 Chirality : 0.042 0.157 3852 Planarity : 0.004 0.064 4362 Dihedral : 6.565 113.000 3547 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.56 % Allowed : 13.01 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.16), residues: 3115 helix: 1.60 (0.15), residues: 1244 sheet: 0.49 (0.24), residues: 516 loop : -0.10 (0.17), residues: 1355 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 470 PHE 0.014 0.001 PHE G 165 TYR 0.013 0.001 TYR D 377 ARG 0.003 0.000 ARG B 213 Details of bonding type rmsd hydrogen bonds : bond 0.03421 ( 1148) hydrogen bonds : angle 4.49590 ( 3318) covalent geometry : bond 0.00204 (24655) covalent geometry : angle 0.49557 (33433) *********************** 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 170 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 130 time to evaluate : 5.600 Fit side-chains revert: symmetry clash REVERT: A 157 VAL cc_start: 0.8746 (OUTLIER) cc_final: 0.8453 (m) REVERT: B 455 ARG cc_start: 0.9035 (ttp80) cc_final: 0.8771 (ttp80) REVERT: D 1 MET cc_start: 0.6275 (tmm) cc_final: 0.4481 (mmp) REVERT: D 37 ARG cc_start: 0.7469 (mtm180) cc_final: 0.7246 (mtm180) REVERT: D 381 GLN cc_start: 0.6076 (mm-40) cc_final: 0.5737 (mm110) REVERT: D 462 VAL cc_start: 0.4479 (t) cc_final: 0.4182 (t) REVERT: G 67 MET cc_start: 0.7423 (mmm) cc_final: 0.6972 (mmp) REVERT: G 171 TYR cc_start: 0.8014 (m-80) cc_final: 0.7706 (m-80) outliers start: 40 outliers final: 34 residues processed: 165 average time/residue: 0.4356 time to fit residues: 122.3806 Evaluate side-chains 146 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 111 time to evaluate : 4.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL 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 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 95 MET Chi-restraints excluded: chain B residue 146 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 48 MET Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 333 ASN Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 404 ARG Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 301 THR 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 14 optimal weight: 10.0000 chunk 219 optimal weight: 0.9990 chunk 209 optimal weight: 0.0000 chunk 4 optimal weight: 0.6980 chunk 247 optimal weight: 4.9990 chunk 173 optimal weight: 10.0000 chunk 230 optimal weight: 4.9990 chunk 44 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 279 optimal weight: 0.5980 chunk 186 optimal weight: 9.9990 overall best weight: 1.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 HIS G 107 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.073063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.057952 restraints weight = 73372.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.059807 restraints weight = 37815.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.061023 restraints weight = 24201.329| |-----------------------------------------------------------------------------| r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1776 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= 0.105 Angle : 0.517 11.289 33433 Z= 0.261 Chirality : 0.043 0.199 3852 Planarity : 0.004 0.063 4362 Dihedral : 6.435 110.690 3546 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.44 % Allowed : 12.89 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.15), residues: 3115 helix: 1.62 (0.15), residues: 1246 sheet: 0.64 (0.24), residues: 503 loop : -0.10 (0.17), residues: 1366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 363 PHE 0.012 0.001 PHE B 395 TYR 0.010 0.001 TYR B 248 ARG 0.002 0.000 ARG E 376 Details of bonding type rmsd hydrogen bonds : bond 0.03521 ( 1148) hydrogen bonds : angle 4.50590 ( 3318) covalent geometry : bond 0.00236 (24655) covalent geometry : angle 0.51734 (33433) ********************** 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 153 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 116 time to evaluate : 4.247 Fit side-chains revert: symmetry clash REVERT: A 157 VAL cc_start: 0.8796 (OUTLIER) cc_final: 0.8519 (m) REVERT: B 455 ARG cc_start: 0.9039 (ttp80) cc_final: 0.8778 (ttp80) REVERT: D 1 MET cc_start: 0.6293 (tmm) cc_final: 0.4564 (mmp) REVERT: D 37 ARG cc_start: 0.7455 (mtm180) cc_final: 0.7222 (mtm180) REVERT: D 381 GLN cc_start: 0.6157 (mm-40) cc_final: 0.5871 (mm110) REVERT: D 462 VAL cc_start: 0.4500 (t) cc_final: 0.4212 (t) REVERT: G 67 MET cc_start: 0.7457 (mmm) cc_final: 0.7048 (mmp) REVERT: G 171 TYR cc_start: 0.8022 (m-80) cc_final: 0.7710 (m-80) outliers start: 37 outliers final: 34 residues processed: 150 average time/residue: 0.4204 time to fit residues: 107.8199 Evaluate side-chains 144 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 109 time to evaluate : 2.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL 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 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 95 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 404 ARG Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 301 THR 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 153 optimal weight: 4.9990 chunk 150 optimal weight: 6.9990 chunk 133 optimal weight: 10.0000 chunk 192 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 197 optimal weight: 8.9990 chunk 22 optimal weight: 4.9990 chunk 235 optimal weight: 7.9990 chunk 147 optimal weight: 10.0000 chunk 162 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN C 189 GLN D 375 GLN D 381 GLN ** G 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.069727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.054523 restraints weight = 74650.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.056321 restraints weight = 38823.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.057504 restraints weight = 25040.061| |-----------------------------------------------------------------------------| r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 24655 Z= 0.295 Angle : 0.665 10.841 33433 Z= 0.342 Chirality : 0.048 0.199 3852 Planarity : 0.005 0.061 4362 Dihedral : 6.882 125.100 3546 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.67 % Allowed : 12.93 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.15), residues: 3115 helix: 1.10 (0.15), residues: 1244 sheet: 0.44 (0.24), residues: 502 loop : -0.42 (0.17), residues: 1369 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.001 HIS G 107 PHE 0.030 0.002 PHE G 165 TYR 0.015 0.002 TYR B 248 ARG 0.010 0.001 ARG D 270 Details of bonding type rmsd hydrogen bonds : bond 0.04968 ( 1148) hydrogen bonds : angle 5.00497 ( 3318) covalent geometry : bond 0.00698 (24655) covalent geometry : angle 0.66460 (33433) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7133.25 seconds wall clock time: 131 minutes 3.82 seconds (7863.82 seconds total)