Starting phenix.real_space_refine on Sat Jun 21 20:08:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yry_34066/06_2025/7yry_34066.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yry_34066/06_2025/7yry_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7yry_34066/06_2025/7yry_34066.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yry_34066/06_2025/7yry_34066.map" model { file = "/net/cci-nas-00/data/ceres_data/7yry_34066/06_2025/7yry_34066.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yry_34066/06_2025/7yry_34066.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 15.80, per 1000 atoms: 0.63 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: 6.39 Conformation dependent library (CDL) restraints added in 3.1 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: 3.09 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: 9.07 Time building geometry restraints manager: 7.44 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: 14879 35.87 - 71.74: 582 71.74 - 107.61: 51 107.61 - 143.49: 1 143.49 - 179.36: 1 Dihedral angle restraints: 15514 sinusoidal: 6145 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 15511 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: 2.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.900 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 56.440 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.100 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:12.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 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 : 17.926 179.358 9544 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (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 TRP 0.027 0.002 TRP g 206 HIS 0.002 0.000 HIS D 190 PHE 0.011 0.001 PHE F 415 TYR 0.023 0.001 TYR g 63 ARG 0.007 0.000 ARG F 20 Details of bonding type rmsd hydrogen bonds : bond 0.18291 ( 1221) hydrogen bonds : angle 6.90789 ( 3537) covalent geometry : bond 0.00248 (25436) covalent geometry : angle 0.54361 (34474) *********************** 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 : 2.574 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: 1.1724 time to fit residues: 408.4422 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 : 3.001 ------------------------------------------------------------------------------- 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 272 optimal weight: 8.9990 chunk 244 optimal weight: 8.9990 chunk 135 optimal weight: 7.9990 chunk 83 optimal weight: 9.9990 chunk 165 optimal weight: 3.9990 chunk 130 optimal weight: 7.9990 chunk 253 optimal weight: 6.9990 chunk 97 optimal weight: 0.4980 chunk 153 optimal weight: 0.9990 chunk 188 optimal weight: 3.9990 chunk 293 optimal weight: 20.0000 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3652 r_free = 0.3652 target = 0.111924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.078006 restraints weight = 49410.629| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.53 r_work: 0.2920 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.0870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 25436 Z= 0.231 Angle : 0.616 9.588 34474 Z= 0.328 Chirality : 0.047 0.197 3979 Planarity : 0.004 0.047 4494 Dihedral : 8.817 151.374 3796 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 5.41 % Allowed : 24.12 % Favored : 70.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.15), residues: 3266 helix: 1.44 (0.15), residues: 1339 sheet: 0.16 (0.23), residues: 525 loop : -1.05 (0.16), residues: 1402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 139 HIS 0.004 0.001 HIS D 190 PHE 0.016 0.001 PHE g 175 TYR 0.030 0.002 TYR E 396 ARG 0.004 0.000 ARG F 20 Details of bonding type rmsd hydrogen bonds : bond 0.06401 ( 1221) hydrogen bonds : angle 5.39964 ( 3537) covalent geometry : bond 0.00565 (25436) covalent geometry : angle 0.61604 (34474) *********************** 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 339 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 197 time to evaluate : 2.955 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 476 PHE cc_start: 0.9277 (OUTLIER) cc_final: 0.8024 (t80) REVERT: C 419 ARG cc_start: -0.0471 (OUTLIER) cc_final: -0.0917 (mtt180) REVERT: C 427 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7620 (mpt-90) REVERT: D 326 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.9098 (mt) REVERT: E 158 MET cc_start: 0.8075 (OUTLIER) cc_final: 0.7712 (mpm) REVERT: E 404 PHE cc_start: 0.5694 (OUTLIER) cc_final: 0.5445 (t80) REVERT: F 36 GLU cc_start: 0.7960 (pm20) cc_final: 0.7670 (pp20) REVERT: F 203 MET cc_start: 0.8638 (OUTLIER) cc_final: 0.8171 (mpp) REVERT: F 249 ILE cc_start: 0.8517 (OUTLIER) cc_final: 0.8078 (pp) REVERT: F 310 ASP cc_start: 0.8646 (OUTLIER) cc_final: 0.8032 (t0) REVERT: g 8 ARG cc_start: 0.6937 (OUTLIER) cc_final: 0.6293 (mpt-90) REVERT: g 267 TYR cc_start: 0.8295 (t80) cc_final: 0.8085 (t80) outliers start: 142 outliers final: 65 residues processed: 314 average time/residue: 1.3324 time to fit residues: 487.0080 Evaluate side-chains 261 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 186 time to evaluate : 2.638 ------------------------------------------------------------------------------- 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 126 LEU 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 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 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 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 219 optimal weight: 4.9990 chunk 290 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 241 optimal weight: 8.9990 chunk 216 optimal weight: 3.9990 chunk 178 optimal weight: 0.1980 chunk 279 optimal weight: 3.9990 chunk 321 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 172 optimal weight: 0.7980 chunk 175 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 190 HIS F 248 ASN ** e 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 127 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.115210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.081730 restraints weight = 48696.533| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.60 r_work: 0.2993 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.0910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 25436 Z= 0.104 Angle : 0.518 9.766 34474 Z= 0.269 Chirality : 0.043 0.203 3979 Planarity : 0.003 0.042 4494 Dihedral : 7.416 140.077 3733 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.70 % Allowed : 25.04 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.15), residues: 3266 helix: 1.71 (0.15), residues: 1334 sheet: 0.35 (0.23), residues: 520 loop : -0.91 (0.16), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP g 206 HIS 0.003 0.000 HIS g 55 PHE 0.014 0.001 PHE g 175 TYR 0.011 0.001 TYR E 396 ARG 0.005 0.000 ARG F 20 Details of bonding type rmsd hydrogen bonds : bond 0.04239 ( 1221) hydrogen bonds : angle 4.87813 ( 3537) covalent geometry : bond 0.00219 (25436) covalent geometry : angle 0.51786 (34474) *********************** 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 307 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 210 time to evaluate : 2.644 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 476 PHE cc_start: 0.9218 (OUTLIER) cc_final: 0.7929 (t80) REVERT: C 427 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7581 (mpt-90) REVERT: E 117 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.8472 (mp0) REVERT: E 158 MET cc_start: 0.7947 (OUTLIER) cc_final: 0.7576 (mpm) REVERT: E 180 GLU cc_start: 0.6714 (OUTLIER) cc_final: 0.6345 (pm20) REVERT: E 404 PHE cc_start: 0.5591 (OUTLIER) cc_final: 0.5311 (t80) REVERT: F 159 MET cc_start: 0.8728 (mmp) cc_final: 0.8041 (mtp) REVERT: F 249 ILE cc_start: 0.8352 (OUTLIER) cc_final: 0.7951 (pp) REVERT: F 310 ASP cc_start: 0.8499 (OUTLIER) cc_final: 0.7931 (t0) REVERT: e 4 MET cc_start: 0.8047 (tpt) cc_final: 0.7826 (tpt) REVERT: e 127 GLN cc_start: 0.5189 (OUTLIER) cc_final: 0.4840 (pp30) REVERT: g 8 ARG cc_start: 0.7158 (OUTLIER) cc_final: 0.6701 (mpt-90) REVERT: g 63 TYR cc_start: 0.8230 (t80) cc_final: 0.7966 (t80) REVERT: g 67 TYR cc_start: 0.8785 (m-80) cc_final: 0.8238 (m-80) REVERT: g 76 VAL cc_start: 0.9419 (OUTLIER) cc_final: 0.9064 (p) REVERT: g 115 PHE cc_start: 0.8621 (p90) cc_final: 0.8256 (p90) REVERT: g 129 TYR cc_start: 0.7222 (p90) cc_final: 0.6933 (p90) outliers start: 97 outliers final: 28 residues processed: 290 average time/residue: 1.3977 time to fit residues: 467.1724 Evaluate side-chains 231 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 192 time to evaluate : 2.959 ------------------------------------------------------------------------------- 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 331 ILE Chi-restraints excluded: chain A residue 476 PHE Chi-restraints excluded: chain B residue 291 VAL 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 270 VAL Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 405 PHE Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain E residue 37 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 216 LEU Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 404 PHE Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 249 ILE 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 127 GLN Chi-restraints excluded: chain g residue 8 ARG Chi-restraints excluded: chain g residue 76 VAL Chi-restraints excluded: chain g residue 210 TYR 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 218 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 88 optimal weight: 9.9990 chunk 279 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 chunk 196 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 73 optimal weight: 10.0000 chunk 262 optimal weight: 0.0010 overall best weight: 2.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 190 HIS ** e 72 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 = 0.3672 r_free = 0.3672 target = 0.113208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.079242 restraints weight = 49403.885| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.54 r_work: 0.2947 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.0997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 25436 Z= 0.168 Angle : 0.558 9.802 34474 Z= 0.293 Chirality : 0.044 0.211 3979 Planarity : 0.004 0.045 4494 Dihedral : 7.016 113.176 3711 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.81 % Allowed : 25.38 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.15), residues: 3266 helix: 1.69 (0.15), residues: 1335 sheet: 0.41 (0.23), residues: 511 loop : -0.95 (0.16), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP g 206 HIS 0.003 0.001 HIS D 190 PHE 0.017 0.001 PHE g 175 TYR 0.034 0.001 TYR E 396 ARG 0.006 0.000 ARG F 20 Details of bonding type rmsd hydrogen bonds : bond 0.05161 ( 1221) hydrogen bonds : angle 4.88398 ( 3537) covalent geometry : bond 0.00405 (25436) covalent geometry : angle 0.55821 (34474) *********************** 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 303 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 203 time to evaluate : 2.668 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.7654 (p0) cc_final: 0.7082 (p0) REVERT: A 476 PHE cc_start: 0.9241 (OUTLIER) cc_final: 0.8066 (t80) REVERT: C 427 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7556 (mpt-90) REVERT: D 425 LEU cc_start: 0.8054 (pt) cc_final: 0.7683 (tp) REVERT: E 117 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8483 (mp0) REVERT: E 158 MET cc_start: 0.7973 (OUTLIER) cc_final: 0.7620 (mpm) REVERT: E 180 GLU cc_start: 0.6722 (OUTLIER) cc_final: 0.6413 (pm20) REVERT: E 404 PHE cc_start: 0.5705 (OUTLIER) cc_final: 0.5463 (t80) REVERT: F 159 MET cc_start: 0.8700 (mmp) cc_final: 0.7913 (mtp) REVERT: F 249 ILE cc_start: 0.8450 (OUTLIER) cc_final: 0.8015 (pp) REVERT: F 310 ASP cc_start: 0.8583 (OUTLIER) cc_final: 0.7942 (t0) REVERT: e 4 MET cc_start: 0.8136 (tpt) cc_final: 0.7888 (tpt) REVERT: g 63 TYR cc_start: 0.8236 (t80) cc_final: 0.7955 (t80) REVERT: g 67 TYR cc_start: 0.8808 (m-80) cc_final: 0.8224 (m-80) outliers start: 100 outliers final: 51 residues processed: 286 average time/residue: 1.5455 time to fit residues: 514.9204 Evaluate side-chains 252 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 193 time to evaluate : 2.851 ------------------------------------------------------------------------------- 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 476 PHE 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 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 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 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 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 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 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 53 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 423 VAL Chi-restraints excluded: chain F residue 450 MET Chi-restraints excluded: chain e residue 9 VAL Chi-restraints excluded: chain g residue 76 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 11 optimal weight: 4.9990 chunk 133 optimal weight: 8.9990 chunk 269 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 chunk 310 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 chunk 154 optimal weight: 4.9990 chunk 286 optimal weight: 2.9990 chunk 260 optimal weight: 3.9990 chunk 230 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 190 HIS g 60 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.111367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.077086 restraints weight = 49550.552| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.35 r_work: 0.2915 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 25436 Z= 0.256 Angle : 0.635 10.381 34474 Z= 0.335 Chirality : 0.047 0.209 3979 Planarity : 0.004 0.050 4494 Dihedral : 7.286 98.242 3710 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 4.92 % Allowed : 24.89 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.15), residues: 3266 helix: 1.42 (0.15), residues: 1340 sheet: 0.25 (0.23), residues: 514 loop : -1.08 (0.15), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP g 206 HIS 0.005 0.001 HIS g 65 PHE 0.019 0.002 PHE g 175 TYR 0.016 0.002 TYR g 267 ARG 0.006 0.000 ARG F 20 Details of bonding type rmsd hydrogen bonds : bond 0.06328 ( 1221) hydrogen bonds : angle 5.07476 ( 3537) covalent geometry : bond 0.00632 (25436) covalent geometry : angle 0.63540 (34474) *********************** 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 328 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 199 time to evaluate : 2.670 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.7713 (p0) cc_final: 0.7236 (p0) REVERT: A 476 PHE cc_start: 0.9275 (OUTLIER) cc_final: 0.8121 (t80) REVERT: C 427 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7629 (mpt-90) REVERT: D 425 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7829 (tp) REVERT: E 117 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8495 (mp0) REVERT: E 158 MET cc_start: 0.8099 (OUTLIER) cc_final: 0.7730 (mpm) REVERT: E 404 PHE cc_start: 0.5695 (OUTLIER) cc_final: 0.5461 (t80) REVERT: F 39 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.7701 (mt) REVERT: F 159 MET cc_start: 0.8758 (mmp) cc_final: 0.7990 (mtp) REVERT: F 249 ILE cc_start: 0.8514 (OUTLIER) cc_final: 0.8072 (pp) REVERT: F 310 ASP cc_start: 0.8706 (OUTLIER) cc_final: 0.8042 (t0) REVERT: g 8 ARG cc_start: 0.7199 (OUTLIER) cc_final: 0.6647 (mpt-90) REVERT: g 39 MET cc_start: 0.7519 (mmp) cc_final: 0.6731 (tpp) REVERT: g 63 TYR cc_start: 0.8331 (t80) cc_final: 0.8110 (t80) REVERT: g 66 ARG cc_start: 0.8468 (ptm160) cc_final: 0.8247 (ptm160) REVERT: g 267 TYR cc_start: 0.8238 (t80) cc_final: 0.8015 (t80) outliers start: 129 outliers final: 65 residues processed: 308 average time/residue: 1.4438 time to fit residues: 519.1090 Evaluate side-chains 271 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 196 time to evaluate : 3.018 ------------------------------------------------------------------------------- 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 324 SER 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 479 GLU Chi-restraints excluded: chain B residue 76 VAL 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 319 THR Chi-restraints excluded: chain B residue 324 SER 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 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 104 GLU 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 32 VAL 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 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 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 35 THR Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 53 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 423 VAL Chi-restraints excluded: chain e residue 9 VAL Chi-restraints excluded: chain g residue 8 ARG Chi-restraints excluded: chain g residue 20 ILE 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 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 293 optimal weight: 8.9990 chunk 83 optimal weight: 7.9990 chunk 285 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 212 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 314 optimal weight: 30.0000 chunk 11 optimal weight: 3.9990 chunk 254 optimal weight: 7.9990 chunk 114 optimal weight: 0.9990 chunk 95 optimal weight: 9.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3661 r_free = 0.3661 target = 0.112622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.079174 restraints weight = 49232.697| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.59 r_work: 0.2936 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 25436 Z= 0.176 Angle : 0.579 12.956 34474 Z= 0.303 Chirality : 0.045 0.211 3979 Planarity : 0.004 0.049 4494 Dihedral : 7.096 87.420 3710 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 4.19 % Allowed : 25.61 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.15), residues: 3266 helix: 1.54 (0.15), residues: 1332 sheet: 0.31 (0.23), residues: 510 loop : -1.07 (0.15), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP g 206 HIS 0.003 0.001 HIS D 190 PHE 0.018 0.001 PHE g 175 TYR 0.036 0.001 TYR E 396 ARG 0.006 0.000 ARG F 20 Details of bonding type rmsd hydrogen bonds : bond 0.05404 ( 1221) hydrogen bonds : angle 4.90678 ( 3537) covalent geometry : bond 0.00424 (25436) covalent geometry : angle 0.57877 (34474) *********************** 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 316 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 206 time to evaluate : 2.874 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.7747 (p0) cc_final: 0.7197 (p0) REVERT: A 476 PHE cc_start: 0.9249 (OUTLIER) cc_final: 0.8059 (t80) REVERT: C 427 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.7611 (mpt-90) REVERT: D 425 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7697 (tp) REVERT: E 117 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8477 (mp0) REVERT: E 158 MET cc_start: 0.8054 (OUTLIER) cc_final: 0.7695 (mpm) REVERT: E 180 GLU cc_start: 0.6809 (OUTLIER) cc_final: 0.6447 (pm20) REVERT: E 404 PHE cc_start: 0.5661 (OUTLIER) cc_final: 0.5401 (t80) REVERT: F 159 MET cc_start: 0.8687 (mmp) cc_final: 0.8059 (mtp) REVERT: F 165 ILE cc_start: 0.9003 (OUTLIER) cc_final: 0.8735 (tp) REVERT: F 249 ILE cc_start: 0.8459 (OUTLIER) cc_final: 0.7992 (pp) REVERT: F 310 ASP cc_start: 0.8620 (OUTLIER) cc_final: 0.7975 (t0) REVERT: e 4 MET cc_start: 0.8182 (tpt) cc_final: 0.7961 (tpt) REVERT: g 39 MET cc_start: 0.7573 (mmp) cc_final: 0.6756 (tpp) REVERT: g 63 TYR cc_start: 0.8427 (t80) cc_final: 0.8194 (t80) REVERT: g 66 ARG cc_start: 0.8410 (ptm160) cc_final: 0.7960 (ptm160) REVERT: g 76 VAL cc_start: 0.9416 (OUTLIER) cc_final: 0.9058 (p) outliers start: 110 outliers final: 62 residues processed: 293 average time/residue: 1.7070 time to fit residues: 582.2490 Evaluate side-chains 267 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 194 time to evaluate : 2.634 ------------------------------------------------------------------------------- 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 381 SER Chi-restraints excluded: chain A residue 476 PHE 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 394 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 427 ARG Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 484 MET 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 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 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 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 464 LEU Chi-restraints excluded: chain F residue 53 ILE 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 423 VAL Chi-restraints excluded: chain F residue 450 MET Chi-restraints excluded: chain e residue 9 VAL Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain g residue 20 ILE 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 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 211 optimal weight: 0.4980 chunk 277 optimal weight: 10.0000 chunk 218 optimal weight: 7.9990 chunk 245 optimal weight: 6.9990 chunk 87 optimal weight: 10.0000 chunk 145 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 44 optimal weight: 7.9990 chunk 163 optimal weight: 5.9990 chunk 274 optimal weight: 6.9990 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 190 HIS E 284 GLN F 248 ASN ** e 5 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 = 0.3637 r_free = 0.3637 target = 0.110974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.077368 restraints weight = 49757.186| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.62 r_work: 0.2898 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 25436 Z= 0.276 Angle : 0.661 11.581 34474 Z= 0.349 Chirality : 0.048 0.227 3979 Planarity : 0.005 0.061 4494 Dihedral : 7.381 84.729 3710 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 5.03 % Allowed : 25.19 % Favored : 69.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.15), residues: 3266 helix: 1.29 (0.15), residues: 1338 sheet: 0.14 (0.23), residues: 515 loop : -1.19 (0.15), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP g 206 HIS 0.006 0.001 HIS g 65 PHE 0.020 0.002 PHE g 175 TYR 0.016 0.002 TYR A 261 ARG 0.008 0.001 ARG e 51 Details of bonding type rmsd hydrogen bonds : bond 0.06592 ( 1221) hydrogen bonds : angle 5.11150 ( 3537) covalent geometry : bond 0.00682 (25436) covalent geometry : angle 0.66148 (34474) *********************** 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 334 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 202 time to evaluate : 2.995 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.7783 (p0) cc_final: 0.7212 (p0) REVERT: A 476 PHE cc_start: 0.9269 (OUTLIER) cc_final: 0.8205 (t80) REVERT: C 427 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.7569 (mpt-90) REVERT: D 425 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7852 (tp) REVERT: E 117 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.8503 (mp0) REVERT: E 158 MET cc_start: 0.8118 (OUTLIER) cc_final: 0.7785 (mpm) REVERT: E 180 GLU cc_start: 0.6866 (OUTLIER) cc_final: 0.6524 (pm20) REVERT: E 404 PHE cc_start: 0.5725 (OUTLIER) cc_final: 0.5458 (t80) REVERT: F 39 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.7731 (mt) REVERT: F 159 MET cc_start: 0.8768 (mmp) cc_final: 0.7965 (mtp) REVERT: F 249 ILE cc_start: 0.8538 (OUTLIER) cc_final: 0.8059 (pp) REVERT: F 310 ASP cc_start: 0.8722 (OUTLIER) cc_final: 0.8064 (t0) REVERT: e 4 MET cc_start: 0.8250 (tpt) cc_final: 0.7919 (tpt) REVERT: e 5 GLN cc_start: 0.8708 (tp40) cc_final: 0.8449 (tp-100) REVERT: e 51 ARG cc_start: 0.8057 (tpt170) cc_final: 0.7810 (tpt170) REVERT: g 8 ARG cc_start: 0.7118 (OUTLIER) cc_final: 0.6829 (mpt-90) REVERT: g 39 MET cc_start: 0.7504 (mmp) cc_final: 0.6651 (tpp) REVERT: g 63 TYR cc_start: 0.8490 (t80) cc_final: 0.8204 (t80) REVERT: g 66 ARG cc_start: 0.8535 (ptm160) cc_final: 0.8090 (ptm160) outliers start: 132 outliers final: 77 residues processed: 312 average time/residue: 1.2419 time to fit residues: 451.9498 Evaluate side-chains 286 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 198 time to evaluate : 2.599 ------------------------------------------------------------------------------- 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 324 SER Chi-restraints excluded: chain A residue 331 ILE 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 B residue 76 VAL 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 319 THR Chi-restraints excluded: chain B residue 324 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 487 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 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 104 GLU Chi-restraints excluded: chain D residue 123 ASP 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 377 ASP 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 32 VAL Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 78 VAL 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 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 35 THR 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 378 ILE Chi-restraints excluded: chain F residue 379 ILE 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 20 ILE 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 253 THR 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 49 optimal weight: 0.6980 chunk 112 optimal weight: 0.8980 chunk 127 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 190 optimal weight: 1.9990 chunk 274 optimal weight: 5.9990 chunk 321 optimal weight: 1.9990 chunk 158 optimal weight: 0.8980 chunk 213 optimal weight: 8.9990 chunk 208 optimal weight: 0.9990 chunk 257 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 190 HIS E 284 GLN F 248 ASN ** e 5 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 = 0.3679 r_free = 0.3679 target = 0.113845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.079564 restraints weight = 49103.127| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.37 r_work: 0.2965 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 25436 Z= 0.123 Angle : 0.564 11.913 34474 Z= 0.293 Chirality : 0.044 0.242 3979 Planarity : 0.004 0.047 4494 Dihedral : 6.973 83.207 3710 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.58 % Allowed : 26.49 % Favored : 69.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.15), residues: 3266 helix: 1.65 (0.15), residues: 1330 sheet: 0.32 (0.23), residues: 527 loop : -1.03 (0.16), residues: 1409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP g 206 HIS 0.002 0.001 HIS D 190 PHE 0.018 0.001 PHE g 175 TYR 0.041 0.001 TYR E 396 ARG 0.006 0.000 ARG F 20 Details of bonding type rmsd hydrogen bonds : bond 0.04822 ( 1221) hydrogen bonds : angle 4.82008 ( 3537) covalent geometry : bond 0.00274 (25436) covalent geometry : angle 0.56413 (34474) *********************** 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 309 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 215 time to evaluate : 2.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.7844 (p0) cc_final: 0.7255 (p0) REVERT: A 435 LYS cc_start: 0.7925 (mppt) cc_final: 0.7694 (mtpt) REVERT: A 476 PHE cc_start: 0.9229 (OUTLIER) cc_final: 0.8014 (t80) REVERT: C 427 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7563 (mpt-90) REVERT: D 425 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7635 (tp) REVERT: E 117 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8454 (mp0) REVERT: E 158 MET cc_start: 0.7997 (OUTLIER) cc_final: 0.7641 (mpm) REVERT: E 180 GLU cc_start: 0.6790 (OUTLIER) cc_final: 0.6442 (pm20) REVERT: E 404 PHE cc_start: 0.5635 (OUTLIER) cc_final: 0.5378 (t80) REVERT: F 159 MET cc_start: 0.8672 (mmp) cc_final: 0.8099 (mtp) REVERT: F 165 ILE cc_start: 0.8953 (OUTLIER) cc_final: 0.8675 (tp) REVERT: F 249 ILE cc_start: 0.8395 (OUTLIER) cc_final: 0.7944 (pp) REVERT: F 310 ASP cc_start: 0.8551 (OUTLIER) cc_final: 0.7928 (t0) REVERT: F 430 ARG cc_start: 0.8960 (OUTLIER) cc_final: 0.8732 (ttp-110) REVERT: e 3 THR cc_start: 0.8878 (t) cc_final: 0.8654 (m) REVERT: e 4 MET cc_start: 0.8228 (tpt) cc_final: 0.7794 (tpt) REVERT: e 5 GLN cc_start: 0.8701 (tp40) cc_final: 0.8484 (tp-100) REVERT: e 26 LYS cc_start: 0.7575 (mppt) cc_final: 0.7029 (mmmm) REVERT: e 70 GLU cc_start: 0.8917 (tp30) cc_final: 0.8658 (tp30) REVERT: g 6 GLU cc_start: 0.6690 (tm-30) cc_final: 0.6221 (tp30) REVERT: g 8 ARG cc_start: 0.7106 (OUTLIER) cc_final: 0.6759 (mpt-90) REVERT: g 39 MET cc_start: 0.7454 (mmp) cc_final: 0.6666 (tpp) REVERT: g 63 TYR cc_start: 0.8436 (t80) cc_final: 0.8200 (t80) REVERT: g 76 VAL cc_start: 0.9390 (OUTLIER) cc_final: 0.9032 (p) outliers start: 94 outliers final: 57 residues processed: 289 average time/residue: 1.2923 time to fit residues: 434.3461 Evaluate side-chains 268 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 198 time to evaluate : 2.666 ------------------------------------------------------------------------------- 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 324 SER Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 476 PHE 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 394 ILE Chi-restraints excluded: chain B residue 507 SER 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 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 416 THR Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 458 ILE 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 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 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 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 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 F residue 430 ARG Chi-restraints excluded: chain e residue 9 VAL Chi-restraints excluded: chain e residue 68 VAL Chi-restraints excluded: chain g residue 8 ARG 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 92 optimal weight: 6.9990 chunk 163 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 132 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 269 optimal weight: 2.9990 chunk 77 optimal weight: 0.0070 chunk 26 optimal weight: 0.9980 chunk 154 optimal weight: 0.0980 chunk 22 optimal weight: 0.9980 chunk 2 optimal weight: 7.9990 overall best weight: 0.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3705 r_free = 0.3705 target = 0.115553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.082732 restraints weight = 48811.000| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.49 r_work: 0.3007 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 25436 Z= 0.108 Angle : 0.554 12.500 34474 Z= 0.284 Chirality : 0.043 0.246 3979 Planarity : 0.004 0.045 4494 Dihedral : 6.531 83.578 3708 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.67 % Allowed : 27.63 % Favored : 69.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.15), residues: 3266 helix: 1.81 (0.15), residues: 1333 sheet: 0.48 (0.23), residues: 529 loop : -0.89 (0.16), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP g 206 HIS 0.002 0.000 HIS F 190 PHE 0.017 0.001 PHE g 175 TYR 0.025 0.001 TYR g 231 ARG 0.008 0.000 ARG F 328 Details of bonding type rmsd hydrogen bonds : bond 0.03876 ( 1221) hydrogen bonds : angle 4.58167 ( 3537) covalent geometry : bond 0.00240 (25436) covalent geometry : angle 0.55445 (34474) *********************** 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 280 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 210 time to evaluate : 2.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.7827 (p0) cc_final: 0.7217 (p0) REVERT: A 476 PHE cc_start: 0.9202 (OUTLIER) cc_final: 0.7885 (t80) REVERT: C 427 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7635 (mpt-90) REVERT: D 104 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7524 (pm20) REVERT: D 425 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7562 (tp) REVERT: E 117 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8467 (mp0) REVERT: E 158 MET cc_start: 0.7888 (OUTLIER) cc_final: 0.7516 (mpm) REVERT: E 180 GLU cc_start: 0.6714 (OUTLIER) cc_final: 0.6385 (pm20) REVERT: F 159 MET cc_start: 0.8667 (mmp) cc_final: 0.8274 (mtp) REVERT: F 249 ILE cc_start: 0.8309 (OUTLIER) cc_final: 0.7941 (pp) REVERT: F 310 ASP cc_start: 0.8447 (OUTLIER) cc_final: 0.7923 (t0) REVERT: F 430 ARG cc_start: 0.8977 (OUTLIER) cc_final: 0.8704 (ttp-110) REVERT: e 3 THR cc_start: 0.8808 (t) cc_final: 0.8587 (m) REVERT: e 4 MET cc_start: 0.8212 (tpt) cc_final: 0.7756 (tpt) REVERT: e 70 GLU cc_start: 0.8847 (tp30) cc_final: 0.8562 (tp30) REVERT: g 6 GLU cc_start: 0.6661 (tm-30) cc_final: 0.6173 (tp30) REVERT: g 8 ARG cc_start: 0.7146 (OUTLIER) cc_final: 0.6806 (mpt-90) REVERT: g 39 MET cc_start: 0.7490 (mmp) cc_final: 0.6770 (tpp) REVERT: g 63 TYR cc_start: 0.8445 (t80) cc_final: 0.8242 (t80) REVERT: g 76 VAL cc_start: 0.9409 (OUTLIER) cc_final: 0.9179 (p) REVERT: g 115 PHE cc_start: 0.8598 (p90) cc_final: 0.8253 (p90) outliers start: 70 outliers final: 36 residues processed: 264 average time/residue: 1.6491 time to fit residues: 507.1221 Evaluate side-chains 243 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 195 time to evaluate : 2.765 ------------------------------------------------------------------------------- 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 274 ILE Chi-restraints excluded: chain A residue 324 SER 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 B residue 291 VAL Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 394 ILE 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 104 GLU Chi-restraints excluded: chain D residue 122 THR 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 173 SER 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 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 249 ILE 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 430 ARG Chi-restraints excluded: chain F residue 450 MET Chi-restraints excluded: chain e residue 9 VAL Chi-restraints excluded: chain e residue 68 VAL Chi-restraints excluded: chain g residue 7 ILE Chi-restraints excluded: chain g residue 8 ARG Chi-restraints excluded: chain g residue 76 VAL 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 219 optimal weight: 0.9990 chunk 101 optimal weight: 0.0970 chunk 116 optimal weight: 5.9990 chunk 35 optimal weight: 8.9990 chunk 280 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 137 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 136 optimal weight: 0.7980 chunk 227 optimal weight: 10.0000 chunk 117 optimal weight: 0.5980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3707 r_free = 0.3707 target = 0.115680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.082758 restraints weight = 48512.040| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.51 r_work: 0.3007 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 25436 Z= 0.107 Angle : 0.552 13.079 34474 Z= 0.282 Chirality : 0.043 0.275 3979 Planarity : 0.004 0.068 4494 Dihedral : 6.262 84.196 3701 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.17 % Allowed : 28.39 % Favored : 69.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.15), residues: 3266 helix: 1.88 (0.15), residues: 1334 sheet: 0.61 (0.23), residues: 507 loop : -0.86 (0.16), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP g 206 HIS 0.002 0.000 HIS F 190 PHE 0.017 0.001 PHE g 175 TYR 0.044 0.001 TYR E 396 ARG 0.007 0.000 ARG D 5 Details of bonding type rmsd hydrogen bonds : bond 0.03831 ( 1221) hydrogen bonds : angle 4.50095 ( 3537) covalent geometry : bond 0.00242 (25436) covalent geometry : angle 0.55227 (34474) ********************** 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 260 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 203 time to evaluate : 2.872 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.7823 (p0) cc_final: 0.7187 (p0) REVERT: A 476 PHE cc_start: 0.9219 (OUTLIER) cc_final: 0.7987 (t80) REVERT: C 427 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7627 (mpt-90) REVERT: D 104 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7487 (pm20) REVERT: D 425 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7665 (tp) REVERT: E 117 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8462 (mp0) REVERT: E 158 MET cc_start: 0.7820 (OUTLIER) cc_final: 0.7402 (mpm) REVERT: E 180 GLU cc_start: 0.6615 (OUTLIER) cc_final: 0.6295 (pm20) REVERT: E 192 MET cc_start: 0.8586 (mmm) cc_final: 0.8314 (mtp) REVERT: F 159 MET cc_start: 0.8646 (mmp) cc_final: 0.8187 (mtp) REVERT: F 249 ILE cc_start: 0.8313 (OUTLIER) cc_final: 0.7926 (pp) REVERT: F 310 ASP cc_start: 0.8468 (OUTLIER) cc_final: 0.7951 (t0) REVERT: F 430 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.8726 (ttp-110) REVERT: e 3 THR cc_start: 0.8810 (t) cc_final: 0.8609 (m) REVERT: e 4 MET cc_start: 0.8234 (tpt) cc_final: 0.7887 (tpt) REVERT: g 8 ARG cc_start: 0.7147 (OUTLIER) cc_final: 0.6808 (mpt-90) REVERT: g 39 MET cc_start: 0.7475 (mmp) cc_final: 0.6781 (tpp) REVERT: g 63 TYR cc_start: 0.8427 (t80) cc_final: 0.8189 (t80) REVERT: g 76 VAL cc_start: 0.9465 (OUTLIER) cc_final: 0.9054 (p) REVERT: g 115 PHE cc_start: 0.8614 (p90) cc_final: 0.8327 (p90) outliers start: 57 outliers final: 39 residues processed: 246 average time/residue: 1.4537 time to fit residues: 411.7538 Evaluate side-chains 246 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 195 time to evaluate : 2.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 91 CYS 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 381 SER Chi-restraints excluded: chain A residue 476 PHE Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 394 ILE 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 78 VAL Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 122 THR 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 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 216 LEU 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 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 430 ARG Chi-restraints excluded: chain e residue 9 VAL Chi-restraints excluded: chain e residue 68 VAL Chi-restraints excluded: chain g residue 7 ILE Chi-restraints excluded: chain g residue 8 ARG Chi-restraints excluded: chain g residue 76 VAL 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 125 optimal weight: 0.9980 chunk 46 optimal weight: 7.9990 chunk 93 optimal weight: 9.9990 chunk 84 optimal weight: 0.8980 chunk 248 optimal weight: 5.9990 chunk 289 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 239 optimal weight: 5.9990 chunk 177 optimal weight: 0.6980 chunk 299 optimal weight: 0.9980 chunk 321 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3702 r_free = 0.3702 target = 0.115343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.082475 restraints weight = 49018.504| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.68 r_work: 0.2991 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 25436 Z= 0.118 Angle : 0.564 13.211 34474 Z= 0.288 Chirality : 0.043 0.240 3979 Planarity : 0.004 0.050 4494 Dihedral : 6.230 83.268 3701 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.44 % Allowed : 28.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.15), residues: 3266 helix: 1.91 (0.15), residues: 1328 sheet: 0.58 (0.23), residues: 516 loop : -0.82 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP g 206 HIS 0.002 0.001 HIS D 190 PHE 0.026 0.001 PHE g 125 TYR 0.023 0.001 TYR g 231 ARG 0.007 0.000 ARG F 20 Details of bonding type rmsd hydrogen bonds : bond 0.04071 ( 1221) hydrogen bonds : angle 4.50703 ( 3537) covalent geometry : bond 0.00276 (25436) covalent geometry : angle 0.56421 (34474) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20949.02 seconds wall clock time: 369 minutes 52.82 seconds (22192.82 seconds total)