Starting phenix.real_space_refine on Sat Aug 8 01:46:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7yry_34066/08_2026/7yry_34066.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yry_34066/08_2026/7yry_34066.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7yry_34066/08_2026/7yry_34066.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yry_34066/08_2026/7yry_34066.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7yry_34066/08_2026/7yry_34066.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7yry_34066/08_2026/7yry_34066.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yry_34066/08_2026/7yry_34066.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yry_34066/08_2026/7yry_34066.map" } resolution = 3.0 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 12 5.49 5 Mg 4 5.21 5 S 99 5.16 5 C 15741 2.51 5 N 4306 2.21 5 O 4894 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25056 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3702 Classifications: {'peptide': 489} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 471} Chain: "B" Number of atoms: 3703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3703 Classifications: {'peptide': 489} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 471} Chain: "C" Number of atoms: 3703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3703 Classifications: {'peptide': 489} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 471} Chain: "D" Number of atoms: 3525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3525 Classifications: {'peptide': 463} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 440} Chain: "E" Number of atoms: 3525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3525 Classifications: {'peptide': 463} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 440} Chain: "F" Number of atoms: 3525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3525 Classifications: {'peptide': 463} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 440} Chain: "e" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1010 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain: "g" Number of atoms: 2234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2234 Classifications: {'peptide': 288} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 279} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.67, per 1000 atoms: 0.23 Number of scatterers: 25056 At special positions: 0 Unit cell: (154.512, 131.335, 133.91, 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 99 16.00 P 12 15.00 Mg 4 11.99 O 4894 8.00 N 4306 7.00 C 15741 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: 2.06 Conformation dependent library (CDL) restraints added in 1.2 seconds 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5970 Finding SS restraints... Secondary structure from input PDB file: 133 helices and 27 sheets defined 47.6% alpha, 16.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 79 through 83 removed outlier: 4.366A pdb=" N SER A 82 " --> pdb=" O ASN A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 105 removed outlier: 3.627A pdb=" N LEU A 104 " --> pdb=" O GLY A 101 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A 105 " --> pdb=" O PRO A 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 101 through 105' Processing helix chain 'A' and resid 151 through 158 removed outlier: 3.549A pdb=" N THR A 156 " --> pdb=" O LYS A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 186 removed outlier: 3.586A pdb=" N MET A 179 " --> pdb=" O GLY A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 216 removed outlier: 3.504A pdb=" N THR A 216 " --> pdb=" O LYS A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 220 Processing helix chain 'A' and resid 232 through 252 Proline residue: A 240 - end of helix removed outlier: 3.865A pdb=" N TYR A 249 " --> pdb=" O THR A 245 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N PHE A 250 " --> pdb=" O MET A 246 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ARG A 251 " --> pdb=" O GLY A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 278 removed outlier: 4.049A pdb=" N GLN A 267 " --> pdb=" O ASP A 263 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA A 268 " --> pdb=" O LEU A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 287 Processing helix chain 'A' and resid 290 through 300 removed outlier: 3.857A pdb=" N HIS A 295 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU A 298 " --> pdb=" O LEU A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 315 Processing helix chain 'A' and resid 340 through 348 Processing helix chain 'A' and resid 357 through 363 Processing helix chain 'A' and resid 378 through 383 removed outlier: 4.290A pdb=" N SER A 381 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA A 382 " --> pdb=" O GLY A 379 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLN A 383 " --> pdb=" O GLY A 380 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 378 through 383' Processing helix chain 'A' and resid 384 through 391 Processing helix chain 'A' and resid 393 through 408 Processing helix chain 'A' and resid 415 through 432 removed outlier: 3.546A pdb=" N ARG A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 454 Processing helix chain 'A' and resid 461 through 463 No H-bonds generated for 'chain 'A' and resid 461 through 463' Processing helix chain 'A' and resid 464 through 480 Processing helix chain 'A' and resid 480 through 491 Processing helix chain 'A' and resid 494 through 512 Processing helix chain 'B' and resid 101 through 105 removed outlier: 3.750A pdb=" N LEU B 104 " --> pdb=" O GLY B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 140 removed outlier: 3.697A pdb=" N ARG B 140 " --> pdb=" O VAL B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 158 Processing helix chain 'B' and resid 176 through 187 Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 218 through 220 No H-bonds generated for 'chain 'B' and resid 218 through 220' Processing helix chain 'B' and resid 232 through 252 Proline residue: B 240 - end of helix removed outlier: 3.699A pdb=" N TYR B 249 " --> pdb=" O THR B 245 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N PHE B 250 " --> pdb=" O MET B 246 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG B 251 " --> pdb=" O GLY B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 278 removed outlier: 3.832A pdb=" N GLN B 267 " --> pdb=" O ASP B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 287 Processing helix chain 'B' and resid 290 through 300 removed outlier: 3.679A pdb=" N ARG B 297 " --> pdb=" O TYR B 293 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU B 298 " --> pdb=" O LEU B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 315 Processing helix chain 'B' and resid 340 through 348 Processing helix chain 'B' and resid 357 through 362 removed outlier: 3.545A pdb=" N PHE B 361 " --> pdb=" O GLU B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 383 removed outlier: 3.971A pdb=" N SER B 381 " --> pdb=" O VAL B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 404 removed outlier: 4.672A pdb=" N GLY B 392 " --> pdb=" O LYS B 388 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLY B 393 " --> pdb=" O LYS B 389 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE B 394 " --> pdb=" O LEU B 390 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU B 404 " --> pdb=" O GLN B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 408 removed outlier: 3.889A pdb=" N ALA B 408 " --> pdb=" O ALA B 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 405 through 408' Processing helix chain 'B' and resid 415 through 432 Processing helix chain 'B' and resid 441 through 454 removed outlier: 3.761A pdb=" N GLN B 445 " --> pdb=" O SER B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 463 No H-bonds generated for 'chain 'B' and resid 461 through 463' Processing helix chain 'B' and resid 464 through 480 Processing helix chain 'B' and resid 480 through 491 Processing helix chain 'B' and resid 494 through 512 removed outlier: 4.101A pdb=" N ALA B 510 " --> pdb=" O GLU B 506 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN B 512 " --> pdb=" O PHE B 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 140 Processing helix chain 'C' and resid 151 through 158 Processing helix chain 'C' and resid 175 through 186 Processing helix chain 'C' and resid 202 through 216 removed outlier: 3.559A pdb=" N ILE C 206 " --> pdb=" O LYS C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 220 removed outlier: 4.182A pdb=" N ALA C 220 " --> pdb=" O GLY C 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 217 through 220' Processing helix chain 'C' and resid 232 through 252 Proline residue: C 240 - end of helix removed outlier: 4.348A pdb=" N PHE C 250 " --> pdb=" O MET C 246 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG C 251 " --> pdb=" O GLY C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 278 removed outlier: 3.862A pdb=" N GLN C 267 " --> pdb=" O ASP C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 287 Processing helix chain 'C' and resid 290 through 300 removed outlier: 3.753A pdb=" N LEU C 298 " --> pdb=" O LEU C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 315 Processing helix chain 'C' and resid 340 through 350 removed outlier: 3.694A pdb=" N THR C 344 " --> pdb=" O ALA C 340 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASN C 345 " --> pdb=" O PHE C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 363 Processing helix chain 'C' and resid 378 through 383 removed outlier: 3.717A pdb=" N SER C 381 " --> pdb=" O VAL C 378 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA C 382 " --> pdb=" O GLY C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 403 removed outlier: 4.708A pdb=" N GLY C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N GLY C 393 " --> pdb=" O LYS C 389 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ILE C 394 " --> pdb=" O LEU C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 411 removed outlier: 3.706A pdb=" N PHE C 407 " --> pdb=" O LEU C 404 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLN C 409 " --> pdb=" O ALA C 406 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA C 411 " --> pdb=" O ALA C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 432 Processing helix chain 'C' and resid 441 through 454 Processing helix chain 'C' and resid 464 through 480 Processing helix chain 'C' and resid 480 through 490 Processing helix chain 'C' and resid 494 through 510 removed outlier: 3.848A pdb=" N ALA C 510 " --> pdb=" O GLU C 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'D' and resid 129 through 136 Processing helix chain 'D' and resid 153 through 166 Processing helix chain 'D' and resid 167 through 169 No H-bonds generated for 'chain 'D' and resid 167 through 169' Processing helix chain 'D' and resid 181 through 195 removed outlier: 3.533A pdb=" N SER D 195 " --> pdb=" O GLU D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 199 No H-bonds generated for 'chain 'D' and resid 197 through 199' Processing helix chain 'D' and resid 211 through 231 removed outlier: 3.661A pdb=" N ARG D 217 " --> pdb=" O GLY D 213 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ALA D 219 " --> pdb=" O ARG D 215 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N LEU D 220 " --> pdb=" O LEU D 216 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N THR D 221 " --> pdb=" O ARG D 217 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY D 222 " --> pdb=" O VAL D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 259 removed outlier: 3.901A pdb=" N THR D 253 " --> pdb=" O ILE D 249 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL D 259 " --> pdb=" O ALA D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 264 Processing helix chain 'D' and resid 275 through 285 removed outlier: 3.850A pdb=" N LEU D 283 " --> pdb=" O GLU D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 307 Processing helix chain 'D' and resid 310 through 317 Processing helix chain 'D' and resid 318 through 320 No H-bonds generated for 'chain 'D' and resid 318 through 320' Processing helix chain 'D' and resid 327 through 332 Processing helix chain 'D' and resid 350 through 355 Processing helix chain 'D' and resid 355 through 382 removed outlier: 3.556A pdb=" N TYR D 359 " --> pdb=" O GLY D 355 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ASP D 377 " --> pdb=" O LYS D 373 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ILE D 378 " --> pdb=" O GLU D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 405 Processing helix chain 'D' and resid 412 through 417 Processing helix chain 'D' and resid 424 through 438 Processing helix chain 'D' and resid 444 through 449 removed outlier: 3.635A pdb=" N PHE D 448 " --> pdb=" O GLU D 445 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TYR D 449 " --> pdb=" O GLN D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 464 Processing helix chain 'E' and resid 79 through 83 Processing helix chain 'E' and resid 129 through 135 Processing helix chain 'E' and resid 153 through 169 removed outlier: 3.572A pdb=" N ASN E 157 " --> pdb=" O GLY E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 194 Processing helix chain 'E' and resid 195 through 199 removed outlier: 5.320A pdb=" N LEU E 198 " --> pdb=" O SER E 195 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ASP E 199 " --> pdb=" O ASN E 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 195 through 199' Processing helix chain 'E' and resid 211 through 231 removed outlier: 3.584A pdb=" N ARG E 215 " --> pdb=" O PRO E 211 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ALA E 219 " --> pdb=" O ARG E 215 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU E 220 " --> pdb=" O LEU E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 263 removed outlier: 3.776A pdb=" N TYR E 252 " --> pdb=" O ASN E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 285 Processing helix chain 'E' and resid 303 through 307 removed outlier: 3.552A pdb=" N ASP E 306 " --> pdb=" O VAL E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 318 removed outlier: 3.925A pdb=" N THR E 316 " --> pdb=" O SER E 312 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA E 318 " --> pdb=" O ALA E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 333 Processing helix chain 'E' and resid 350 through 355 Processing helix chain 'E' and resid 355 through 382 removed outlier: 3.912A pdb=" N LYS E 376 " --> pdb=" O TYR E 372 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ASP E 377 " --> pdb=" O LYS E 373 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ILE E 378 " --> pdb=" O GLU E 374 " (cutoff:3.500A) Processing helix chain 'E' and resid 391 through 405 removed outlier: 3.563A pdb=" N PHE E 405 " --> pdb=" O ILE E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 424 through 438 removed outlier: 3.662A pdb=" N THR E 428 " --> pdb=" O PRO E 424 " (cutoff:3.500A) Processing helix chain 'E' and resid 444 through 449 removed outlier: 4.073A pdb=" N TYR E 449 " --> pdb=" O GLN E 446 " (cutoff:3.500A) Processing helix chain 'E' and resid 453 through 464 Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.812A pdb=" N THR F 82 " --> pdb=" O GLY F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 118 removed outlier: 3.559A pdb=" N GLN F 118 " --> pdb=" O TYR F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 129 through 136 Processing helix chain 'F' and resid 154 through 168 Processing helix chain 'F' and resid 181 through 195 Processing helix chain 'F' and resid 197 through 201 removed outlier: 3.691A pdb=" N VAL F 201 " --> pdb=" O LEU F 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 217 removed outlier: 3.522A pdb=" N ARG F 215 " --> pdb=" O PRO F 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 218 through 232 removed outlier: 3.766A pdb=" N GLY F 222 " --> pdb=" O VAL F 218 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 238 removed outlier: 4.176A pdb=" N LYS F 238 " --> pdb=" O GLU F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 264 Processing helix chain 'F' and resid 275 through 285 Processing helix chain 'F' and resid 303 through 307 removed outlier: 3.558A pdb=" N ASP F 306 " --> pdb=" O VAL F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 318 Processing helix chain 'F' and resid 327 through 333 removed outlier: 3.615A pdb=" N ALA F 331 " --> pdb=" O SER F 327 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER F 333 " --> pdb=" O ASP F 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 355 Processing helix chain 'F' and resid 355 through 383 removed outlier: 3.948A pdb=" N TYR F 359 " --> pdb=" O GLY F 355 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASP F 377 " --> pdb=" O LYS F 373 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ILE F 378 " --> pdb=" O GLU F 374 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY F 383 " --> pdb=" O ILE F 379 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 405 Processing helix chain 'F' and resid 412 through 417 Processing helix chain 'F' and resid 424 through 438 removed outlier: 3.643A pdb=" N THR F 428 " --> pdb=" O PRO F 424 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE F 429 " --> pdb=" O LEU F 425 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG F 430 " --> pdb=" O LYS F 426 " (cutoff:3.500A) Processing helix chain 'F' and resid 444 through 449 Processing helix chain 'F' and resid 453 through 464 Processing helix chain 'e' and resid 91 through 125 removed outlier: 4.574A pdb=" N ALA e 97 " --> pdb=" O ALA e 93 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ARG e 98 " --> pdb=" O ILE e 94 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ALA e 119 " --> pdb=" O ALA e 115 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ALA e 120 " --> pdb=" O ALA e 116 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA e 122 " --> pdb=" O LEU e 118 " (cutoff:3.500A) Processing helix chain 'e' and resid 128 through 133 removed outlier: 3.595A pdb=" N ARG e 132 " --> pdb=" O LEU e 128 " (cutoff:3.500A) Processing helix chain 'g' and resid 3 through 37 Processing helix chain 'g' and resid 42 through 60 removed outlier: 3.968A pdb=" N ALA g 46 " --> pdb=" O GLY g 42 " (cutoff:3.500A) Processing helix chain 'g' and resid 65 through 69 removed outlier: 3.749A pdb=" N MET g 68 " --> pdb=" O HIS g 65 " (cutoff:3.500A) Processing helix chain 'g' and resid 90 through 108 removed outlier: 3.692A pdb=" N GLU g 108 " --> pdb=" O LYS g 104 " (cutoff:3.500A) Processing helix chain 'g' and resid 119 through 128 Processing helix chain 'g' and resid 150 through 161 Processing helix chain 'g' and resid 213 through 242 removed outlier: 4.401A pdb=" N LEU g 217 " --> pdb=" O GLU g 213 " (cutoff:3.500A) Processing helix chain 'g' and resid 244 through 288 Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 67 removed outlier: 4.840A pdb=" N GLU A 52 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N ARG A 94 " --> pdb=" O MET A 53 " (cutoff:3.500A) removed outlier: 8.523A pdb=" N GLU A 55 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N THR A 92 " --> pdb=" O GLU A 55 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ARG A 41 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N VAL A 35 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ILE A 39 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N GLY A 73 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ARG D 51 " --> pdb=" O GLN D 42 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N GLN D 44 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N VAL D 49 " --> pdb=" O GLN D 44 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLN D 8 " --> pdb=" O ASP D 15 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N GLU D 17 " --> pdb=" O ILE D 6 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ILE D 6 " --> pdb=" O GLU D 17 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 100 removed outlier: 3.628A pdb=" N VAL A 100 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LEU A 126 " --> pdb=" O VAL A 100 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 108 through 109 removed outlier: 3.670A pdb=" N ILE A 199 " --> pdb=" O ASP A 262 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA A 257 " --> pdb=" O SER A 324 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LEU A 167 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N LEU A 356 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE A 169 " --> pdb=" O LEU A 356 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 146 through 147 removed outlier: 4.651A pdb=" N VAL A 160 " --> pdb=" O VAL A 147 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 61 through 67 removed outlier: 4.606A pdb=" N GLU B 52 " --> pdb=" O ALA B 64 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N MET B 53 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ARG B 41 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VAL B 35 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ILE B 39 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N GLY B 73 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N THR F 38 " --> pdb=" O MET F 55 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ARG F 51 " --> pdb=" O GLN F 42 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N GLN F 44 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N VAL F 49 " --> pdb=" O GLN F 44 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN F 8 " --> pdb=" O ASP F 15 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N GLU F 17 " --> pdb=" O ILE F 6 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ILE F 6 " --> pdb=" O GLU F 17 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 97 through 100 removed outlier: 4.565A pdb=" N LEU B 126 " --> pdb=" O VAL B 100 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 108 through 109 Processing sheet with id=AA8, first strand: chain 'B' and resid 146 through 147 removed outlier: 4.454A pdb=" N VAL B 160 " --> pdb=" O VAL B 147 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 330 through 332 removed outlier: 10.333A pdb=" N GLN B 353 " --> pdb=" O GLY B 372 " (cutoff:3.500A) removed outlier: 8.594A pdb=" N GLY B 372 " --> pdb=" O GLN B 353 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N PHE B 355 " --> pdb=" O ASN B 370 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 61 through 67 removed outlier: 6.672A pdb=" N ARG C 41 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N VAL C 35 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ILE C 39 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N SER C 71 " --> pdb=" O LEU C 67 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N LEU C 67 " --> pdb=" O SER C 71 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLY C 73 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ARG E 51 " --> pdb=" O GLN E 42 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N GLN E 44 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N VAL E 49 " --> pdb=" O GLN E 44 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL E 13 " --> pdb=" O ILE E 9 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ILE E 9 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ASP E 15 " --> pdb=" O ILE E 7 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 97 through 100 removed outlier: 4.110A pdb=" N LEU C 126 " --> pdb=" O VAL C 100 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 107 through 109 removed outlier: 6.504A pdb=" N ARG C 107 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ALA C 226 " --> pdb=" O ARG C 107 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL C 109 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N ALA C 228 " --> pdb=" O VAL C 109 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR C 261 " --> pdb=" O LEU C 328 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY C 323 " --> pdb=" O VAL C 305 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 107 through 109 removed outlier: 6.504A pdb=" N ARG C 107 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ALA C 226 " --> pdb=" O ARG C 107 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL C 109 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N ALA C 228 " --> pdb=" O VAL C 109 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR C 261 " --> pdb=" O LEU C 328 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLU C 166 " --> pdb=" O PRO C 329 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N ILE C 331 " --> pdb=" O GLU C 166 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE C 168 " --> pdb=" O ILE C 331 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU C 167 " --> pdb=" O ILE C 354 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 146 through 147 removed outlier: 4.550A pdb=" N VAL C 160 " --> pdb=" O VAL C 147 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 75 through 77 Processing sheet with id=AB7, first strand: chain 'D' and resid 86 through 87 removed outlier: 3.531A pdb=" N VAL D 178 " --> pdb=" O ASP D 247 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL D 144 " --> pdb=" O GLN D 299 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N VAL D 301 " --> pdb=" O VAL D 144 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N LEU D 146 " --> pdb=" O VAL D 301 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 124 through 125 removed outlier: 3.555A pdb=" N LEU D 125 " --> pdb=" O PHE D 138 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N PHE D 138 " --> pdb=" O LEU D 125 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'E' and resid 75 through 77 Processing sheet with id=AC1, first strand: chain 'E' and resid 86 through 87 removed outlier: 6.483A pdb=" N LEU E 244 " --> pdb=" O ILE E 298 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N ALA E 300 " --> pdb=" O LEU E 244 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N VAL E 246 " --> pdb=" O ALA E 300 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 124 through 125 removed outlier: 4.334A pdb=" N PHE E 138 " --> pdb=" O LEU E 125 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 241 through 242 Processing sheet with id=AC4, first strand: chain 'F' and resid 75 through 77 Processing sheet with id=AC5, first strand: chain 'F' and resid 86 through 87 removed outlier: 6.793A pdb=" N MET F 87 " --> pdb=" O TYR F 205 " (cutoff:3.500A) removed outlier: 8.659A pdb=" N GLN F 207 " --> pdb=" O MET F 87 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU F 172 " --> pdb=" O ASP F 241 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA F 300 " --> pdb=" O VAL F 246 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LYS F 143 " --> pdb=" O ALA F 322 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N VAL F 324 " --> pdb=" O LYS F 143 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N GLY F 145 " --> pdb=" O VAL F 324 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'e' and resid 17 through 20 removed outlier: 3.851A pdb=" N VAL e 76 " --> pdb=" O GLN e 5 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'e' and resid 31 through 34 removed outlier: 4.150A pdb=" N LEU e 23 " --> pdb=" O ILE e 34 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG e 51 " --> pdb=" O ILE e 24 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N LYS e 26 " --> pdb=" O PRO e 49 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL e 52 " --> pdb=" O GLU e 60 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'e' and resid 44 through 45 removed outlier: 3.592A pdb=" N GLY e 67 " --> pdb=" O LEU e 45 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'g' and resid 113 through 118 removed outlier: 6.485A pdb=" N VAL g 76 " --> pdb=" O GLN g 114 " (cutoff:3.500A) removed outlier: 8.623A pdb=" N ALA g 116 " --> pdb=" O VAL g 76 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N TYR g 78 " --> pdb=" O ALA g 116 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N ILE g 118 " --> pdb=" O TYR g 78 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE g 80 " --> pdb=" O ILE g 118 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE g 79 " --> pdb=" O TYR g 169 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL g 81 " --> pdb=" O VAL g 171 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ASN g 173 " --> pdb=" O VAL g 81 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU g 186 " --> pdb=" O LEU g 170 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER g 172 " --> pdb=" O LYS g 184 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS g 184 " --> pdb=" O SER g 172 " (cutoff:3.500A) 1237 hydrogen bonds defined for protein. 3537 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: 5.45 Time building geometry restraints manager: 2.80 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: 8453 1.34 - 1.46: 4816 1.46 - 1.58: 11968 1.58 - 1.70: 15 1.70 - 1.82: 184 Bond restraints: 25436 Sorted by residual: bond pdb=" C VAL g 176 " pdb=" N ASN g 177 " ideal model delta sigma weight residual 1.332 1.264 0.068 1.40e-02 5.10e+03 2.35e+01 bond pdb=" O3 PO4 E 601 " pdb=" P PO4 E 601 " ideal model delta sigma weight residual 1.569 1.509 0.060 2.00e-02 2.50e+03 8.94e+00 bond pdb=" O4 PO4 E 601 " pdb=" P PO4 E 601 " ideal model delta sigma weight residual 1.568 1.510 0.058 2.00e-02 2.50e+03 8.40e+00 bond pdb=" O2 PO4 E 601 " pdb=" P PO4 E 601 " ideal model delta sigma weight residual 1.567 1.510 0.057 2.00e-02 2.50e+03 8.17e+00 bond pdb=" O1 PO4 E 601 " pdb=" P PO4 E 601 " ideal model delta sigma weight residual 1.565 1.510 0.055 2.00e-02 2.50e+03 7.58e+00 ... (remaining 25431 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 34222 2.54 - 5.08: 217 5.08 - 7.61: 24 7.61 - 10.15: 9 10.15 - 12.69: 2 Bond angle restraints: 34474 Sorted by residual: angle pdb=" CB MET E 55 " pdb=" CG MET E 55 " pdb=" SD MET E 55 " ideal model delta sigma weight residual 112.70 125.39 -12.69 3.00e+00 1.11e-01 1.79e+01 angle pdb=" C GLU F 389 " pdb=" CA GLU F 389 " pdb=" CB GLU F 389 " ideal model delta sigma weight residual 110.42 118.14 -7.72 1.99e+00 2.53e-01 1.51e+01 angle pdb=" CA ILE g 226 " pdb=" CB ILE g 226 " pdb=" CG1 ILE g 226 " ideal model delta sigma weight residual 110.40 116.71 -6.31 1.70e+00 3.46e-01 1.38e+01 angle pdb=" N ILE e 94 " pdb=" CA ILE e 94 " pdb=" C ILE e 94 " ideal model delta sigma weight residual 111.81 108.72 3.09 8.60e-01 1.35e+00 1.29e+01 angle pdb=" CA GLU F 389 " pdb=" CB GLU F 389 " pdb=" CG GLU F 389 " ideal model delta sigma weight residual 114.10 120.71 -6.61 2.00e+00 2.50e-01 1.09e+01 ... (remaining 34469 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.87: 14820 35.87 - 71.74: 553 71.74 - 107.61: 46 107.61 - 143.49: 1 143.49 - 179.36: 1 Dihedral angle restraints: 15421 sinusoidal: 6052 harmonic: 9369 Sorted by residual: dihedral pdb=" C5' ADP D 502 " pdb=" O5' ADP D 502 " pdb=" PA ADP D 502 " pdb=" O2A ADP D 502 " ideal model delta sinusoidal sigma weight residual -60.00 119.36 -179.36 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O1B ADP D 502 " pdb=" O3A ADP D 502 " pdb=" PB ADP D 502 " pdb=" PA ADP D 502 " ideal model delta sinusoidal sigma weight residual -60.00 61.57 -121.57 1 2.00e+01 2.50e-03 3.66e+01 dihedral pdb=" CA MET F 203 " pdb=" C MET F 203 " pdb=" N VAL F 204 " pdb=" CA VAL F 204 " ideal model delta harmonic sigma weight residual 180.00 157.71 22.29 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 15418 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2867 0.040 - 0.080: 775 0.080 - 0.120: 295 0.120 - 0.161: 40 0.161 - 0.201: 2 Chirality restraints: 3979 Sorted by residual: chirality pdb=" CB ILE e 24 " pdb=" CA ILE e 24 " pdb=" CG1 ILE e 24 " pdb=" CG2 ILE e 24 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA GLU F 389 " pdb=" N GLU F 389 " pdb=" C GLU F 389 " pdb=" CB GLU F 389 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.46e-01 chirality pdb=" CB ILE g 226 " pdb=" CA ILE g 226 " pdb=" CG1 ILE g 226 " pdb=" CG2 ILE g 226 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.93e-01 ... (remaining 3976 not shown) Planarity restraints: 4494 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL g 176 " 0.017 2.00e-02 2.50e+03 3.30e-02 1.09e+01 pdb=" C VAL g 176 " -0.057 2.00e-02 2.50e+03 pdb=" O VAL g 176 " 0.021 2.00e-02 2.50e+03 pdb=" N ASN g 177 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN g 177 " -0.014 2.00e-02 2.50e+03 2.70e-02 7.30e+00 pdb=" C ASN g 177 " 0.047 2.00e-02 2.50e+03 pdb=" O ASN g 177 " -0.017 2.00e-02 2.50e+03 pdb=" N ALA g 178 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP F 310 " 0.030 5.00e-02 4.00e+02 4.51e-02 3.25e+00 pdb=" N PRO F 311 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO F 311 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO F 311 " 0.025 5.00e-02 4.00e+02 ... (remaining 4491 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 207 2.61 - 3.18: 21105 3.18 - 3.76: 37313 3.76 - 4.33: 50646 4.33 - 4.90: 86049 Nonbonded interactions: 195320 Sorted by model distance: nonbonded pdb=" O2G ATP B 601 " pdb="MG MG B 602 " model vdw 2.041 2.170 nonbonded pdb="MG MG C 601 " pdb=" O2B ATP C 602 " model vdw 2.051 2.170 nonbonded pdb=" OG1 THR A 177 " pdb="MG MG A 602 " model vdw 2.066 2.170 nonbonded pdb=" N GLU D 104 " pdb=" OE1 GLU D 104 " model vdw 2.167 3.120 nonbonded pdb="MG MG D 501 " pdb=" O3B ADP D 502 " model vdw 2.171 2.170 ... (remaining 195315 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 26 through 514) selection = (chain 'B' and (resid 26 through 513 or (resid 514 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name \ CE2 or name CZ or name OH )))) selection = (chain 'C' and (resid 26 through 513 or (resid 514 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name \ CE2 or name CZ or name OH )))) } ncs_group { reference = (chain 'D' and resid 2 through 464) selection = (chain 'E' and resid 2 through 464) selection = chain 'F' } 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: 2.840 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: 0.530 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 24.420 Find NCS groups from input model: 0.600 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:6.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 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 : 0.002 0.068 25436 Z= 0.120 Angle : 0.544 12.692 34474 Z= 0.280 Chirality : 0.043 0.201 3979 Planarity : 0.003 0.045 4494 Dihedral : 17.649 179.358 9451 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.35 % Allowed : 26.64 % Favored : 70.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: 0.38 (0.15), residues: 3266 helix: 1.60 (0.15), residues: 1310 sheet: 0.20 (0.24), residues: 491 loop : -0.98 (0.15), residues: 1465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 20 TYR 0.023 0.001 TYR g 63 PHE 0.011 0.001 PHE F 415 TRP 0.027 0.002 TRP g 206 HIS 0.002 0.000 HIS D 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 (25436) covalent geometry : angle 0.54361 / 0.28 (34474) hydrogen bonds : bond 0.18291 / 12.18 ( 1221) hydrogen bonds : angle 6.90789 / 4.76 ( 3537) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 213 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 266 MET cc_start: 0.7148 (mpt) cc_final: 0.6892 (mpp) REVERT: E 404 PHE cc_start: 0.5689 (OUTLIER) cc_final: 0.5429 (t80) REVERT: e 22 MET cc_start: 0.3467 (tmm) cc_final: 0.3228 (tpp) REVERT: g 6 GLU cc_start: 0.6541 (tm-30) cc_final: 0.6334 (tp30) REVERT: g 39 MET cc_start: 0.7600 (mmp) cc_final: 0.6803 (tpp) REVERT: g 115 PHE cc_start: 0.8722 (p90) cc_final: 0.8262 (p90) REVERT: g 229 MET cc_start: 0.7984 (mmt) cc_final: 0.7758 (mmm) outliers start: 88 outliers final: 74 residues processed: 296 average time/residue: 0.5911 time to fit residues: 206.2286 Evaluate side-chains 268 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 193 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 507 SER Chi-restraints excluded: chain B residue 509 LYS Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 62 LYS Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 123 ASP Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain E residue 5 ARG Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 404 PHE Chi-restraints excluded: chain E residue 409 PHE Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 257 THR Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 353 VAL Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain e residue 10 SER Chi-restraints excluded: chain e residue 44 LEU Chi-restraints excluded: chain e residue 77 THR Chi-restraints excluded: chain e residue 114 SER Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain g residue 16 SER Chi-restraints excluded: chain g residue 18 GLN Chi-restraints excluded: chain g residue 60 ASN Chi-restraints excluded: chain g residue 92 ASN Chi-restraints excluded: chain g residue 129 TYR Chi-restraints excluded: chain g residue 166 ASP Chi-restraints excluded: chain g residue 198 ASP Chi-restraints excluded: chain g residue 206 TRP Chi-restraints excluded: chain g residue 228 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 197 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 61.0452 > 50:) chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 10.0000 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 148 GLN E 190 HIS F 248 ASN ** e 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.111667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.078179 restraints weight = 49762.252| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.61 r_work: 0.2908 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.0879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 25436 Z= 0.260 Angle : 0.635 9.558 34474 Z= 0.339 Chirality : 0.047 0.211 3979 Planarity : 0.004 0.049 4494 Dihedral : 7.503 150.428 3703 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 5.64 % Allowed : 24.09 % Favored : 70.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: 0.22 (0.15), residues: 3266 helix: 1.40 (0.15), residues: 1339 sheet: 0.12 (0.23), residues: 529 loop : -1.08 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 20 TYR 0.028 0.002 TYR E 396 PHE 0.015 0.002 PHE g 175 TRP 0.006 0.001 TRP B 139 HIS 0.005 0.001 HIS D 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00632 / 0.26 (25436) covalent geometry : angle 0.63511 / 0.34 (34474) hydrogen bonds : bond 0.06684 / 4.43 ( 1221) hydrogen bonds : angle 5.46568 / 3.81 ( 3537) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 197 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.7739 (p0) cc_final: 0.7407 (p0) REVERT: A 476 PHE cc_start: 0.9286 (OUTLIER) cc_final: 0.8038 (t80) REVERT: C 419 ARG cc_start: -0.0407 (OUTLIER) cc_final: -0.0863 (mtt180) REVERT: C 427 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7592 (mpt-90) REVERT: D 326 LEU cc_start: 0.9380 (OUTLIER) cc_final: 0.9103 (mt) REVERT: E 158 MET cc_start: 0.8105 (OUTLIER) cc_final: 0.7735 (mpm) REVERT: E 404 PHE cc_start: 0.5679 (OUTLIER) cc_final: 0.5435 (t80) REVERT: F 36 GLU cc_start: 0.7992 (pm20) cc_final: 0.7696 (pp20) REVERT: F 203 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.8198 (mpp) REVERT: F 249 ILE cc_start: 0.8535 (OUTLIER) cc_final: 0.8099 (pp) REVERT: F 310 ASP cc_start: 0.8675 (OUTLIER) cc_final: 0.8042 (t0) REVERT: g 8 ARG cc_start: 0.6933 (OUTLIER) cc_final: 0.6298 (mpt-90) REVERT: g 267 TYR cc_start: 0.8291 (t80) cc_final: 0.8081 (t80) outliers start: 148 outliers final: 69 residues processed: 320 average time/residue: 0.6338 time to fit residues: 237.4800 Evaluate side-chains 263 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 184 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain A residue 476 PHE Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 473 ILE Chi-restraints excluded: chain B residue 507 SER Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 419 ARG Chi-restraints excluded: chain C residue 427 ARG Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 249 ILE Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 458 ILE Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain E residue 382 LEU Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 404 PHE Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain E residue 464 LEU Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 203 MET Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 249 ILE Chi-restraints excluded: chain F residue 257 THR Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 310 ASP Chi-restraints excluded: chain F residue 353 VAL Chi-restraints excluded: chain F residue 378 ILE Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain e residue 9 VAL Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain g residue 8 ARG Chi-restraints excluded: chain g residue 18 GLN Chi-restraints excluded: chain g residue 32 MET Chi-restraints excluded: chain g residue 92 ASN Chi-restraints excluded: chain g residue 129 TYR Chi-restraints excluded: chain g residue 133 VAL Chi-restraints excluded: chain g residue 142 ASP Chi-restraints excluded: chain g residue 210 TYR Chi-restraints excluded: chain g residue 253 THR Chi-restraints excluded: chain g residue 279 ILE Chi-restraints excluded: chain g residue 281 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 255 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 95 optimal weight: 9.9990 chunk 296 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 291 optimal weight: 5.9990 chunk 257 optimal weight: 0.0020 chunk 136 optimal weight: 5.9990 chunk 293 optimal weight: 20.0000 overall best weight: 1.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 190 HIS E 348 GLN F 248 ASN ** e 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.112862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.079259 restraints weight = 49355.945| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 2.49 r_work: 0.2947 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.0891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 25436 Z= 0.157 Angle : 0.562 11.489 34474 Z= 0.295 Chirality : 0.044 0.207 3979 Planarity : 0.004 0.045 4494 Dihedral : 6.321 137.427 3643 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 4.34 % Allowed : 25.15 % Favored : 70.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: 0.35 (0.15), residues: 3266 helix: 1.54 (0.15), residues: 1333 sheet: 0.23 (0.23), residues: 516 loop : -1.03 (0.16), residues: 1417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 20 TYR 0.012 0.001 TYR D 252 PHE 0.017 0.001 PHE g 175 TRP 0.013 0.001 TRP g 206 HIS 0.003 0.001 HIS D 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (25436) covalent geometry : angle 0.56246 / 0.30 (34474) hydrogen bonds : bond 0.05442 / 3.60 ( 1221) hydrogen bonds : angle 5.11330 / 3.58 ( 3537) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 198 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.7699 (p0) cc_final: 0.7205 (p0) REVERT: A 476 PHE cc_start: 0.9246 (OUTLIER) cc_final: 0.8060 (t80) REVERT: C 427 ARG cc_start: 0.8045 (OUTLIER) cc_final: 0.7519 (mpt-90) REVERT: C 475 TYR cc_start: 0.8331 (t80) cc_final: 0.7609 (t80) REVERT: E 117 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8488 (mp0) REVERT: E 158 MET cc_start: 0.8024 (OUTLIER) cc_final: 0.7672 (mpm) REVERT: E 180 GLU cc_start: 0.6758 (OUTLIER) cc_final: 0.6399 (pm20) REVERT: E 404 PHE cc_start: 0.5727 (OUTLIER) cc_final: 0.5482 (t80) REVERT: F 39 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.7693 (mt) REVERT: F 159 MET cc_start: 0.8652 (mmp) cc_final: 0.7792 (mtp) REVERT: F 249 ILE cc_start: 0.8450 (OUTLIER) cc_final: 0.8016 (pp) REVERT: F 310 ASP cc_start: 0.8570 (OUTLIER) cc_final: 0.7951 (t0) REVERT: g 8 ARG cc_start: 0.7038 (OUTLIER) cc_final: 0.6496 (mpt-90) REVERT: g 63 TYR cc_start: 0.8271 (t80) cc_final: 0.8049 (t80) outliers start: 114 outliers final: 57 residues processed: 291 average time/residue: 0.6590 time to fit residues: 223.2630 Evaluate side-chains 254 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 187 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain A residue 476 PHE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 473 ILE Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 427 ARG Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 458 ILE Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 180 GLU Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain E residue 382 LEU Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 404 PHE Chi-restraints excluded: chain E residue 451 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 249 ILE Chi-restraints excluded: chain F residue 257 THR Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 310 ASP Chi-restraints excluded: chain F residue 378 ILE Chi-restraints excluded: chain F residue 379 ILE Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain e residue 9 VAL Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain g residue 8 ARG Chi-restraints excluded: chain g residue 32 MET Chi-restraints excluded: chain g residue 76 VAL Chi-restraints excluded: chain g residue 92 ASN Chi-restraints excluded: chain g residue 129 TYR Chi-restraints excluded: chain g residue 166 ASP Chi-restraints excluded: chain g residue 210 TYR Chi-restraints excluded: chain g residue 279 ILE Chi-restraints excluded: chain g residue 281 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 109 optimal weight: 1.9990 chunk 252 optimal weight: 4.9990 chunk 194 optimal weight: 2.9990 chunk 231 optimal weight: 0.9990 chunk 88 optimal weight: 9.9990 chunk 126 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 160 optimal weight: 5.9990 chunk 232 optimal weight: 9.9990 chunk 288 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 190 HIS F 248 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.111757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.078704 restraints weight = 48814.352| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.55 r_work: 0.2926 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8887 moved from start: 0.1050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 25436 Z= 0.200 Angle : 0.585 10.043 34474 Z= 0.309 Chirality : 0.046 0.223 3979 Planarity : 0.004 0.049 4494 Dihedral : 6.000 110.898 3629 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 4.95 % Allowed : 24.77 % Favored : 70.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: 0.29 (0.15), residues: 3266 helix: 1.48 (0.15), residues: 1338 sheet: 0.22 (0.23), residues: 520 loop : -1.08 (0.15), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 20 TYR 0.033 0.001 TYR E 396 PHE 0.019 0.001 PHE g 175 TRP 0.015 0.002 TRP g 206 HIS 0.004 0.001 HIS D 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.20 (25436) covalent geometry : angle 0.58516 / 0.31 (34474) hydrogen bonds : bond 0.05794 / 3.82 ( 1221) hydrogen bonds : angle 5.04327 / 3.53 ( 3537) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 199 time to evaluate : 1.096 Fit side-chains revert: symmetry clash REVERT: A 123 ASP cc_start: 0.7692 (p0) cc_final: 0.7117 (p0) REVERT: A 476 PHE cc_start: 0.9261 (OUTLIER) cc_final: 0.8097 (t80) REVERT: C 427 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.7556 (mpt-90) REVERT: E 117 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8497 (mp0) REVERT: E 158 MET cc_start: 0.8069 (OUTLIER) cc_final: 0.7711 (mpm) REVERT: E 192 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.8341 (mmm) REVERT: E 404 PHE cc_start: 0.5702 (OUTLIER) cc_final: 0.5464 (t80) REVERT: F 39 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7605 (mt) REVERT: F 159 MET cc_start: 0.8710 (mmp) cc_final: 0.7857 (mtp) REVERT: F 249 ILE cc_start: 0.8489 (OUTLIER) cc_final: 0.8033 (pp) REVERT: F 310 ASP cc_start: 0.8665 (OUTLIER) cc_final: 0.7987 (t0) REVERT: g 8 ARG cc_start: 0.7125 (OUTLIER) cc_final: 0.6545 (mpt-90) REVERT: g 63 TYR cc_start: 0.8293 (t80) cc_final: 0.8044 (t80) outliers start: 130 outliers final: 63 residues processed: 305 average time/residue: 0.6344 time to fit residues: 226.8406 Evaluate side-chains 261 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 188 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 476 PHE Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 473 ILE Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 427 ARG Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 249 ILE Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 458 ILE Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 382 LEU Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 404 PHE Chi-restraints excluded: chain E residue 451 VAL Chi-restraints excluded: chain E residue 464 LEU Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 249 ILE Chi-restraints excluded: chain F residue 257 THR Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 310 ASP Chi-restraints excluded: chain F residue 353 VAL Chi-restraints excluded: chain F residue 378 ILE Chi-restraints excluded: chain F residue 379 ILE Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain e residue 9 VAL Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain g residue 8 ARG Chi-restraints excluded: chain g residue 76 VAL Chi-restraints excluded: chain g residue 129 TYR Chi-restraints excluded: chain g residue 133 VAL Chi-restraints excluded: chain g residue 142 ASP Chi-restraints excluded: chain g residue 210 TYR Chi-restraints excluded: chain g residue 279 ILE Chi-restraints excluded: chain g residue 281 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 165 optimal weight: 4.9990 chunk 134 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 262 optimal weight: 7.9990 chunk 162 optimal weight: 5.9990 chunk 81 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 240 optimal weight: 1.9990 chunk 318 optimal weight: 10.0000 chunk 254 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 190 HIS F 248 ASN e 127 GLN g 60 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.113114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.078742 restraints weight = 49112.171| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.37 r_work: 0.2952 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.1048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 25436 Z= 0.152 Angle : 0.560 12.821 34474 Z= 0.291 Chirality : 0.044 0.209 3979 Planarity : 0.004 0.047 4494 Dihedral : 5.650 94.818 3624 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 4.88 % Allowed : 24.92 % Favored : 70.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: 0.43 (0.15), residues: 3266 helix: 1.62 (0.15), residues: 1326 sheet: 0.35 (0.23), residues: 508 loop : -1.03 (0.15), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG e 51 TYR 0.013 0.001 TYR C 475 PHE 0.018 0.001 PHE g 175 TRP 0.017 0.002 TRP g 206 HIS 0.003 0.001 HIS D 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 (25436) covalent geometry : angle 0.55994 / 0.29 (34474) hydrogen bonds : bond 0.05086 / 3.35 ( 1221) hydrogen bonds : angle 4.87443 / 3.42 ( 3537) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 203 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.7708 (p0) cc_final: 0.7229 (p0) REVERT: A 476 PHE cc_start: 0.9244 (OUTLIER) cc_final: 0.8042 (t80) REVERT: C 427 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7565 (mpt-90) REVERT: D 425 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7667 (tp) REVERT: E 25 LYS cc_start: 0.8945 (OUTLIER) cc_final: 0.8708 (mtmm) REVERT: E 117 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8473 (mp0) REVERT: E 158 MET cc_start: 0.8019 (OUTLIER) cc_final: 0.7663 (mpm) REVERT: E 180 GLU cc_start: 0.6738 (OUTLIER) cc_final: 0.6390 (pm20) REVERT: E 404 PHE cc_start: 0.5632 (OUTLIER) cc_final: 0.5377 (t80) REVERT: F 39 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7656 (mt) REVERT: F 159 MET cc_start: 0.8684 (mmp) cc_final: 0.7988 (mtp) REVERT: F 165 ILE cc_start: 0.8984 (OUTLIER) cc_final: 0.8717 (tp) REVERT: F 249 ILE cc_start: 0.8429 (OUTLIER) cc_final: 0.7985 (pp) REVERT: F 310 ASP cc_start: 0.8581 (OUTLIER) cc_final: 0.7932 (t0) REVERT: g 8 ARG cc_start: 0.7140 (OUTLIER) cc_final: 0.6599 (mpt-90) REVERT: g 39 MET cc_start: 0.7540 (mmp) cc_final: 0.6738 (tpp) REVERT: g 63 TYR cc_start: 0.8305 (t80) cc_final: 0.8097 (t80) REVERT: g 76 VAL cc_start: 0.9411 (OUTLIER) cc_final: 0.9052 (p) REVERT: g 129 TYR cc_start: 0.7375 (OUTLIER) cc_final: 0.6942 (p90) outliers start: 128 outliers final: 67 residues processed: 308 average time/residue: 0.6538 time to fit residues: 234.8860 Evaluate side-chains 273 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 191 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 476 PHE Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 473 ILE Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 427 ARG Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain D residue 405 PHE Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 458 ILE Chi-restraints excluded: chain E residue 25 LYS Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 173 SER Chi-restraints excluded: chain E residue 180 GLU Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 404 PHE Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain E residue 451 VAL Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 249 ILE Chi-restraints excluded: chain F residue 257 THR Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 310 ASP Chi-restraints excluded: chain F residue 378 ILE Chi-restraints excluded: chain F residue 379 ILE Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain e residue 9 VAL Chi-restraints excluded: chain e residue 75 VAL Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain g residue 8 ARG Chi-restraints excluded: chain g residue 32 MET Chi-restraints excluded: chain g residue 76 VAL Chi-restraints excluded: chain g residue 87 LEU Chi-restraints excluded: chain g residue 129 TYR Chi-restraints excluded: chain g residue 142 ASP Chi-restraints excluded: chain g residue 166 ASP Chi-restraints excluded: chain g residue 210 TYR Chi-restraints excluded: chain g residue 219 ASN Chi-restraints excluded: chain g residue 279 ILE Chi-restraints excluded: chain g residue 281 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 19 optimal weight: 0.6980 chunk 86 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 chunk 304 optimal weight: 3.9990 chunk 126 optimal weight: 0.9990 chunk 45 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 175 optimal weight: 3.9990 chunk 196 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 190 HIS E 284 GLN F 248 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.113607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.079023 restraints weight = 48824.958| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.40 r_work: 0.2949 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 25436 Z= 0.144 Angle : 0.556 11.457 34474 Z= 0.289 Chirality : 0.044 0.201 3979 Planarity : 0.004 0.047 4494 Dihedral : 5.536 85.268 3624 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 4.69 % Allowed : 25.27 % Favored : 70.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: 0.51 (0.15), residues: 3266 helix: 1.68 (0.15), residues: 1326 sheet: 0.38 (0.23), residues: 509 loop : -0.98 (0.16), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 20 TYR 0.035 0.001 TYR E 396 PHE 0.018 0.001 PHE g 175 TRP 0.017 0.001 TRP g 206 HIS 0.003 0.001 HIS g 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.14 (25436) covalent geometry : angle 0.55595 / 0.29 (34474) hydrogen bonds : bond 0.04889 / 3.22 ( 1221) hydrogen bonds : angle 4.79926 / 3.37 ( 3537) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 200 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.7742 (p0) cc_final: 0.7215 (p0) REVERT: A 476 PHE cc_start: 0.9213 (OUTLIER) cc_final: 0.8041 (t80) REVERT: C 427 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7552 (mpt-90) REVERT: D 425 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7651 (tp) REVERT: E 117 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8452 (mp0) REVERT: E 158 MET cc_start: 0.7974 (OUTLIER) cc_final: 0.7623 (mpm) REVERT: E 180 GLU cc_start: 0.6784 (OUTLIER) cc_final: 0.6402 (pm20) REVERT: E 192 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.8332 (mmm) REVERT: E 404 PHE cc_start: 0.5582 (OUTLIER) cc_final: 0.5334 (t80) REVERT: F 39 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7600 (mt) REVERT: F 159 MET cc_start: 0.8683 (mmp) cc_final: 0.8130 (mtp) REVERT: F 165 ILE cc_start: 0.8964 (OUTLIER) cc_final: 0.8701 (tp) REVERT: F 249 ILE cc_start: 0.8428 (OUTLIER) cc_final: 0.7989 (pp) REVERT: F 310 ASP cc_start: 0.8544 (OUTLIER) cc_final: 0.7887 (t0) REVERT: F 430 ARG cc_start: 0.8992 (OUTLIER) cc_final: 0.8775 (ttp-110) REVERT: g 8 ARG cc_start: 0.7131 (OUTLIER) cc_final: 0.6621 (mpt-90) REVERT: g 39 MET cc_start: 0.7524 (mmp) cc_final: 0.6731 (tpp) REVERT: g 76 VAL cc_start: 0.9444 (OUTLIER) cc_final: 0.9097 (p) REVERT: g 129 TYR cc_start: 0.7415 (OUTLIER) cc_final: 0.6985 (p90) outliers start: 123 outliers final: 71 residues processed: 302 average time/residue: 0.6305 time to fit residues: 223.4477 Evaluate side-chains 281 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 194 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 476 PHE Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 427 ARG Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain D residue 405 PHE Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 458 ILE Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 173 SER Chi-restraints excluded: chain E residue 180 GLU Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 299 GLN Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 404 PHE Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain E residue 451 VAL Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain F residue 249 ILE Chi-restraints excluded: chain F residue 257 THR Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 310 ASP Chi-restraints excluded: chain F residue 378 ILE Chi-restraints excluded: chain F residue 379 ILE Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain F residue 430 ARG Chi-restraints excluded: chain e residue 9 VAL Chi-restraints excluded: chain e residue 75 VAL Chi-restraints excluded: chain g residue 8 ARG Chi-restraints excluded: chain g residue 32 MET Chi-restraints excluded: chain g residue 76 VAL Chi-restraints excluded: chain g residue 87 LEU Chi-restraints excluded: chain g residue 94 ASN Chi-restraints excluded: chain g residue 129 TYR Chi-restraints excluded: chain g residue 166 ASP Chi-restraints excluded: chain g residue 210 TYR Chi-restraints excluded: chain g residue 219 ASN Chi-restraints excluded: chain g residue 279 ILE Chi-restraints excluded: chain g residue 281 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 285 optimal weight: 20.0000 chunk 182 optimal weight: 5.9990 chunk 164 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 202 optimal weight: 8.9990 chunk 147 optimal weight: 0.0980 chunk 146 optimal weight: 0.7980 chunk 62 optimal weight: 9.9990 chunk 119 optimal weight: 3.9990 chunk 47 optimal weight: 8.9990 chunk 132 optimal weight: 6.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 190 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.112208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.078571 restraints weight = 49271.937| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.59 r_work: 0.2927 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 25436 Z= 0.199 Angle : 0.603 12.320 34474 Z= 0.314 Chirality : 0.046 0.204 3979 Planarity : 0.004 0.048 4494 Dihedral : 5.643 82.165 3621 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 5.18 % Allowed : 25.00 % Favored : 69.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: 0.38 (0.15), residues: 3266 helix: 1.54 (0.15), residues: 1333 sheet: 0.32 (0.23), residues: 510 loop : -1.03 (0.16), residues: 1423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 20 TYR 0.025 0.001 TYR g 231 PHE 0.019 0.001 PHE g 175 TRP 0.023 0.002 TRP g 206 HIS 0.004 0.001 HIS D 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.20 (25436) covalent geometry : angle 0.60283 / 0.31 (34474) hydrogen bonds : bond 0.05632 / 3.71 ( 1221) hydrogen bonds : angle 4.90646 / 3.45 ( 3537) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 199 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.7830 (p0) cc_final: 0.7245 (p0) REVERT: A 476 PHE cc_start: 0.9261 (OUTLIER) cc_final: 0.8078 (t80) REVERT: C 427 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7596 (mpt-90) REVERT: D 425 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7766 (tp) REVERT: E 117 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8489 (mp0) REVERT: E 158 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.7696 (mpm) REVERT: E 180 GLU cc_start: 0.6847 (OUTLIER) cc_final: 0.6486 (pm20) REVERT: E 404 PHE cc_start: 0.5651 (OUTLIER) cc_final: 0.5392 (t80) REVERT: F 39 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7595 (mt) REVERT: F 159 MET cc_start: 0.8691 (mmp) cc_final: 0.7998 (mtp) REVERT: F 165 ILE cc_start: 0.9032 (OUTLIER) cc_final: 0.8773 (tp) REVERT: F 249 ILE cc_start: 0.8470 (OUTLIER) cc_final: 0.8004 (pp) REVERT: F 310 ASP cc_start: 0.8663 (OUTLIER) cc_final: 0.8003 (t0) REVERT: e 31 GLU cc_start: 0.8100 (tm-30) cc_final: 0.7834 (tm-30) REVERT: g 8 ARG cc_start: 0.7098 (OUTLIER) cc_final: 0.6562 (mpt-90) REVERT: g 39 MET cc_start: 0.7461 (mmp) cc_final: 0.6613 (tpp) REVERT: g 63 TYR cc_start: 0.8328 (t80) cc_final: 0.8123 (t80) REVERT: g 76 VAL cc_start: 0.9433 (OUTLIER) cc_final: 0.9086 (p) REVERT: g 267 TYR cc_start: 0.8235 (t80) cc_final: 0.7993 (t80) outliers start: 136 outliers final: 82 residues processed: 312 average time/residue: 0.5510 time to fit residues: 202.1300 Evaluate side-chains 291 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 196 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 476 PHE Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 473 ILE Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 427 ARG Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 249 ILE Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 458 ILE Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 180 GLU Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 299 GLN Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 404 PHE Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain E residue 451 VAL Chi-restraints excluded: chain E residue 464 LEU Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 249 ILE Chi-restraints excluded: chain F residue 257 THR Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 310 ASP Chi-restraints excluded: chain F residue 353 VAL Chi-restraints excluded: chain F residue 378 ILE Chi-restraints excluded: chain F residue 379 ILE Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain F residue 450 MET Chi-restraints excluded: chain e residue 9 VAL Chi-restraints excluded: chain e residue 75 VAL Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain g residue 8 ARG Chi-restraints excluded: chain g residue 32 MET Chi-restraints excluded: chain g residue 76 VAL Chi-restraints excluded: chain g residue 94 ASN Chi-restraints excluded: chain g residue 129 TYR Chi-restraints excluded: chain g residue 133 VAL Chi-restraints excluded: chain g residue 210 TYR Chi-restraints excluded: chain g residue 219 ASN Chi-restraints excluded: chain g residue 279 ILE Chi-restraints excluded: chain g residue 281 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 152 optimal weight: 5.9990 chunk 150 optimal weight: 1.9990 chunk 210 optimal weight: 7.9990 chunk 89 optimal weight: 6.9990 chunk 105 optimal weight: 8.9990 chunk 114 optimal weight: 1.9990 chunk 201 optimal weight: 5.9990 chunk 286 optimal weight: 3.9990 chunk 250 optimal weight: 8.9990 chunk 104 optimal weight: 0.0970 chunk 8 optimal weight: 1.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 190 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.113190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.079586 restraints weight = 49165.010| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.60 r_work: 0.2938 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 25436 Z= 0.158 Angle : 0.580 11.712 34474 Z= 0.301 Chirality : 0.045 0.200 3979 Planarity : 0.004 0.047 4494 Dihedral : 5.507 79.139 3621 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 4.23 % Allowed : 26.14 % Favored : 69.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: 0.47 (0.15), residues: 3266 helix: 1.64 (0.15), residues: 1325 sheet: 0.39 (0.23), residues: 508 loop : -0.99 (0.16), residues: 1433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 20 TYR 0.041 0.001 TYR E 396 PHE 0.018 0.001 PHE g 175 TRP 0.022 0.002 TRP g 206 HIS 0.003 0.001 HIS D 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 (25436) covalent geometry : angle 0.58014 / 0.30 (34474) hydrogen bonds : bond 0.05065 / 3.34 ( 1221) hydrogen bonds : angle 4.81061 / 3.38 ( 3537) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 204 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.7865 (p0) cc_final: 0.7267 (p0) REVERT: A 476 PHE cc_start: 0.9237 (OUTLIER) cc_final: 0.8059 (t80) REVERT: B 157 MET cc_start: 0.8328 (mtm) cc_final: 0.8117 (mtp) REVERT: C 427 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7563 (mpt-90) REVERT: D 326 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9083 (mt) REVERT: D 425 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7723 (tp) REVERT: E 117 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.8503 (mp0) REVERT: E 158 MET cc_start: 0.8026 (OUTLIER) cc_final: 0.7677 (mpm) REVERT: E 180 GLU cc_start: 0.6841 (OUTLIER) cc_final: 0.6465 (pm20) REVERT: E 404 PHE cc_start: 0.5596 (OUTLIER) cc_final: 0.5282 (t80) REVERT: F 39 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7617 (mt) REVERT: F 159 MET cc_start: 0.8680 (mmp) cc_final: 0.8116 (mtp) REVERT: F 165 ILE cc_start: 0.8993 (OUTLIER) cc_final: 0.8724 (tp) REVERT: F 249 ILE cc_start: 0.8432 (OUTLIER) cc_final: 0.7989 (pp) REVERT: F 310 ASP cc_start: 0.8584 (OUTLIER) cc_final: 0.7941 (t0) REVERT: e 3 THR cc_start: 0.8992 (t) cc_final: 0.8780 (m) REVERT: e 31 GLU cc_start: 0.8228 (tm-30) cc_final: 0.7745 (tm-30) REVERT: g 39 MET cc_start: 0.7472 (mmp) cc_final: 0.6626 (tpp) REVERT: g 76 VAL cc_start: 0.9436 (OUTLIER) cc_final: 0.9091 (p) REVERT: g 229 MET cc_start: 0.8230 (mmm) cc_final: 0.8016 (mmm) outliers start: 111 outliers final: 78 residues processed: 294 average time/residue: 0.5242 time to fit residues: 180.6618 Evaluate side-chains 283 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 192 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 476 PHE Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 427 ARG Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 458 ILE Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 180 GLU Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 299 GLN Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 404 PHE Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain E residue 451 VAL Chi-restraints excluded: chain E residue 464 LEU Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 249 ILE Chi-restraints excluded: chain F residue 257 THR Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 310 ASP Chi-restraints excluded: chain F residue 353 VAL Chi-restraints excluded: chain F residue 378 ILE Chi-restraints excluded: chain F residue 379 ILE Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain e residue 9 VAL Chi-restraints excluded: chain e residue 10 SER Chi-restraints excluded: chain e residue 75 VAL Chi-restraints excluded: chain e residue 114 SER Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain g residue 32 MET Chi-restraints excluded: chain g residue 76 VAL Chi-restraints excluded: chain g residue 94 ASN Chi-restraints excluded: chain g residue 129 TYR Chi-restraints excluded: chain g residue 133 VAL Chi-restraints excluded: chain g residue 142 ASP Chi-restraints excluded: chain g residue 206 TRP Chi-restraints excluded: chain g residue 210 TYR Chi-restraints excluded: chain g residue 219 ASN Chi-restraints excluded: chain g residue 279 ILE Chi-restraints excluded: chain g residue 281 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 206 optimal weight: 0.6980 chunk 50 optimal weight: 5.9990 chunk 21 optimal weight: 0.5980 chunk 177 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 chunk 116 optimal weight: 2.9990 chunk 123 optimal weight: 8.9990 chunk 309 optimal weight: 9.9990 chunk 29 optimal weight: 8.9990 chunk 224 optimal weight: 10.0000 chunk 147 optimal weight: 0.0670 overall best weight: 1.0722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 190 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.114832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.081268 restraints weight = 49213.519| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.59 r_work: 0.2984 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 25436 Z= 0.116 Angle : 0.560 12.520 34474 Z= 0.287 Chirality : 0.044 0.187 3979 Planarity : 0.004 0.045 4494 Dihedral : 5.207 78.712 3618 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.28 % Allowed : 27.21 % Favored : 69.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: 0.64 (0.15), residues: 3266 helix: 1.77 (0.15), residues: 1326 sheet: 0.50 (0.23), residues: 512 loop : -0.90 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 20 TYR 0.015 0.001 TYR g 231 PHE 0.017 0.001 PHE g 175 TRP 0.025 0.002 TRP g 206 HIS 0.002 0.000 HIS F 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (25436) covalent geometry : angle 0.55979 / 0.29 (34474) hydrogen bonds : bond 0.04219 / 2.79 ( 1221) hydrogen bonds : angle 4.63254 / 3.25 ( 3537) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 205 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.7871 (p0) cc_final: 0.7241 (p0) REVERT: A 476 PHE cc_start: 0.9204 (OUTLIER) cc_final: 0.7987 (t80) REVERT: C 427 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.7582 (mpt-90) REVERT: D 104 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7441 (pm20) REVERT: D 425 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7654 (tp) REVERT: E 117 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8493 (mp0) REVERT: E 158 MET cc_start: 0.7920 (OUTLIER) cc_final: 0.7547 (mpm) REVERT: E 180 GLU cc_start: 0.6743 (OUTLIER) cc_final: 0.6408 (pm20) REVERT: F 159 MET cc_start: 0.8724 (mmp) cc_final: 0.8230 (mtp) REVERT: F 165 ILE cc_start: 0.8901 (OUTLIER) cc_final: 0.8637 (tp) REVERT: F 249 ILE cc_start: 0.8339 (OUTLIER) cc_final: 0.7931 (pp) REVERT: F 310 ASP cc_start: 0.8500 (OUTLIER) cc_final: 0.7906 (t0) REVERT: F 430 ARG cc_start: 0.8967 (OUTLIER) cc_final: 0.8722 (ttp-110) REVERT: e 26 LYS cc_start: 0.7956 (mppt) cc_final: 0.6594 (tptt) REVERT: e 31 GLU cc_start: 0.7963 (tm-30) cc_final: 0.7492 (tm-30) REVERT: e 70 GLU cc_start: 0.8877 (tp30) cc_final: 0.8610 (tp30) REVERT: g 39 MET cc_start: 0.7436 (mmp) cc_final: 0.6655 (tpp) REVERT: g 63 TYR cc_start: 0.8298 (t80) cc_final: 0.8057 (t80) REVERT: g 76 VAL cc_start: 0.9397 (OUTLIER) cc_final: 0.9159 (p) REVERT: g 115 PHE cc_start: 0.8599 (p90) cc_final: 0.8151 (p90) REVERT: g 129 TYR cc_start: 0.7403 (OUTLIER) cc_final: 0.6983 (p90) outliers start: 86 outliers final: 50 residues processed: 278 average time/residue: 0.6307 time to fit residues: 202.8086 Evaluate side-chains 256 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 193 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 476 PHE Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 427 ARG Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 123 ASP Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 180 GLU Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 249 ILE Chi-restraints excluded: chain F residue 310 ASP Chi-restraints excluded: chain F residue 353 VAL Chi-restraints excluded: chain F residue 378 ILE Chi-restraints excluded: chain F residue 379 ILE Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain F residue 430 ARG Chi-restraints excluded: chain F residue 450 MET Chi-restraints excluded: chain e residue 10 SER Chi-restraints excluded: chain e residue 75 VAL Chi-restraints excluded: chain e residue 114 SER Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain g residue 76 VAL Chi-restraints excluded: chain g residue 129 TYR Chi-restraints excluded: chain g residue 206 TRP Chi-restraints excluded: chain g residue 210 TYR Chi-restraints excluded: chain g residue 219 ASN Chi-restraints excluded: chain g residue 281 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 294 optimal weight: 1.9990 chunk 257 optimal weight: 0.9990 chunk 62 optimal weight: 9.9990 chunk 125 optimal weight: 9.9990 chunk 285 optimal weight: 10.0000 chunk 261 optimal weight: 0.9990 chunk 272 optimal weight: 2.9990 chunk 279 optimal weight: 4.9990 chunk 222 optimal weight: 9.9990 chunk 68 optimal weight: 8.9990 chunk 127 optimal weight: 0.6980 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 190 HIS g 36 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.114084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.080815 restraints weight = 48478.054| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.46 r_work: 0.2973 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 25436 Z= 0.136 Angle : 0.575 13.141 34474 Z= 0.295 Chirality : 0.044 0.184 3979 Planarity : 0.004 0.047 4494 Dihedral : 5.072 78.364 3610 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.78 % Allowed : 27.82 % Favored : 69.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: 3266 helix: 1.77 (0.15), residues: 1327 sheet: 0.55 (0.23), residues: 508 loop : -0.88 (0.16), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 20 TYR 0.040 0.001 TYR E 396 PHE 0.018 0.001 PHE g 175 TRP 0.022 0.002 TRP g 206 HIS 0.003 0.001 HIS D 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (25436) covalent geometry : angle 0.57542 / 0.29 (34474) hydrogen bonds : bond 0.04529 / 2.99 ( 1221) hydrogen bonds : angle 4.63704 / 3.26 ( 3537) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 193 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.7851 (p0) cc_final: 0.7225 (p0) REVERT: A 476 PHE cc_start: 0.9219 (OUTLIER) cc_final: 0.8022 (t80) REVERT: C 427 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.7603 (mpt-90) REVERT: D 104 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7443 (pm20) REVERT: D 425 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7742 (tp) REVERT: E 117 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8480 (mp0) REVERT: E 158 MET cc_start: 0.7917 (OUTLIER) cc_final: 0.7531 (mpm) REVERT: E 180 GLU cc_start: 0.6798 (OUTLIER) cc_final: 0.6448 (pm20) REVERT: E 266 MET cc_start: 0.7398 (mpp) cc_final: 0.7146 (mmt) REVERT: E 404 PHE cc_start: 0.5665 (OUTLIER) cc_final: 0.5321 (t80) REVERT: F 159 MET cc_start: 0.8709 (mmp) cc_final: 0.8122 (mtp) REVERT: F 165 ILE cc_start: 0.8954 (OUTLIER) cc_final: 0.8697 (tp) REVERT: F 249 ILE cc_start: 0.8381 (OUTLIER) cc_final: 0.7954 (pp) REVERT: F 310 ASP cc_start: 0.8511 (OUTLIER) cc_final: 0.7906 (t0) REVERT: F 430 ARG cc_start: 0.8957 (OUTLIER) cc_final: 0.8693 (ttp-110) REVERT: e 4 MET cc_start: 0.8323 (tpt) cc_final: 0.7866 (tpt) REVERT: e 26 LYS cc_start: 0.7977 (mppt) cc_final: 0.7727 (mmtm) REVERT: e 70 GLU cc_start: 0.8869 (tp30) cc_final: 0.8606 (tp30) REVERT: g 8 ARG cc_start: 0.7111 (OUTLIER) cc_final: 0.6803 (mpt-90) REVERT: g 36 GLN cc_start: 0.8157 (OUTLIER) cc_final: 0.7732 (mm-40) REVERT: g 39 MET cc_start: 0.7395 (mmp) cc_final: 0.6646 (tpt) REVERT: g 63 TYR cc_start: 0.8230 (t80) cc_final: 0.8023 (t80) REVERT: g 76 VAL cc_start: 0.9480 (OUTLIER) cc_final: 0.8985 (p) REVERT: g 115 PHE cc_start: 0.8614 (p90) cc_final: 0.8148 (p90) REVERT: g 129 TYR cc_start: 0.7407 (OUTLIER) cc_final: 0.6982 (p90) REVERT: g 229 MET cc_start: 0.8135 (mmm) cc_final: 0.7920 (mmm) REVERT: g 267 TYR cc_start: 0.8268 (t80) cc_final: 0.8058 (t80) outliers start: 73 outliers final: 52 residues processed: 254 average time/residue: 0.6503 time to fit residues: 190.6190 Evaluate side-chains 257 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 189 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 476 PHE Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 427 ARG Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 180 GLU Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 404 PHE Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 249 ILE Chi-restraints excluded: chain F residue 310 ASP Chi-restraints excluded: chain F residue 353 VAL Chi-restraints excluded: chain F residue 378 ILE Chi-restraints excluded: chain F residue 379 ILE Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain F residue 426 LYS Chi-restraints excluded: chain F residue 430 ARG Chi-restraints excluded: chain F residue 450 MET Chi-restraints excluded: chain e residue 10 SER Chi-restraints excluded: chain e residue 114 SER Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain g residue 8 ARG Chi-restraints excluded: chain g residue 36 GLN Chi-restraints excluded: chain g residue 76 VAL Chi-restraints excluded: chain g residue 94 ASN Chi-restraints excluded: chain g residue 129 TYR Chi-restraints excluded: chain g residue 206 TRP Chi-restraints excluded: chain g residue 210 TYR Chi-restraints excluded: chain g residue 219 ASN Chi-restraints excluded: chain g residue 281 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 82 optimal weight: 6.9990 chunk 169 optimal weight: 5.9990 chunk 277 optimal weight: 8.9990 chunk 275 optimal weight: 1.9990 chunk 320 optimal weight: 10.0000 chunk 189 optimal weight: 4.9990 chunk 207 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 270 optimal weight: 4.9990 chunk 177 optimal weight: 0.8980 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 190 HIS ** g 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.114163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.080113 restraints weight = 48219.684| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.34 r_work: 0.2969 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.118 25436 Z= 0.186 Angle : 0.710 59.143 34474 Z= 0.391 Chirality : 0.049 1.231 3979 Planarity : 0.004 0.046 4494 Dihedral : 5.088 78.341 3610 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.37 % Favored : 96.60 % Rotamer: Outliers : 3.01 % Allowed : 27.74 % Favored : 69.25 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.15), residues: 3266 helix: 1.76 (0.15), residues: 1327 sheet: 0.56 (0.23), residues: 508 loop : -0.89 (0.16), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG g 75 TYR 0.022 0.001 TYR E 396 PHE 0.017 0.001 PHE g 175 TRP 0.015 0.002 TRP g 206 HIS 0.003 0.001 HIS D 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.19 (25436) covalent geometry : angle 0.71037 / 0.39 (34474) hydrogen bonds : bond 0.04646 / 3.06 ( 1221) hydrogen bonds : angle 4.64468 / 3.26 ( 3537) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8685.91 seconds wall clock time: 148 minutes 45.74 seconds (8925.74 seconds total)