Starting phenix.real_space_refine on Thu Mar 5 18:06:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hhc_34760/03_2026/8hhc_34760.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hhc_34760/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8hhc_34760/03_2026/8hhc_34760.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hhc_34760/03_2026/8hhc_34760.map" model { file = "/net/cci-nas-00/data/ceres_data/8hhc_34760/03_2026/8hhc_34760.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hhc_34760/03_2026/8hhc_34760.cif" } 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-5986/lib/python3.9/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: 5.32, per 1000 atoms: 0.22 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: 2.15 Conformation dependent library (CDL) restraints added in 960.3 milliseconds 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5712 Finding SS restraints... Secondary structure from input PDB file: 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: 0.63 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: 4.83 Time building geometry restraints manager: 2.83 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: 13863 17.71 - 35.42: 925 35.42 - 53.13: 207 53.13 - 70.84: 61 70.84 - 88.54: 26 Dihedral angle restraints: 15082 sinusoidal: 6157 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 15079 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: 4.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 22.370 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 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 : 13.661 88.544 9370 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 covalent geometry : bond 0.00544 (24655) covalent geometry : angle 0.65312 (33434) hydrogen bonds : bond 0.14116 ( 1176) hydrogen bonds : angle 6.19419 ( 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 : 0.911 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: 0.1293 time to fit residues: 26.2577 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 : 0.917 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 200 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.073296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.054114 restraints weight = 69749.970| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 2.82 r_work: 0.2750 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.0633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 24655 Z= 0.164 Angle : 0.542 8.896 33434 Z= 0.285 Chirality : 0.044 0.151 3852 Planarity : 0.004 0.045 4362 Dihedral : 8.119 88.267 3569 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.31 % Allowed : 3.35 % Favored : 96.34 % 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: 0.92 (0.15), residues: 3115 helix: 1.36 (0.15), residues: 1238 sheet: 0.75 (0.22), residues: 528 loop : -0.06 (0.17), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 164 TYR 0.009 0.001 TYR C 248 PHE 0.016 0.001 PHE C 494 HIS 0.006 0.001 HIS F 363 Details of bonding type rmsd covalent geometry : bond 0.00387 (24655) covalent geometry : angle 0.54249 (33434) hydrogen bonds : bond 0.04805 ( 1176) hydrogen bonds : angle 5.09190 ( 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 117 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 109 time to evaluate : 0.867 Fit side-chains REVERT: B 62 MET cc_start: 0.9318 (ttp) cc_final: 0.9108 (ttm) REVERT: D 226 MET cc_start: 0.8936 (ptm) cc_final: 0.8722 (ptp) outliers start: 8 outliers final: 6 residues processed: 111 average time/residue: 0.1299 time to fit residues: 25.1063 Evaluate side-chains 113 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 107 time to evaluate : 0.876 ------------------------------------------------------------------------------- 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 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: 5.9990 chunk 283 optimal weight: 10.0000 chunk 140 optimal weight: 9.9990 chunk 161 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 167 optimal weight: 6.9990 chunk 215 optimal weight: 2.9990 chunk 31 optimal weight: 9.9990 chunk 112 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 34 HIS D 217 GLN G 173 ASN G 174 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.072313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.053202 restraints weight = 70190.027| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 2.81 r_work: 0.2726 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.0799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 24655 Z= 0.216 Angle : 0.568 8.028 33434 Z= 0.296 Chirality : 0.046 0.157 3852 Planarity : 0.004 0.046 4362 Dihedral : 7.893 89.784 3569 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % 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: 0.79 (0.15), residues: 3115 helix: 1.32 (0.15), residues: 1229 sheet: 0.56 (0.22), residues: 545 loop : -0.15 (0.17), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 164 TYR 0.012 0.001 TYR A 195 PHE 0.017 0.002 PHE A 494 HIS 0.007 0.001 HIS F 363 Details of bonding type rmsd covalent geometry : bond 0.00520 (24655) covalent geometry : angle 0.56792 (33434) hydrogen bonds : bond 0.04968 ( 1176) hydrogen bonds : angle 4.97320 ( 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 : 0.625 Fit side-chains REVERT: A 357 ILE cc_start: 0.8963 (OUTLIER) cc_final: 0.8708 (mp) REVERT: D 226 MET cc_start: 0.8953 (ptm) cc_final: 0.8747 (ptp) outliers start: 24 outliers final: 18 residues processed: 123 average time/residue: 0.1320 time to fit residues: 28.2537 Evaluate side-chains 127 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 0.889 ------------------------------------------------------------------------------- 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: 1.9990 chunk 124 optimal weight: 0.6980 chunk 282 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 86 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 249 optimal weight: 0.8980 chunk 245 optimal weight: 0.0970 chunk 303 optimal weight: 7.9990 chunk 110 optimal weight: 1.9990 chunk 123 optimal weight: 7.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 174 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.074514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.055398 restraints weight = 68866.719| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 2.83 r_work: 0.2781 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.1130 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= 0.101 Angle : 0.472 8.447 33434 Z= 0.246 Chirality : 0.042 0.148 3852 Planarity : 0.004 0.043 4362 Dihedral : 7.271 86.440 3569 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.86 % Allowed : 6.39 % Favored : 92.76 % 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: 1.16 (0.15), residues: 3115 helix: 1.70 (0.15), residues: 1241 sheet: 0.72 (0.22), residues: 520 loop : 0.01 (0.17), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 164 TYR 0.009 0.001 TYR A 195 PHE 0.015 0.001 PHE A 494 HIS 0.004 0.000 HIS F 363 Details of bonding type rmsd covalent geometry : bond 0.00218 (24655) covalent geometry : angle 0.47163 (33434) hydrogen bonds : bond 0.03695 ( 1176) hydrogen bonds : angle 4.59629 ( 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 142 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 0.773 Fit side-chains REVERT: A 261 ASP cc_start: 0.6844 (m-30) cc_final: 0.6522 (m-30) REVERT: A 357 ILE cc_start: 0.8920 (OUTLIER) cc_final: 0.8649 (mp) REVERT: D 445 TYR cc_start: 0.7331 (m-80) cc_final: 0.6665 (m-80) outliers start: 22 outliers final: 8 residues processed: 136 average time/residue: 0.1352 time to fit residues: 31.3976 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 : 0.897 ------------------------------------------------------------------------------- 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 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 68 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: 7.9990 chunk 124 optimal weight: 8.9990 chunk 275 optimal weight: 7.9990 chunk 242 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 186 optimal weight: 6.9990 chunk 101 optimal weight: 5.9990 chunk 127 optimal weight: 9.9990 chunk 50 optimal weight: 4.9990 chunk 75 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 174 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.072249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.053105 restraints weight = 69738.778| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 2.77 r_work: 0.2722 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.1041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 24655 Z= 0.298 Angle : 0.627 9.614 33434 Z= 0.324 Chirality : 0.048 0.170 3852 Planarity : 0.005 0.046 4362 Dihedral : 7.543 84.744 3569 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.60 % Allowed : 7.36 % Favored : 91.04 % 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: 0.67 (0.15), residues: 3115 helix: 1.28 (0.15), residues: 1235 sheet: 0.45 (0.22), residues: 538 loop : -0.26 (0.17), residues: 1342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 296 TYR 0.013 0.002 TYR A 195 PHE 0.020 0.002 PHE F 257 HIS 0.007 0.001 HIS F 363 Details of bonding type rmsd covalent geometry : bond 0.00719 (24655) covalent geometry : angle 0.62686 (33434) hydrogen bonds : bond 0.05332 ( 1176) hydrogen bonds : angle 4.98262 ( 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 155 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 114 time to evaluate : 0.744 Fit side-chains REVERT: A 357 ILE cc_start: 0.8919 (OUTLIER) cc_final: 0.8670 (mp) REVERT: C 164 ARG cc_start: 0.8825 (OUTLIER) cc_final: 0.7230 (pmt-80) REVERT: F 10 MET cc_start: 0.8804 (mtp) cc_final: 0.8410 (mtm) outliers start: 41 outliers final: 23 residues processed: 144 average time/residue: 0.1419 time to fit residues: 34.2882 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 : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 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 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 E residue 109 ILE 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 213 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: 1.9990 chunk 150 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 291 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 238 optimal weight: 8.9990 chunk 32 optimal weight: 9.9990 chunk 252 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.074562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.055348 restraints weight = 68514.623| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 2.78 r_work: 0.2782 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.1215 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= 0.110 Angle : 0.493 13.372 33434 Z= 0.254 Chirality : 0.043 0.146 3852 Planarity : 0.004 0.045 4362 Dihedral : 7.077 87.660 3569 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.13 % Allowed : 7.87 % Favored : 91.00 % 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: 1.04 (0.15), residues: 3115 helix: 1.65 (0.15), residues: 1236 sheet: 0.63 (0.23), residues: 519 loop : -0.10 (0.17), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 365 TYR 0.010 0.001 TYR D 341 PHE 0.021 0.001 PHE C 460 HIS 0.004 0.001 HIS F 363 Details of bonding type rmsd covalent geometry : bond 0.00243 (24655) covalent geometry : angle 0.49281 (33434) hydrogen bonds : bond 0.03928 ( 1176) hydrogen bonds : angle 4.63401 ( 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 141 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 112 time to evaluate : 0.915 Fit side-chains REVERT: A 357 ILE cc_start: 0.8917 (OUTLIER) cc_final: 0.8658 (mp) REVERT: C 164 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.7272 (pmt-80) REVERT: F 10 MET cc_start: 0.8728 (mtp) cc_final: 0.8358 (mtm) REVERT: G 131 MET cc_start: 0.4861 (OUTLIER) cc_final: 0.3951 (mpt) outliers start: 29 outliers final: 17 residues processed: 133 average time/residue: 0.1267 time to fit residues: 28.8273 Evaluate side-chains 129 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.853 ------------------------------------------------------------------------------- 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 C residue 129 ILE Chi-restraints excluded: chain C residue 164 ARG 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 469 MET Chi-restraints excluded: chain E residue 162 VAL 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 68 LEU Chi-restraints excluded: chain G residue 131 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 297 optimal weight: 5.9990 chunk 110 optimal weight: 0.8980 chunk 224 optimal weight: 9.9990 chunk 30 optimal weight: 8.9990 chunk 294 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 169 optimal weight: 5.9990 chunk 162 optimal weight: 10.0000 chunk 134 optimal weight: 7.9990 chunk 35 optimal weight: 10.0000 chunk 180 optimal weight: 10.0000 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.072398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.053285 restraints weight = 69388.536| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 2.77 r_work: 0.2727 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 24655 Z= 0.272 Angle : 0.603 12.454 33434 Z= 0.311 Chirality : 0.047 0.157 3852 Planarity : 0.005 0.048 4362 Dihedral : 7.242 81.513 3569 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.36 % Allowed : 8.22 % Favored : 90.42 % 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: 0.67 (0.15), residues: 3115 helix: 1.34 (0.15), residues: 1232 sheet: 0.46 (0.23), residues: 526 loop : -0.32 (0.17), residues: 1357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 296 TYR 0.012 0.002 TYR A 195 PHE 0.030 0.002 PHE C 460 HIS 0.007 0.001 HIS F 363 Details of bonding type rmsd covalent geometry : bond 0.00654 (24655) covalent geometry : angle 0.60265 (33434) hydrogen bonds : bond 0.05071 ( 1176) hydrogen bonds : angle 4.89753 ( 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 142 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 107 time to evaluate : 0.794 Fit side-chains REVERT: A 357 ILE cc_start: 0.8971 (OUTLIER) cc_final: 0.8719 (mp) REVERT: C 164 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.7187 (pmt-80) REVERT: F 10 MET cc_start: 0.8788 (mtp) cc_final: 0.8417 (mtm) REVERT: G 131 MET cc_start: 0.4796 (OUTLIER) cc_final: 0.3839 (mpt) outliers start: 35 outliers final: 28 residues processed: 134 average time/residue: 0.1393 time to fit residues: 31.7401 Evaluate side-chains 138 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 107 time to evaluate : 0.777 ------------------------------------------------------------------------------- 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 129 ILE Chi-restraints excluded: chain C residue 164 ARG Chi-restraints excluded: chain C residue 225 THR 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 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 202 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 264 optimal weight: 7.9990 chunk 184 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 187 optimal weight: 8.9990 chunk 102 optimal weight: 3.9990 chunk 308 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 162 optimal weight: 1.9990 chunk 157 optimal weight: 0.9990 chunk 139 optimal weight: 3.9990 chunk 205 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.073818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.054667 restraints weight = 68398.628| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 2.77 r_work: 0.2763 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 24655 Z= 0.145 Angle : 0.510 11.744 33434 Z= 0.263 Chirality : 0.044 0.146 3852 Planarity : 0.004 0.046 4362 Dihedral : 6.922 82.791 3569 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.21 % Allowed : 8.57 % Favored : 90.23 % 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: 1.57 (0.15), residues: 1228 sheet: 0.52 (0.23), residues: 528 loop : -0.22 (0.17), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 365 TYR 0.010 0.001 TYR D 341 PHE 0.025 0.001 PHE C 460 HIS 0.005 0.001 HIS F 363 Details of bonding type rmsd covalent geometry : bond 0.00340 (24655) covalent geometry : angle 0.51025 (33434) hydrogen bonds : bond 0.04201 ( 1176) hydrogen bonds : angle 4.69095 ( 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 143 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 112 time to evaluate : 0.798 Fit side-chains revert: symmetry clash REVERT: A 357 ILE cc_start: 0.8925 (OUTLIER) cc_final: 0.8664 (mp) REVERT: F 10 MET cc_start: 0.8755 (mtp) cc_final: 0.8405 (mtm) REVERT: G 131 MET cc_start: 0.4692 (OUTLIER) cc_final: 0.3776 (mpt) outliers start: 31 outliers final: 28 residues processed: 134 average time/residue: 0.1382 time to fit residues: 31.5094 Evaluate side-chains 140 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 110 time to evaluate : 0.850 ------------------------------------------------------------------------------- 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 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 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 469 MET Chi-restraints excluded: chain E residue 162 VAL 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 202 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 252 optimal weight: 3.9990 chunk 137 optimal weight: 9.9990 chunk 281 optimal weight: 7.9990 chunk 235 optimal weight: 5.9990 chunk 236 optimal weight: 0.6980 chunk 79 optimal weight: 4.9990 chunk 263 optimal weight: 3.9990 chunk 67 optimal weight: 7.9990 chunk 183 optimal weight: 9.9990 chunk 239 optimal weight: 2.9990 chunk 88 optimal weight: 7.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.073296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.054133 restraints weight = 69056.504| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 2.78 r_work: 0.2751 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 24655 Z= 0.184 Angle : 0.537 11.356 33434 Z= 0.276 Chirality : 0.044 0.145 3852 Planarity : 0.004 0.048 4362 Dihedral : 6.878 80.775 3569 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.44 % Allowed : 8.41 % 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: 0.82 (0.15), residues: 3115 helix: 1.51 (0.15), residues: 1228 sheet: 0.49 (0.23), residues: 526 loop : -0.25 (0.17), residues: 1361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 365 TYR 0.012 0.001 TYR D 341 PHE 0.024 0.001 PHE C 460 HIS 0.005 0.001 HIS F 363 Details of bonding type rmsd covalent geometry : bond 0.00439 (24655) covalent geometry : angle 0.53713 (33434) hydrogen bonds : bond 0.04474 ( 1176) hydrogen bonds : angle 4.73243 ( 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 146 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 109 time to evaluate : 0.860 Fit side-chains revert: symmetry clash REVERT: A 357 ILE cc_start: 0.8931 (OUTLIER) cc_final: 0.8672 (mp) REVERT: F 10 MET cc_start: 0.8774 (mtp) cc_final: 0.8427 (mtm) REVERT: G 131 MET cc_start: 0.4719 (OUTLIER) cc_final: 0.3741 (mpt) outliers start: 37 outliers final: 30 residues processed: 139 average time/residue: 0.1378 time to fit residues: 32.6211 Evaluate side-chains 141 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 109 time to evaluate : 0.905 ------------------------------------------------------------------------------- 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 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 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 D residue 340 ILE Chi-restraints excluded: chain D residue 384 ILE Chi-restraints excluded: chain D residue 469 MET Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 384 ILE Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 168 ILE 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 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: 2.9990 chunk 296 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 134 optimal weight: 0.4980 chunk 224 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 257 optimal weight: 7.9990 chunk 180 optimal weight: 6.9990 chunk 229 optimal weight: 9.9990 chunk 168 optimal weight: 0.0980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.074917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.055716 restraints weight = 68416.727| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 2.78 r_work: 0.2791 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 24655 Z= 0.104 Angle : 0.480 11.167 33434 Z= 0.247 Chirality : 0.043 0.149 3852 Planarity : 0.004 0.044 4362 Dihedral : 6.496 82.030 3569 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.01 % Allowed : 9.00 % Favored : 89.99 % 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: 1.10 (0.15), residues: 3115 helix: 1.74 (0.15), residues: 1235 sheet: 0.58 (0.23), residues: 529 loop : -0.08 (0.17), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 365 TYR 0.010 0.001 TYR D 341 PHE 0.027 0.001 PHE C 460 HIS 0.004 0.001 HIS F 363 Details of bonding type rmsd covalent geometry : bond 0.00228 (24655) covalent geometry : angle 0.47963 (33434) hydrogen bonds : bond 0.03703 ( 1176) hydrogen bonds : angle 4.53522 ( 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 137 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 111 time to evaluate : 0.915 Fit side-chains revert: symmetry clash REVERT: A 357 ILE cc_start: 0.8859 (OUTLIER) cc_final: 0.8615 (mp) REVERT: D 445 TYR cc_start: 0.7271 (m-80) cc_final: 0.6704 (m-80) REVERT: G 131 MET cc_start: 0.4720 (OUTLIER) cc_final: 0.3819 (mpt) outliers start: 26 outliers final: 21 residues processed: 131 average time/residue: 0.1379 time to fit residues: 30.3953 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 : 0.826 ------------------------------------------------------------------------------- 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 C residue 129 ILE Chi-restraints excluded: chain C residue 164 ARG 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 162 VAL Chi-restraints excluded: chain E residue 456 VAL 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 224 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: 5.9990 chunk 52 optimal weight: 2.9990 chunk 167 optimal weight: 6.9990 chunk 120 optimal weight: 2.9990 chunk 159 optimal weight: 10.0000 chunk 86 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 230 optimal weight: 4.9990 chunk 232 optimal weight: 2.9990 chunk 178 optimal weight: 6.9990 chunk 127 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 174 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.073334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.054179 restraints weight = 68781.662| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 2.77 r_work: 0.2750 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 24655 Z= 0.195 Angle : 0.543 10.906 33434 Z= 0.279 Chirality : 0.045 0.143 3852 Planarity : 0.004 0.047 4362 Dihedral : 6.653 79.264 3569 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.29 % Allowed : 8.68 % Favored : 90.03 % 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: 1.59 (0.15), residues: 1234 sheet: 0.53 (0.23), residues: 529 loop : -0.18 (0.17), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 191 TYR 0.013 0.001 TYR D 341 PHE 0.030 0.001 PHE C 460 HIS 0.006 0.001 HIS F 363 Details of bonding type rmsd covalent geometry : bond 0.00465 (24655) covalent geometry : angle 0.54264 (33434) hydrogen bonds : bond 0.04472 ( 1176) hydrogen bonds : angle 4.69654 ( 3354) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4160.07 seconds wall clock time: 72 minutes 19.49 seconds (4339.49 seconds total)