Starting phenix.real_space_refine on Sun Jul 5 00:08:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hhc_34760/07_2026/8hhc_34760.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hhc_34760/07_2026/8hhc_34760.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8hhc_34760/07_2026/8hhc_34760.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hhc_34760/07_2026/8hhc_34760.cif" model { file = "/net/cci-nas-00/data/ceres_data/8hhc_34760/07_2026/8hhc_34760.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hhc_34760/07_2026/8hhc_34760.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hhc_34760/07_2026/8hhc_34760.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hhc_34760/07_2026/8hhc_34760.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 16 5.49 5 Mg 5 5.21 5 S 77 5.16 5 C 15277 2.51 5 N 4214 2.21 5 O 4660 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24249 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3661 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 23, 'TRANS': 454} Chain: "B" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3661 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 23, 'TRANS': 454} Chain: "C" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3661 Classifications: {'peptide': 478} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 454} Chain: "D" Number of atoms: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3630 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 447} Chain: "E" Number of atoms: 3623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3623 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 446} Chain: "F" Number of atoms: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3630 Classifications: {'peptide': 471} Link IDs: {'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: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 272} Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {' MG': 1, 'ATP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.59, per 1000 atoms: 0.23 Number of scatterers: 24249 At special positions: 0 Unit cell: (127.6, 121.44, 154.88, 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 4660 8.00 N 4214 7.00 C 15277 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.04 Conformation dependent library (CDL) restraints added in 1.2 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 22 sheets defined 48.4% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 78 through 82 removed outlier: 4.020A pdb=" N GLY A 81 " --> pdb=" O PRO A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 104 Processing helix chain 'A' and resid 135 through 139 removed outlier: 3.953A pdb=" N ARG A 139 " --> pdb=" O VAL A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 157 removed outlier: 3.966A pdb=" N LEU A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 186 removed outlier: 3.552A pdb=" N GLN A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) 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 252 removed outlier: 3.685A pdb=" N LEU A 235 " --> pdb=" O PRO A 231 " (cutoff:3.500A) Proline residue: A 239 - end of helix removed outlier: 3.702A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS A 252 " --> pdb=" O TYR A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 277 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 351 Processing helix chain 'A' and resid 372 through 393 removed outlier: 3.825A pdb=" N GLY A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N THR A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LEU A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ARG A 383 " --> pdb=" O ALA A 379 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LEU A 384 " --> pdb=" O GLY A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 396 No H-bonds generated for 'chain 'A' and resid 394 through 396' Processing helix chain 'A' and resid 405 through 421 removed outlier: 4.287A pdb=" N ALA A 411 " --> pdb=" O GLN A 407 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS A 421 " --> pdb=" O VAL A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 442 Processing helix chain 'A' and resid 449 through 468 removed outlier: 4.547A pdb=" N ARG A 454 " --> pdb=" O VAL A 450 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ARG A 455 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLN A 466 " --> pdb=" O LEU A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 479 removed outlier: 3.919A pdb=" N HIS A 474 " --> pdb=" O HIS A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 498 Processing helix chain 'B' and resid 100 through 104 Processing helix chain 'B' and resid 150 through 157 Processing helix chain 'B' and resid 174 through 186 removed outlier: 3.552A 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 251 removed outlier: 3.767A pdb=" N LEU B 235 " --> pdb=" O PRO B 231 " (cutoff:3.500A) Proline residue: B 239 - end of helix removed outlier: 3.628A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 277 removed outlier: 3.901A pdb=" N GLN B 266 " --> pdb=" O ASP B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 286 Processing helix chain 'B' and resid 287 through 288 No H-bonds generated for 'chain 'B' and resid 287 through 288' Processing helix chain 'B' and resid 289 through 299 removed outlier: 3.779A pdb=" N HIS B 294 " --> pdb=" O ILE B 290 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG B 296 " --> pdb=" O TYR B 292 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LEU B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 338 Processing helix chain 'B' and resid 345 through 351 Processing helix chain 'B' and resid 372 through 399 removed outlier: 3.511A pdb=" N LYS B 376 " --> pdb=" O ILE B 372 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS B 377 " --> pdb=" O LYS B 373 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N VAL B 378 " --> pdb=" O ALA B 374 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY B 380 " --> pdb=" O LYS B 376 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N THR B 381 " --> pdb=" O LYS B 377 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU B 384 " --> pdb=" O GLY B 380 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU B 391 " --> pdb=" O ALA B 387 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU B 392 " --> pdb=" O ALA B 388 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ALA B 394 " --> pdb=" O ARG B 390 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N PHE B 395 " --> pdb=" O GLU B 391 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN B 397 " --> pdb=" O GLU B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 420 removed outlier: 3.598A pdb=" N ALA B 408 " --> pdb=" O LYS B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 442 Processing helix chain 'B' and resid 452 through 468 removed outlier: 3.715A pdb=" N LEU B 462 " --> pdb=" O LYS B 458 " (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: 3.675A pdb=" N LEU C 103 " --> pdb=" O GLY C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 139 Processing helix chain 'C' and resid 150 through 157 Processing helix chain 'C' and resid 174 through 186 removed outlier: 3.624A pdb=" N GLN C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 189 No H-bonds generated for 'chain 'C' and resid 187 through 189' Processing helix chain 'C' and resid 201 through 216 Processing helix chain 'C' and resid 217 through 219 No H-bonds generated for 'chain 'C' and resid 217 through 219' Processing helix chain 'C' and resid 231 through 253 removed outlier: 3.653A pdb=" N LEU C 235 " --> pdb=" O PRO C 231 " (cutoff:3.500A) Proline residue: C 239 - end of helix removed outlier: 3.597A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 277 removed outlier: 4.152A pdb=" N GLN C 266 " --> pdb=" O ASP C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 286 Processing helix chain 'C' and resid 287 through 288 No H-bonds generated for 'chain 'C' and resid 287 through 288' Processing helix chain 'C' and resid 289 through 299 Processing helix chain 'C' and resid 305 through 309 Processing helix chain 'C' and resid 328 through 338 Processing helix chain 'C' and resid 345 through 351 Processing helix chain 'C' and resid 372 through 396 removed outlier: 3.906A pdb=" N VAL C 378 " --> pdb=" O ALA C 374 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLY C 380 " --> pdb=" O LYS C 376 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N THR C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 421 removed outlier: 3.727A pdb=" N LYS C 409 " --> pdb=" O ALA C 405 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG C 412 " --> pdb=" O ALA C 408 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY C 413 " --> pdb=" O LYS C 409 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA C 414 " --> pdb=" O LEU C 410 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS C 421 " --> pdb=" O VAL C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 442 removed outlier: 4.038A pdb=" N LEU C 435 " --> pdb=" O GLU C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 468 removed outlier: 4.650A pdb=" N ARG C 454 " --> pdb=" O VAL C 450 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N ARG C 455 " --> pdb=" O GLU C 451 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU C 462 " --> pdb=" O LYS C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 479 Processing helix chain 'C' and resid 483 through 498 Processing helix chain 'D' and resid 88 through 92 Processing helix chain 'D' and resid 139 through 146 Processing helix chain 'D' and resid 163 through 179 removed outlier: 3.764A pdb=" N HIS D 173 " --> pdb=" O GLN D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 206 Processing helix chain 'D' and resid 207 through 209 No H-bonds generated for 'chain 'D' and resid 207 through 209' Processing helix chain 'D' and resid 221 through 244 removed outlier: 5.142A pdb=" N ALA D 229 " --> pdb=" O ARG D 225 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N LEU D 230 " --> pdb=" O MET D 226 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR D 238 " --> pdb=" O THR D 234 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE D 239 " --> pdb=" O MET D 235 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN D 243 " --> pdb=" O PHE D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 269 removed outlier: 3.623A pdb=" N PHE D 257 " --> pdb=" O ASN D 253 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY D 261 " --> pdb=" O PHE D 257 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA D 266 " --> pdb=" O SER D 262 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU D 267 " --> pdb=" O GLU D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 290 Processing helix chain 'D' and resid 309 through 312 Processing helix chain 'D' and resid 315 through 323 removed outlier: 4.193A pdb=" N SER D 323 " --> pdb=" O ALA D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 338 Processing helix chain 'D' and resid 355 through 360 Processing helix chain 'D' and resid 360 through 388 removed outlier: 3.788A pdb=" N LYS D 378 " --> pdb=" O LEU D 374 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLU D 379 " --> pdb=" O GLN D 375 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU D 380 " --> pdb=" O ARG D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 410 removed outlier: 4.435A pdb=" N ARG D 404 " --> pdb=" O VAL D 400 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLN D 407 " --> pdb=" O ALA D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 422 removed outlier: 3.867A pdb=" N THR D 421 " --> pdb=" O ALA D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 443 Processing helix chain 'D' and resid 449 through 454 removed outlier: 3.637A pdb=" N PHE D 453 " --> pdb=" O GLU D 450 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG D 454 " --> pdb=" O ASP D 451 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 470 removed outlier: 4.337A pdb=" N VAL D 463 " --> pdb=" O ILE D 459 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N GLU D 464 " --> pdb=" O GLU D 460 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 92 Processing helix chain 'E' and resid 139 through 146 Processing helix chain 'E' and resid 163 through 179 Processing helix chain 'E' and resid 191 through 206 Processing helix chain 'E' and resid 207 through 209 No H-bonds generated for 'chain 'E' and resid 207 through 209' Processing helix chain 'E' and resid 221 through 243 removed outlier: 5.406A pdb=" N ALA E 229 " --> pdb=" O ARG E 225 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N LEU E 230 " --> pdb=" O MET E 226 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N PHE E 239 " --> pdb=" O MET E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 269 removed outlier: 3.888A pdb=" N PHE E 257 " --> pdb=" O ASN E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 277 Processing helix chain 'E' and resid 280 through 290 Processing helix chain 'E' and resid 308 through 312 Processing helix chain 'E' and resid 315 through 322 Processing helix chain 'E' and resid 332 through 339 Processing helix chain 'E' and resid 360 through 380 Processing helix chain 'E' and resid 380 through 387 Processing helix chain 'E' and resid 388 through 392 Processing helix chain 'E' and resid 393 through 410 removed outlier: 3.568A pdb=" N ARG E 404 " --> pdb=" O VAL E 400 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 416 No H-bonds generated for 'chain 'E' and resid 414 through 416' 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: 3.594A pdb=" N ARG E 454 " --> pdb=" O ASP E 451 " (cutoff:3.500A) Processing helix chain 'E' and resid 458 through 470 removed outlier: 4.019A pdb=" N VAL E 462 " --> pdb=" O ARG E 458 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL E 463 " --> pdb=" O ILE E 459 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 92 Processing helix chain 'F' and resid 124 through 128 Processing helix chain 'F' and resid 139 through 146 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 242 removed outlier: 5.003A pdb=" N ALA F 229 " --> pdb=" O ARG F 225 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N LEU F 230 " --> pdb=" O MET F 226 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE F 239 " --> pdb=" O MET F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 266 removed outlier: 4.050A pdb=" N THR F 258 " --> pdb=" O ILE F 254 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA F 266 " --> pdb=" O SER F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 290 Processing helix chain 'F' and resid 309 through 312 Processing helix chain 'F' and resid 315 through 322 removed outlier: 3.553A pdb=" N THR F 321 " --> pdb=" O ALA F 317 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE F 322 " --> pdb=" O PRO F 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 325 No H-bonds generated for 'chain 'F' and resid 323 through 325' Processing helix chain 'F' and resid 332 through 338 Processing helix chain 'F' and resid 355 through 360 Processing helix chain 'F' and resid 360 through 380 Processing helix chain 'F' and resid 380 through 388 Processing helix chain 'F' and resid 389 through 392 removed outlier: 3.535A pdb=" N LEU F 392 " --> pdb=" O MET F 389 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 389 through 392' Processing helix chain 'F' and resid 393 through 410 removed outlier: 3.717A pdb=" N ARG F 405 " --> pdb=" O HIS F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 419 removed outlier: 4.048A 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: 3.650A pdb=" N ARG F 454 " --> pdb=" O ASP F 451 " (cutoff:3.500A) Processing helix chain 'F' and resid 458 through 467 removed outlier: 3.681A pdb=" N VAL F 462 " --> pdb=" O ARG F 458 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL F 463 " --> pdb=" O ILE F 459 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 58 removed outlier: 3.758A pdb=" N THR G 17 " --> pdb=" O ALA G 13 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN G 19 " --> pdb=" O LYS G 15 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILE G 20 " --> pdb=" O LYS G 16 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS G 31 " --> pdb=" O VAL G 27 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL G 43 " --> pdb=" O ALA G 39 " (cutoff:3.500A) Proline residue: G 44 - end of helix removed outlier: 3.921A pdb=" N LEU G 58 " --> pdb=" O ALA G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 107 removed outlier: 3.841A pdb=" N VAL G 95 " --> pdb=" O TYR G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 129 Processing helix chain 'G' and resid 145 through 162 removed outlier: 4.882A pdb=" N GLU G 151 " --> pdb=" O ALA G 147 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ILE G 152 " --> pdb=" O ASP G 148 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU G 159 " --> pdb=" O LYS G 155 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE G 160 " --> pdb=" O THR G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 283 removed outlier: 3.857A pdb=" N VAL G 215 " --> pdb=" O GLU G 211 " (cutoff:3.500A) Proline residue: G 218 - end of helix removed outlier: 3.871A pdb=" N ALA G 228 " --> pdb=" O LEU G 224 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 35 removed outlier: 6.563A pdb=" N ARG A 40 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N VAL A 34 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ILE A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN A 65 " --> pdb=" O GLY A 72 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL A 74 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ALA A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LEU A 76 " --> pdb=" O GLY A 61 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N GLY A 61 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLU A 51 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N LEU A 52 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR A 91 " --> pdb=" O LEU A 52 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 99 removed outlier: 3.994A 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: 6.431A pdb=" N VAL A 108 " --> pdb=" O THR A 225 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 318 through 321 removed outlier: 6.887A pdb=" N ILE A 167 " --> pdb=" O VAL A 319 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N THR A 321 " --> pdb=" O ILE A 167 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N GLY A 169 " --> pdb=" O THR A 321 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASP A 170 " --> pdb=" O LEU A 344 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 60 through 66 removed outlier: 4.252A pdb=" N GLU B 51 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N LEU B 52 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ARG B 40 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N VAL B 34 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ILE B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ASN B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N LEU B 66 " --> pdb=" O ASN B 70 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLY B 72 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N GLU F 75 " --> pdb=" O GLN F 33 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N GLN F 33 " --> pdb=" O GLU F 75 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ARG F 60 " --> pdb=" O ALA F 51 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N HIS F 53 " --> pdb=" O THR F 58 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N THR F 58 " --> pdb=" O HIS F 53 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL F 13 " --> pdb=" O VAL F 9 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N VAL F 9 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ASP F 15 " --> pdb=" O ILE F 7 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 96 through 99 removed outlier: 4.228A pdb=" N GLU B 125 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 107 through 108 removed outlier: 3.606A pdb=" N TYR B 260 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU B 166 " --> pdb=" O ILE B 342 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 145 through 146 removed outlier: 4.600A pdb=" N ILE B 159 " --> pdb=" O LEU B 146 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 28 through 35 removed outlier: 6.394A pdb=" N ARG C 40 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N VAL C 34 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ILE C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN C 65 " --> pdb=" O GLY C 72 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL C 74 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N ALA C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLU C 51 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N LEU C 52 " --> pdb=" O THR C 91 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR C 91 " --> pdb=" O LEU C 52 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 96 through 99 removed outlier: 3.826A pdb=" N GLU C 125 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 107 through 108 removed outlier: 3.586A pdb=" N TYR C 260 " --> pdb=" O LEU C 316 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 3 through 10 removed outlier: 5.654A pdb=" N VAL D 6 " --> pdb=" O LYS D 17 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LYS D 17 " --> pdb=" O VAL D 6 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N THR D 58 " --> pdb=" O HIS D 53 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N HIS D 53 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ARG D 60 " --> pdb=" O ALA D 51 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N GLN D 33 " --> pdb=" O GLU D 75 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N GLU D 75 " --> pdb=" O GLN D 33 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 84 through 86 Processing sheet with id=AB5, first strand: chain 'D' and resid 95 through 96 removed outlier: 3.675A pdb=" N ILE D 182 " --> pdb=" O ASP D 246 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N VAL D 247 " --> pdb=" O THR D 301 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ILE D 303 " --> pdb=" O VAL D 247 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU D 249 " --> pdb=" O ILE D 303 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N ALA D 305 " --> pdb=" O LEU D 249 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ILE D 251 " --> pdb=" O ALA D 305 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N TYR D 307 " --> pdb=" O ILE D 251 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILE D 154 " --> pdb=" O GLN D 304 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N ILE D 306 " --> pdb=" O ILE D 154 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N LEU D 156 " --> pdb=" O ILE D 306 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 3 through 10 removed outlier: 5.848A pdb=" N VAL E 6 " --> pdb=" O LYS E 17 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N LYS E 17 " --> pdb=" O VAL E 6 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL E 13 " --> pdb=" O MET E 10 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N THR E 58 " --> pdb=" O HIS E 53 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N HIS E 53 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ARG E 60 " --> pdb=" O ALA E 51 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N GLN E 33 " --> pdb=" O GLU E 75 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N GLU E 75 " --> pdb=" O GLN E 33 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 84 through 86 Processing sheet with id=AB8, first strand: chain 'E' and resid 95 through 96 removed outlier: 6.512A pdb=" N PHE E 96 " --> pdb=" O PHE E 215 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N GLN E 217 " --> pdb=" O PHE E 96 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE E 154 " --> pdb=" O GLN E 304 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 134 through 135 removed outlier: 4.409A pdb=" N TYR E 148 " --> pdb=" O LEU E 135 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 84 through 86 Processing sheet with id=AC2, first strand: chain 'F' and resid 95 through 96 removed outlier: 6.697A pdb=" N PHE F 96 " --> pdb=" O PHE F 215 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL F 247 " --> pdb=" O THR F 301 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N ILE F 303 " --> pdb=" O VAL F 247 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU F 249 " --> pdb=" O ILE F 303 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N ALA F 305 " --> pdb=" O LEU F 249 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ILE F 251 " --> pdb=" O ALA F 305 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N TYR F 307 " --> pdb=" O ILE F 251 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE F 154 " --> pdb=" O GLN F 304 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ILE F 306 " --> pdb=" O ILE F 154 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N LEU F 156 " --> pdb=" O ILE F 306 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LYS F 153 " --> pdb=" O ALA F 327 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N THR F 329 " --> pdb=" O LYS F 153 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLY F 155 " --> pdb=" O THR F 329 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 134 through 135 removed outlier: 4.119A pdb=" N TYR F 148 " --> pdb=" O LEU F 135 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 133 through 137 removed outlier: 6.927A pdb=" N VAL G 133 " --> pdb=" O TYR G 113 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ILE G 115 " --> pdb=" O VAL G 133 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LEU G 135 " --> pdb=" O ILE G 115 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE G 137 " --> pdb=" O VAL G 117 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N THR G 76 " --> pdb=" O ALA G 114 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N ILE G 116 " --> pdb=" O THR G 76 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N TYR G 78 " --> pdb=" O ILE G 116 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ILE G 118 " --> pdb=" O TYR G 78 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL G 80 " --> pdb=" O ILE G 118 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N ASN G 173 " --> pdb=" O ILE G 81 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU G 168 " --> pdb=" O LEU G 188 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N GLN G 180 " --> pdb=" O VAL G 176 " (cutoff:3.500A) 1176 hydrogen bonds defined for protein. 3354 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.69 Time building geometry restraints manager: 2.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8239 1.34 - 1.46: 4727 1.46 - 1.58: 11519 1.58 - 1.70: 16 1.70 - 1.81: 154 Bond restraints: 24655 Sorted by residual: bond pdb=" CB PRO G 207 " pdb=" CG PRO G 207 " ideal model delta sigma weight residual 1.492 1.641 -0.149 5.00e-02 4.00e+02 8.90e+00 bond pdb=" O3 PO4 A 603 " pdb=" P PO4 A 603 " ideal model delta sigma weight residual 1.569 1.510 0.059 2.00e-02 2.50e+03 8.82e+00 bond pdb=" O4 PO4 A 603 " pdb=" P PO4 A 603 " ideal model delta sigma weight residual 1.568 1.510 0.058 2.00e-02 2.50e+03 8.34e+00 bond pdb=" O2 PO4 A 603 " pdb=" P PO4 A 603 " ideal model delta sigma weight residual 1.567 1.509 0.058 2.00e-02 2.50e+03 8.27e+00 bond pdb=" O1 PO4 A 603 " pdb=" P PO4 A 603 " ideal model delta sigma weight residual 1.565 1.511 0.054 2.00e-02 2.50e+03 7.23e+00 ... (remaining 24650 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.58: 33122 2.58 - 5.17: 286 5.17 - 7.75: 21 7.75 - 10.33: 3 10.33 - 12.91: 2 Bond angle restraints: 33434 Sorted by residual: angle pdb=" CA PRO G 207 " pdb=" N PRO G 207 " pdb=" CD PRO G 207 " ideal model delta sigma weight residual 112.00 99.09 12.91 1.40e+00 5.10e-01 8.51e+01 angle pdb=" C SER D 393 " pdb=" N ASP D 394 " pdb=" CA ASP D 394 " ideal model delta sigma weight residual 121.54 132.21 -10.67 1.91e+00 2.74e-01 3.12e+01 angle pdb=" N PRO G 207 " pdb=" CD PRO G 207 " pdb=" CG PRO G 207 " ideal model delta sigma weight residual 103.20 95.84 7.36 1.50e+00 4.44e-01 2.41e+01 angle pdb=" C PHE G 42 " pdb=" N VAL G 43 " pdb=" CA VAL G 43 " ideal model delta sigma weight residual 120.33 123.65 -3.32 8.00e-01 1.56e+00 1.73e+01 angle pdb=" C LEU F 455 " pdb=" N VAL F 456 " pdb=" CA VAL F 456 " ideal model delta sigma weight residual 123.08 119.08 4.00 1.01e+00 9.80e-01 1.57e+01 ... (remaining 33429 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 13796 17.71 - 35.42: 897 35.42 - 53.13: 161 53.13 - 70.84: 50 70.84 - 88.54: 23 Dihedral angle restraints: 14927 sinusoidal: 6002 harmonic: 8925 Sorted by residual: dihedral pdb=" CA ARG C 164 " pdb=" C ARG C 164 " pdb=" N GLU C 165 " pdb=" CA GLU C 165 " ideal model delta harmonic sigma weight residual 180.00 -159.64 -20.36 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA GLN C 397 " pdb=" C GLN C 397 " pdb=" N PHE C 398 " pdb=" CA PHE C 398 " ideal model delta harmonic sigma weight residual 180.00 160.35 19.65 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA PHE F 215 " pdb=" C PHE F 215 " pdb=" N GLY F 216 " pdb=" CA GLY F 216 " ideal model delta harmonic sigma weight residual 180.00 161.18 18.82 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 14924 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 2476 0.039 - 0.078: 976 0.078 - 0.117: 340 0.117 - 0.156: 58 0.156 - 0.195: 2 Chirality restraints: 3852 Sorted by residual: chirality pdb=" CB ILE D 172 " pdb=" CA ILE D 172 " pdb=" CG1 ILE D 172 " pdb=" CG2 ILE D 172 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.53e-01 chirality pdb=" CA ARG C 164 " pdb=" N ARG C 164 " pdb=" C ARG C 164 " pdb=" CB ARG C 164 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.14e-01 chirality pdb=" CA PHE D 215 " pdb=" N PHE D 215 " pdb=" C PHE D 215 " pdb=" CB PHE D 215 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.16 2.00e-01 2.50e+01 6.02e-01 ... (remaining 3849 not shown) Planarity restraints: 4362 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU G 206 " -0.086 5.00e-02 4.00e+02 1.21e-01 2.35e+01 pdb=" N PRO G 207 " 0.209 5.00e-02 4.00e+02 pdb=" CA PRO G 207 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO G 207 " -0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER D 393 " -0.012 2.00e-02 2.50e+03 2.39e-02 5.72e+00 pdb=" C SER D 393 " 0.041 2.00e-02 2.50e+03 pdb=" O SER D 393 " -0.016 2.00e-02 2.50e+03 pdb=" N ASP D 394 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG G 71 " 0.032 5.00e-02 4.00e+02 4.82e-02 3.72e+00 pdb=" N PRO G 72 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO G 72 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO G 72 " 0.027 5.00e-02 4.00e+02 ... (remaining 4359 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.40: 66 2.40 - 3.03: 14539 3.03 - 3.65: 35399 3.65 - 4.28: 53372 4.28 - 4.90: 92356 Nonbonded interactions: 195732 Sorted by model distance: nonbonded pdb=" OG1 THR D 165 " pdb="MG MG D 502 " model vdw 1.776 2.170 nonbonded pdb="MG MG F 601 " pdb=" O3G ATP F 602 " model vdw 1.914 2.170 nonbonded pdb=" OG1 THR F 165 " pdb="MG MG F 601 " model vdw 1.959 2.170 nonbonded pdb=" O3B ATP D 501 " pdb="MG MG D 502 " model vdw 1.964 2.170 nonbonded pdb=" O2B ATP C 600 " pdb="MG MG C 601 " model vdw 1.967 2.170 ... (remaining 195727 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 602) selection = chain 'B' selection = chain 'C' } ncs_group { reference = (chain 'D' and resid 1 through 470) selection = chain 'E' selection = (chain 'F' and resid 1 through 470) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 23.110 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 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 : 0.005 0.149 24655 Z= 0.234 Angle : 0.653 12.913 33434 Z= 0.367 Chirality : 0.046 0.195 3852 Planarity : 0.005 0.121 4362 Dihedral : 13.078 88.544 9215 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.86 % Favored : 97.11 % Rotamer: Outliers : 0.04 % Allowed : 0.23 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.15), residues: 3115 helix: 1.18 (0.15), residues: 1236 sheet: 0.93 (0.23), residues: 510 loop : -0.08 (0.17), residues: 1369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 89 TYR 0.012 0.001 TYR A 286 PHE 0.017 0.002 PHE A 494 HIS 0.008 0.001 HIS F 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.23 (24655) covalent geometry : angle 0.65312 / 0.37 (33434) hydrogen bonds : bond 0.14116 / 9.37 ( 1176) hydrogen bonds : angle 6.19419 / 4.36 ( 3354) *********************** 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 118 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 117 time to evaluate : 0.936 Fit side-chains REVERT: G 46 MET cc_start: 0.5592 (mmm) cc_final: 0.5313 (tpp) outliers start: 1 outliers final: 0 residues processed: 118 average time/residue: 0.1462 time to fit residues: 29.4976 Evaluate side-chains 107 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.4980 chunk 298 optimal weight: 8.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 200 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.073344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.054173 restraints weight = 69758.472| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 2.81 r_work: 0.2751 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8929 moved from start: 0.0656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 24655 Z= 0.162 Angle : 0.540 8.812 33434 Z= 0.283 Chirality : 0.044 0.151 3852 Planarity : 0.004 0.045 4362 Dihedral : 5.521 87.539 3414 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.35 % Allowed : 3.35 % Favored : 96.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.15), residues: 3115 helix: 1.37 (0.15), residues: 1236 sheet: 0.74 (0.22), residues: 528 loop : -0.05 (0.17), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 89 TYR 0.009 0.001 TYR A 195 PHE 0.016 0.001 PHE C 494 HIS 0.006 0.001 HIS F 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 (24655) covalent geometry : angle 0.53968 / 0.28 (33434) hydrogen bonds : bond 0.04686 / 3.17 ( 1176) hydrogen bonds : angle 5.06130 / 3.55 ( 3354) *********************** 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 118 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 109 time to evaluate : 0.888 Fit side-chains REVERT: D 226 MET cc_start: 0.8931 (ptm) cc_final: 0.8709 (ptp) outliers start: 9 outliers final: 7 residues processed: 112 average time/residue: 0.1430 time to fit residues: 27.8020 Evaluate side-chains 114 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 107 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain G residue 24 MET Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 244 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 111 optimal weight: 8.9990 chunk 88 optimal weight: 4.9990 chunk 283 optimal weight: 9.9990 chunk 140 optimal weight: 9.9990 chunk 161 optimal weight: 9.9990 chunk 10 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 167 optimal weight: 5.9990 chunk 215 optimal weight: 0.9990 chunk 31 optimal weight: 10.0000 chunk 112 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 34 HIS G 173 ASN G 174 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.072456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.053354 restraints weight = 70062.370| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 2.81 r_work: 0.2731 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8948 moved from start: 0.0786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 24655 Z= 0.207 Angle : 0.555 7.944 33434 Z= 0.289 Chirality : 0.045 0.152 3852 Planarity : 0.004 0.045 4362 Dihedral : 5.559 89.144 3414 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.93 % Allowed : 5.30 % Favored : 93.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.15), residues: 3115 helix: 1.36 (0.15), residues: 1230 sheet: 0.58 (0.22), residues: 545 loop : -0.14 (0.17), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 164 TYR 0.011 0.001 TYR A 195 PHE 0.016 0.001 PHE A 494 HIS 0.006 0.001 HIS F 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.21 (24655) covalent geometry : angle 0.55514 / 0.29 (33434) hydrogen bonds : bond 0.04868 / 3.29 ( 1176) hydrogen bonds : angle 4.95393 / 3.46 ( 3354) *********************** 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 133 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 109 time to evaluate : 0.892 Fit side-chains REVERT: A 357 ILE cc_start: 0.8955 (OUTLIER) cc_final: 0.8701 (mp) REVERT: D 226 MET cc_start: 0.8955 (ptm) cc_final: 0.8746 (ptp) outliers start: 24 outliers final: 18 residues processed: 123 average time/residue: 0.1465 time to fit residues: 31.3262 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 : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 469 MET Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain G residue 24 MET Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain G residue 244 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 201 optimal weight: 4.9990 chunk 124 optimal weight: 0.2980 chunk 282 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 chunk 86 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 249 optimal weight: 0.9980 chunk 245 optimal weight: 7.9990 chunk 303 optimal weight: 4.9990 chunk 110 optimal weight: 0.8980 chunk 123 optimal weight: 8.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 217 GLN G 174 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.073805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.054670 restraints weight = 69131.237| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 2.82 r_work: 0.2766 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 moved from start: 0.1031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 24655 Z= 0.120 Angle : 0.490 11.504 33434 Z= 0.253 Chirality : 0.043 0.147 3852 Planarity : 0.004 0.042 4362 Dihedral : 5.283 88.670 3414 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.97 % Allowed : 6.31 % Favored : 92.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.15), residues: 3115 helix: 1.65 (0.15), residues: 1235 sheet: 0.67 (0.22), residues: 530 loop : -0.08 (0.17), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 164 TYR 0.010 0.001 TYR A 195 PHE 0.015 0.001 PHE A 494 HIS 0.005 0.001 HIS F 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (24655) covalent geometry : angle 0.48961 / 0.25 (33434) hydrogen bonds : bond 0.04011 / 2.72 ( 1176) hydrogen bonds : angle 4.67411 / 3.27 ( 3354) *********************** 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 144 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 119 time to evaluate : 0.987 Fit side-chains REVERT: A 357 ILE cc_start: 0.8929 (OUTLIER) cc_final: 0.8663 (mp) REVERT: G 46 MET cc_start: 0.5926 (tpp) cc_final: 0.5583 (tpp) outliers start: 25 outliers final: 15 residues processed: 135 average time/residue: 0.1504 time to fit residues: 34.5604 Evaluate side-chains 125 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 469 MET Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain G residue 244 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 238 optimal weight: 8.9990 chunk 185 optimal weight: 10.0000 chunk 124 optimal weight: 8.9990 chunk 275 optimal weight: 6.9990 chunk 242 optimal weight: 3.9990 chunk 74 optimal weight: 10.0000 chunk 186 optimal weight: 5.9990 chunk 101 optimal weight: 10.0000 chunk 127 optimal weight: 10.0000 chunk 50 optimal weight: 0.7980 chunk 75 optimal weight: 8.9990 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 174 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.072533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.053045 restraints weight = 69347.153| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 2.77 r_work: 0.2726 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8914 moved from start: 0.1019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 24655 Z= 0.277 Angle : 0.607 11.405 33434 Z= 0.314 Chirality : 0.047 0.164 3852 Planarity : 0.005 0.047 4362 Dihedral : 5.622 89.063 3414 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.71 % Allowed : 7.09 % Favored : 91.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.15), residues: 3115 helix: 1.27 (0.15), residues: 1235 sheet: 0.46 (0.22), residues: 538 loop : -0.27 (0.17), residues: 1342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 296 TYR 0.013 0.002 TYR A 195 PHE 0.019 0.002 PHE F 257 HIS 0.007 0.001 HIS F 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00667 / 0.28 (24655) covalent geometry : angle 0.60687 / 0.31 (33434) hydrogen bonds : bond 0.05216 / 3.53 ( 1176) hydrogen bonds : angle 4.96269 / 3.46 ( 3354) *********************** 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 157 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 113 time to evaluate : 0.802 Fit side-chains REVERT: A 357 ILE cc_start: 0.8975 (OUTLIER) cc_final: 0.8717 (mp) REVERT: C 164 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.7178 (pmt-80) REVERT: D 226 MET cc_start: 0.8911 (ptm) cc_final: 0.8696 (ptp) REVERT: F 10 MET cc_start: 0.8793 (mtp) cc_final: 0.8394 (mtm) REVERT: G 168 LEU cc_start: 0.7628 (OUTLIER) cc_final: 0.7395 (tt) outliers start: 44 outliers final: 28 residues processed: 145 average time/residue: 0.1483 time to fit residues: 36.1704 Evaluate side-chains 140 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 109 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 164 ARG Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 469 MET Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 384 ILE Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain G residue 24 MET Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain G residue 244 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 9 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 291 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 238 optimal weight: 0.6980 chunk 32 optimal weight: 9.9990 chunk 252 optimal weight: 0.9990 chunk 83 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.074607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.055465 restraints weight = 68299.126| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 2.78 r_work: 0.2784 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 24655 Z= 0.103 Angle : 0.487 10.593 33434 Z= 0.251 Chirality : 0.043 0.148 3852 Planarity : 0.004 0.043 4362 Dihedral : 5.247 89.309 3414 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.32 % Allowed : 7.87 % Favored : 90.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.15), residues: 3115 helix: 1.66 (0.15), residues: 1236 sheet: 0.66 (0.22), residues: 528 loop : -0.10 (0.17), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 97 TYR 0.009 0.001 TYR E 238 PHE 0.021 0.001 PHE C 460 HIS 0.004 0.001 HIS F 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (24655) covalent geometry : angle 0.48710 / 0.25 (33434) hydrogen bonds : bond 0.03903 / 2.66 ( 1176) hydrogen bonds : angle 4.62529 / 3.24 ( 3354) *********************** 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 147 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 113 time to evaluate : 0.967 Fit side-chains REVERT: A 357 ILE cc_start: 0.8920 (OUTLIER) cc_final: 0.8661 (mp) REVERT: C 164 ARG cc_start: 0.8692 (OUTLIER) cc_final: 0.7224 (pmt-80) REVERT: F 10 MET cc_start: 0.8716 (mtp) cc_final: 0.8200 (mmm) REVERT: G 46 MET cc_start: 0.5831 (tpp) cc_final: 0.5578 (tpp) REVERT: G 131 MET cc_start: 0.4880 (OUTLIER) cc_final: 0.3951 (mpt) REVERT: G 168 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.7348 (tt) outliers start: 34 outliers final: 19 residues processed: 136 average time/residue: 0.1414 time to fit residues: 32.7934 Evaluate side-chains 132 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 109 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 164 ARG Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 469 MET Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain G residue 24 MET Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain G residue 206 GLU Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 244 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 297 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 224 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 294 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 169 optimal weight: 7.9990 chunk 162 optimal weight: 10.0000 chunk 134 optimal weight: 0.0770 chunk 35 optimal weight: 10.0000 chunk 180 optimal weight: 3.9990 overall best weight: 3.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 174 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.073195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.054023 restraints weight = 69089.074| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 2.77 r_work: 0.2748 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 24655 Z= 0.207 Angle : 0.546 9.778 33434 Z= 0.281 Chirality : 0.045 0.145 3852 Planarity : 0.004 0.045 4362 Dihedral : 5.371 89.928 3414 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.44 % Allowed : 7.98 % Favored : 90.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.15), residues: 3115 helix: 1.53 (0.15), residues: 1235 sheet: 0.56 (0.23), residues: 528 loop : -0.19 (0.17), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 296 TYR 0.010 0.001 TYR A 195 PHE 0.027 0.001 PHE C 460 HIS 0.006 0.001 HIS F 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.21 (24655) covalent geometry : angle 0.54612 / 0.28 (33434) hydrogen bonds : bond 0.04566 / 3.10 ( 1176) hydrogen bonds : angle 4.74267 / 3.31 ( 3354) *********************** 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 146 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 109 time to evaluate : 0.927 Fit side-chains revert: symmetry clash REVERT: A 357 ILE cc_start: 0.8930 (OUTLIER) cc_final: 0.8673 (mp) REVERT: F 10 MET cc_start: 0.8767 (mtp) cc_final: 0.8417 (mtm) REVERT: G 46 MET cc_start: 0.5831 (tpp) cc_final: 0.5554 (tpp) REVERT: G 131 MET cc_start: 0.4862 (OUTLIER) cc_final: 0.3922 (mpt) REVERT: G 168 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.7323 (tt) outliers start: 37 outliers final: 30 residues processed: 137 average time/residue: 0.1308 time to fit residues: 30.4842 Evaluate side-chains 141 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 108 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 164 ARG Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 469 MET Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 384 ILE Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain G residue 24 MET Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 244 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 264 optimal weight: 10.0000 chunk 184 optimal weight: 8.9990 chunk 24 optimal weight: 8.9990 chunk 187 optimal weight: 6.9990 chunk 102 optimal weight: 0.9980 chunk 308 optimal weight: 7.9990 chunk 22 optimal weight: 0.9980 chunk 162 optimal weight: 6.9990 chunk 157 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 205 optimal weight: 5.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.074018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.054846 restraints weight = 68378.221| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 2.77 r_work: 0.2769 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 24655 Z= 0.141 Angle : 0.503 9.588 33434 Z= 0.258 Chirality : 0.043 0.146 3852 Planarity : 0.004 0.044 4362 Dihedral : 5.242 88.986 3414 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.32 % Allowed : 8.53 % Favored : 90.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.15), residues: 3115 helix: 1.64 (0.15), residues: 1231 sheet: 0.59 (0.23), residues: 528 loop : -0.14 (0.17), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 365 TYR 0.009 0.001 TYR A 195 PHE 0.024 0.001 PHE C 460 HIS 0.005 0.001 HIS F 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (24655) covalent geometry : angle 0.50326 / 0.26 (33434) hydrogen bonds : bond 0.04122 / 2.80 ( 1176) hydrogen bonds : angle 4.63479 / 3.24 ( 3354) *********************** 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 146 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 112 time to evaluate : 0.963 Fit side-chains revert: symmetry clash REVERT: A 357 ILE cc_start: 0.8900 (OUTLIER) cc_final: 0.8638 (mp) REVERT: F 10 MET cc_start: 0.8767 (mtp) cc_final: 0.8410 (mtm) REVERT: G 46 MET cc_start: 0.5895 (tpp) cc_final: 0.5586 (tpp) REVERT: G 131 MET cc_start: 0.4766 (OUTLIER) cc_final: 0.3858 (mpt) outliers start: 34 outliers final: 27 residues processed: 135 average time/residue: 0.1449 time to fit residues: 33.3162 Evaluate side-chains 139 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 110 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 164 ARG Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 384 ILE Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 469 MET Chi-restraints excluded: chain E residue 384 ILE Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain G residue 24 MET Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 244 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 252 optimal weight: 3.9990 chunk 137 optimal weight: 8.9990 chunk 281 optimal weight: 7.9990 chunk 235 optimal weight: 1.9990 chunk 236 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 263 optimal weight: 2.9990 chunk 67 optimal weight: 0.0020 chunk 183 optimal weight: 9.9990 chunk 239 optimal weight: 0.9990 chunk 88 optimal weight: 8.9990 overall best weight: 1.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.074931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.055723 restraints weight = 68541.961| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 2.79 r_work: 0.2791 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 24655 Z= 0.105 Angle : 0.478 9.109 33434 Z= 0.244 Chirality : 0.043 0.145 3852 Planarity : 0.004 0.042 4362 Dihedral : 5.050 88.331 3414 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.05 % Allowed : 8.84 % Favored : 90.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.15), residues: 3115 helix: 1.77 (0.15), residues: 1235 sheet: 0.63 (0.23), residues: 521 loop : -0.06 (0.17), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 365 TYR 0.009 0.001 TYR G 78 PHE 0.022 0.001 PHE C 460 HIS 0.004 0.001 HIS F 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (24655) covalent geometry : angle 0.47774 / 0.24 (33434) hydrogen bonds : bond 0.03697 / 2.52 ( 1176) hydrogen bonds : angle 4.51112 / 3.16 ( 3354) *********************** 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 137 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 110 time to evaluate : 1.002 Fit side-chains revert: symmetry clash REVERT: A 357 ILE cc_start: 0.8847 (OUTLIER) cc_final: 0.8596 (mp) REVERT: D 445 TYR cc_start: 0.7270 (m-80) cc_final: 0.6687 (m-80) REVERT: F 10 MET cc_start: 0.8722 (mtp) cc_final: 0.8373 (mtm) REVERT: G 46 MET cc_start: 0.5612 (tpp) cc_final: 0.5304 (tpp) REVERT: G 131 MET cc_start: 0.4727 (OUTLIER) cc_final: 0.3825 (mpt) outliers start: 27 outliers final: 23 residues processed: 131 average time/residue: 0.1418 time to fit residues: 31.6934 Evaluate side-chains 134 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 109 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 164 ARG Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain E residue 384 ILE Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain G residue 24 MET Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 244 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 65 optimal weight: 5.9990 chunk 296 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 chunk 134 optimal weight: 0.7980 chunk 224 optimal weight: 10.0000 chunk 107 optimal weight: 0.7980 chunk 257 optimal weight: 0.9990 chunk 180 optimal weight: 5.9990 chunk 229 optimal weight: 10.0000 chunk 168 optimal weight: 5.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 425 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.076226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.057024 restraints weight = 68229.385| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 2.79 r_work: 0.2825 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 24655 Z= 0.089 Angle : 0.457 9.841 33434 Z= 0.232 Chirality : 0.042 0.144 3852 Planarity : 0.004 0.040 4362 Dihedral : 4.771 87.659 3414 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.93 % Allowed : 9.00 % Favored : 90.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.15), residues: 3115 helix: 1.90 (0.15), residues: 1252 sheet: 0.66 (0.23), residues: 536 loop : 0.12 (0.18), residues: 1327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 365 TYR 0.010 0.001 TYR A 461 PHE 0.018 0.001 PHE C 460 HIS 0.003 0.000 HIS F 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00192 / 0.09 (24655) covalent geometry : angle 0.45651 / 0.23 (33434) hydrogen bonds : bond 0.03225 / 2.20 ( 1176) hydrogen bonds : angle 4.34003 / 3.05 ( 3354) ********************** 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 143 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 0.983 Fit side-chains revert: symmetry clash REVERT: A 357 ILE cc_start: 0.8799 (OUTLIER) cc_final: 0.8559 (mp) REVERT: D 445 TYR cc_start: 0.7306 (m-80) cc_final: 0.6760 (m-80) REVERT: G 46 MET cc_start: 0.5515 (tpp) cc_final: 0.5133 (tpp) REVERT: G 131 MET cc_start: 0.4664 (OUTLIER) cc_final: 0.3783 (mpt) outliers start: 24 outliers final: 18 residues processed: 137 average time/residue: 0.1484 time to fit residues: 34.0166 Evaluate side-chains 133 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 164 ARG Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain G residue 24 MET Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 244 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 82 optimal weight: 0.0370 chunk 52 optimal weight: 7.9990 chunk 167 optimal weight: 9.9990 chunk 120 optimal weight: 6.9990 chunk 159 optimal weight: 10.0000 chunk 86 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 230 optimal weight: 0.4980 chunk 232 optimal weight: 5.9990 chunk 178 optimal weight: 5.9990 chunk 127 optimal weight: 3.9990 overall best weight: 2.9064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 174 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.074228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.055024 restraints weight = 68573.531| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 2.77 r_work: 0.2775 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 24655 Z= 0.164 Angle : 0.511 9.428 33434 Z= 0.261 Chirality : 0.044 0.142 3852 Planarity : 0.004 0.041 4362 Dihedral : 4.978 88.848 3414 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.09 % Allowed : 9.00 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.15), residues: 3115 helix: 1.80 (0.15), residues: 1240 sheet: 0.60 (0.23), residues: 536 loop : 0.03 (0.17), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 191 TYR 0.011 0.001 TYR D 341 PHE 0.026 0.001 PHE C 460 HIS 0.006 0.001 HIS E 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.16 (24655) covalent geometry : angle 0.51088 / 0.26 (33434) hydrogen bonds : bond 0.04055 / 2.76 ( 1176) hydrogen bonds : angle 4.53731 / 3.18 ( 3354) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4480.48 seconds wall clock time: 77 minutes 53.66 seconds (4673.66 seconds total)