Starting phenix.real_space_refine on Sun Aug 24 18:07:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8spx_40689/08_2025/8spx_40689.cif Found real_map, /net/cci-nas-00/data/ceres_data/8spx_40689/08_2025/8spx_40689.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8spx_40689/08_2025/8spx_40689.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8spx_40689/08_2025/8spx_40689.map" model { file = "/net/cci-nas-00/data/ceres_data/8spx_40689/08_2025/8spx_40689.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8spx_40689/08_2025/8spx_40689.cif" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.029 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 18 5.49 5 Mg 6 5.21 5 S 68 5.16 5 C 13845 2.51 5 N 3826 2.21 5 O 4237 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22000 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3650 Classifications: {'peptide': 476} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 453} Chain: "B" Number of atoms: 3636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3636 Classifications: {'peptide': 474} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 451} Chain: "C" Number of atoms: 3644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3644 Classifications: {'peptide': 475} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 452} Chain: "D" Number of atoms: 3631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3631 Classifications: {'peptide': 471} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 447} Chain: "E" Number of atoms: 3623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3623 Classifications: {'peptide': 470} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 446} Chain: "F" Number of atoms: 3623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3623 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 446} Chain: "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: 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: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.84, per 1000 atoms: 0.22 Number of scatterers: 22000 At special positions: 0 Unit cell: (109.2, 119.28, 125.16, 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 68 16.00 P 18 15.00 Mg 6 11.99 O 4237 8.00 N 3826 7.00 C 13845 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: 1.44 Conformation dependent library (CDL) restraints added in 717.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 5648 Ramachandran restraints generated. 2824 Oldfield, 0 Emsley, 2824 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5150 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 22 sheets defined 44.4% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 78 through 82 removed outlier: 4.092A pdb=" N GLY A 81 " --> pdb=" O PRO A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 157 Processing helix chain 'A' and resid 174 through 186 Processing helix chain 'A' and resid 201 through 215 Processing helix chain 'A' and resid 217 through 219 No H-bonds generated for 'chain 'A' and resid 217 through 219' Processing helix chain 'A' and resid 232 through 253 removed outlier: 3.752A pdb=" N PHE A 236 " --> pdb=" O ALA A 232 " (cutoff:3.500A) Proline residue: A 239 - end of helix removed outlier: 3.804A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 277 removed outlier: 3.514A pdb=" N LEU A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 299 Processing helix chain 'A' and resid 322 through 325 Processing helix chain 'A' and resid 328 through 338 removed outlier: 3.703A pdb=" N ILE A 337 " --> pdb=" O ASN A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 351 Processing helix chain 'A' and resid 372 through 379 Processing helix chain 'A' and resid 381 through 399 Processing helix chain 'A' and resid 403 through 419 removed outlier: 3.693A pdb=" N VAL A 417 " --> pdb=" O GLY A 413 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU A 418 " --> pdb=" O ALA A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 442 removed outlier: 3.827A pdb=" N GLN A 433 " --> pdb=" O PRO A 429 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL A 434 " --> pdb=" O VAL A 430 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LEU A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE A 436 " --> pdb=" O LYS A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 451 No H-bonds generated for 'chain 'A' and resid 449 through 451' Processing helix chain 'A' and resid 452 through 467 Processing helix chain 'A' and resid 468 through 479 removed outlier: 3.984A pdb=" N LEU A 472 " --> pdb=" O GLY A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 498 removed outlier: 4.013A pdb=" N LEU A 487 " --> pdb=" O ASN A 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 104 removed outlier: 3.800A pdb=" N LEU B 103 " --> pdb=" O GLY B 100 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE B 104 " --> pdb=" O GLU B 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 100 through 104' Processing helix chain 'B' and resid 150 through 157 Processing helix chain 'B' and resid 175 through 186 removed outlier: 3.695A pdb=" N ALA B 179 " --> pdb=" O LYS B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 215 removed outlier: 3.561A pdb=" N HIS B 215 " --> pdb=" O THR B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 219 removed outlier: 4.350A pdb=" N ASP B 219 " --> pdb=" O GLY B 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 216 through 219' Processing helix chain 'B' and resid 231 through 253 removed outlier: 3.769A pdb=" N LEU B 235 " --> pdb=" O PRO B 231 " (cutoff:3.500A) Proline residue: B 239 - end of helix removed outlier: 3.716A pdb=" N MET B 245 " --> pdb=" O ALA B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 277 removed outlier: 4.016A pdb=" N GLN B 266 " --> pdb=" O ASP B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 299 Processing helix chain 'B' and resid 322 through 325 Processing helix chain 'B' and resid 328 through 338 Processing helix chain 'B' and resid 345 through 350 Processing helix chain 'B' and resid 372 through 397 removed outlier: 4.109A pdb=" N THR B 381 " --> pdb=" O LYS B 377 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLU B 391 " --> pdb=" O ALA B 387 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU B 392 " --> pdb=" O ALA B 388 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA B 394 " --> pdb=" O ARG B 390 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N PHE B 395 " --> pdb=" O GLU B 391 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLN B 397 " --> pdb=" O GLU B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 420 removed outlier: 3.691A pdb=" N GLN B 407 " --> pdb=" O ASP B 403 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA B 408 " --> pdb=" O LYS B 404 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS B 409 " --> pdb=" O ALA B 405 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU B 410 " --> pdb=" O THR B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 442 Processing helix chain 'B' and resid 449 through 467 removed outlier: 4.303A pdb=" N ARG B 454 " --> pdb=" O VAL B 450 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ARG B 455 " --> pdb=" O GLU B 451 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS B 458 " --> pdb=" O ARG B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 479 removed outlier: 3.990A pdb=" N LEU B 472 " --> pdb=" O GLY B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 498 removed outlier: 3.525A pdb=" N PHE B 494 " --> pdb=" O ALA B 490 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS B 496 " --> pdb=" O GLU B 492 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR B 497 " --> pdb=" O ALA B 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 157 Processing helix chain 'C' and resid 174 through 186 Processing helix chain 'C' and resid 201 through 215 removed outlier: 3.518A pdb=" N VAL C 205 " --> pdb=" O LYS C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 253 removed outlier: 3.502A pdb=" N LEU C 235 " --> pdb=" O PRO C 231 " (cutoff:3.500A) Proline residue: C 239 - end of helix removed outlier: 3.927A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 277 removed outlier: 3.530A pdb=" N GLN C 266 " --> pdb=" O ASP C 262 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU C 272 " --> pdb=" O ALA C 268 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU C 273 " --> pdb=" O ALA C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 299 removed outlier: 4.141A pdb=" N TYR C 292 " --> pdb=" O GLY C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 309 Processing helix chain 'C' and resid 328 through 338 Processing helix chain 'C' and resid 372 through 379 Processing helix chain 'C' and resid 381 through 399 removed outlier: 4.127A pdb=" N ALA C 387 " --> pdb=" O ARG C 383 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA C 394 " --> pdb=" O ARG C 390 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE C 398 " --> pdb=" O ALA C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 421 removed outlier: 3.653A pdb=" N LYS C 421 " --> pdb=" O VAL C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 442 Processing helix chain 'C' and resid 443 through 447 removed outlier: 4.045A pdb=" N ASP C 447 " --> pdb=" O PHE C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 467 Processing helix chain 'C' and resid 468 through 479 removed outlier: 3.940A pdb=" N LEU C 472 " --> pdb=" O GLY C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 498 Processing helix chain 'D' and resid 139 through 146 Processing helix chain 'D' and resid 163 through 180 removed outlier: 3.663A pdb=" N GLU D 178 " --> pdb=" O ASN D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 206 removed outlier: 3.959A pdb=" N TYR D 199 " --> pdb=" O GLY D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 209 No H-bonds generated for 'chain 'D' and resid 207 through 209' Processing helix chain 'D' and resid 221 through 242 removed outlier: 3.604A pdb=" N ARG D 225 " --> pdb=" O PRO D 221 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ALA D 229 " --> pdb=" O ARG D 225 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LEU D 230 " --> pdb=" O MET D 226 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TYR D 238 " --> pdb=" O THR D 234 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE D 239 " --> pdb=" O MET D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 269 removed outlier: 3.874A pdb=" N THR D 258 " --> pdb=" O ILE D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 290 removed outlier: 3.695A pdb=" N LEU D 288 " --> pdb=" O GLU D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 323 removed outlier: 3.930A pdb=" N SER D 323 " --> pdb=" O ALA D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 339 Processing helix chain 'D' and resid 360 through 387 removed outlier: 3.842A pdb=" N LYS D 369 " --> pdb=" O GLN D 365 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N ASP D 382 " --> pdb=" O LYS D 378 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ILE D 383 " --> pdb=" O GLU D 379 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE D 384 " --> pdb=" O LEU D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 391 Processing helix chain 'D' and resid 393 through 409 removed outlier: 3.776A pdb=" N ARG D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE D 408 " --> pdb=" O ARG D 404 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE D 409 " --> pdb=" O ARG D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 442 Processing helix chain 'D' and resid 449 through 454 removed outlier: 3.524A pdb=" N ARG D 454 " --> pdb=" O ASP D 451 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 470 removed outlier: 3.695A pdb=" N VAL D 462 " --> pdb=" O ARG D 458 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL D 463 " --> pdb=" O ILE D 459 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 92 removed outlier: 3.647A pdb=" N THR E 91 " --> pdb=" O GLY E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 128 removed outlier: 3.652A pdb=" N LEU E 128 " --> pdb=" O PHE E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 146 Processing helix chain 'E' and resid 163 through 179 Processing helix chain 'E' and resid 191 through 206 removed outlier: 3.530A pdb=" N GLY E 195 " --> pdb=" O ARG E 191 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASN E 196 " --> pdb=" O THR E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 209 No H-bonds generated for 'chain 'E' and resid 207 through 209' Processing helix chain 'E' and resid 221 through 242 removed outlier: 3.657A pdb=" N ARG E 225 " --> pdb=" O PRO E 221 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ALA E 229 " --> pdb=" O ARG E 225 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LEU E 230 " --> pdb=" O MET E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 266 removed outlier: 4.031A pdb=" N ALA E 266 " --> pdb=" O SER E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 269 No H-bonds generated for 'chain 'E' and resid 267 through 269' Processing helix chain 'E' and resid 280 through 292 removed outlier: 3.999A pdb=" N ARG E 291 " --> pdb=" O GLN E 287 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ILE E 292 " --> pdb=" O LEU E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 323 removed outlier: 4.064A pdb=" N SER E 323 " --> pdb=" O ALA E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 339 removed outlier: 4.119A pdb=" N ALA E 336 " --> pdb=" O GLU E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 355 through 360 Processing helix chain 'E' and resid 360 through 388 removed outlier: 4.299A pdb=" N ASP E 382 " --> pdb=" O LYS E 378 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE E 386 " --> pdb=" O ASP E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 393 through 410 removed outlier: 3.681A pdb=" N PHE E 408 " --> pdb=" O ARG E 404 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE E 409 " --> pdb=" O ARG E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 422 Processing helix chain 'E' and resid 429 through 442 Processing helix chain 'E' and resid 449 through 454 Processing helix chain 'E' and resid 458 through 470 Processing helix chain 'F' and resid 88 through 92 removed outlier: 3.833A pdb=" N THR F 91 " --> pdb=" O GLY F 88 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU F 92 " --> pdb=" O GLU F 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 88 through 92' Processing helix chain 'F' and resid 139 through 146 Processing helix chain 'F' and resid 163 through 179 Processing helix chain 'F' and resid 191 through 206 Processing helix chain 'F' and resid 221 through 242 removed outlier: 3.537A pdb=" N ARG F 225 " --> pdb=" O PRO F 221 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N ALA F 229 " --> pdb=" O ARG F 225 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N LEU F 230 " --> pdb=" O MET F 226 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N TYR F 238 " --> pdb=" O THR F 234 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N PHE F 239 " --> pdb=" O MET F 235 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ARG F 240 " --> pdb=" O ALA F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 269 removed outlier: 3.830A pdb=" N PHE F 257 " --> pdb=" O ASN F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 290 Processing helix chain 'F' and resid 315 through 323 removed outlier: 3.581A pdb=" N SER F 323 " --> pdb=" O ALA F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 337 Processing helix chain 'F' and resid 355 through 360 Processing helix chain 'F' and resid 360 through 388 removed outlier: 4.378A pdb=" N ASP F 382 " --> pdb=" O LYS F 378 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ILE F 383 " --> pdb=" O GLU F 379 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE F 386 " --> pdb=" O ASP F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 410 removed outlier: 3.894A pdb=" N ARG F 405 " --> pdb=" O HIS F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 416 No H-bonds generated for 'chain 'F' and resid 414 through 416' Processing helix chain 'F' and resid 417 through 422 Processing helix chain 'F' and resid 429 through 443 Processing helix chain 'F' and resid 449 through 454 Processing helix chain 'F' and resid 458 through 470 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 6.838A pdb=" N VAL A 74 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N ALA A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N GLU A 51 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N LEU A 52 " --> pdb=" O THR A 91 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 99 Processing sheet with id=AA3, first strand: chain 'A' and resid 107 through 108 removed outlier: 6.614A pdb=" N VAL A 108 " --> pdb=" O THR A 225 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N SER A 227 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL A 319 " --> pdb=" O ILE A 167 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLY A 169 " --> pdb=" O VAL A 319 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 145 through 146 removed outlier: 4.614A pdb=" N ILE A 159 " --> pdb=" O LEU A 146 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 29 through 35 removed outlier: 3.513A pdb=" N GLN B 33 " --> pdb=" O ARG B 40 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N GLY B 72 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLY B 29 " --> pdb=" O VAL B 88 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 96 through 99 Processing sheet with id=AA7, first strand: chain 'B' and resid 107 through 108 removed outlier: 6.390A pdb=" N VAL B 108 " --> pdb=" O THR B 225 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ILE B 192 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N VAL B 259 " --> pdb=" O ILE B 192 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE B 194 " --> pdb=" O VAL B 259 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TYR B 260 " --> pdb=" O LEU B 316 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 107 through 108 removed outlier: 6.390A pdb=" N VAL B 108 " --> pdb=" O THR B 225 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ILE B 192 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N VAL B 259 " --> pdb=" O ILE B 192 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE B 194 " --> pdb=" O VAL B 259 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TYR B 260 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU B 166 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N LEU B 344 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE B 168 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN B 341 " --> pdb=" O VAL B 363 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 60 through 66 removed outlier: 4.430A pdb=" N GLU C 51 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N ARG C 93 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N GLU C 54 " --> pdb=" O THR C 91 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N THR C 91 " --> pdb=" O GLU C 54 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ARG C 40 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N VAL C 34 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N GLY C 72 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N MET C 60 " --> pdb=" O LEU C 76 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N GLU D 75 " --> pdb=" O GLN D 33 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N GLN D 33 " --> pdb=" O GLU D 75 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N HIS D 34 " --> pdb=" O ILE D 44 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ILE D 44 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ARG D 60 " --> pdb=" O ALA D 51 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N HIS D 53 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N THR D 58 " --> pdb=" O HIS D 53 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL D 14 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N VAL D 13 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N VAL D 9 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ASP D 15 " --> pdb=" O ILE D 7 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 96 through 99 Processing sheet with id=AB2, first strand: chain 'C' and resid 107 through 108 removed outlier: 6.241A pdb=" N VAL C 108 " --> pdb=" O THR C 225 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N SER C 227 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL C 256 " --> pdb=" O THR C 314 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N LEU C 316 " --> pdb=" O VAL C 256 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL C 258 " --> pdb=" O LEU C 316 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 318 through 320 removed outlier: 6.810A pdb=" N LEU C 166 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N LEU C 344 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ILE C 168 " --> pdb=" O LEU C 344 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 85 through 86 Processing sheet with id=AB5, first strand: chain 'D' and resid 95 through 96 removed outlier: 6.827A pdb=" N ILE D 182 " --> pdb=" O LEU D 248 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N PHE D 250 " --> pdb=" O ILE D 182 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL D 184 " --> pdb=" O PHE D 250 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N ASP D 252 " --> pdb=" O VAL D 184 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N ALA D 186 " --> pdb=" O ASP D 252 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ILE D 154 " --> pdb=" O GLN D 304 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ILE D 306 " --> pdb=" O ILE D 154 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N LEU D 156 " --> pdb=" O ILE D 306 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LYS D 153 " --> pdb=" O ALA D 327 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N THR D 329 " --> pdb=" O LYS D 153 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N GLY D 155 " --> pdb=" O THR D 329 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 134 through 135 removed outlier: 3.678A pdb=" N LEU D 135 " --> pdb=" O TYR D 148 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N TYR D 148 " --> pdb=" O LEU D 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'E' and resid 3 through 10 removed outlier: 6.695A pdb=" N ASP E 15 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N VAL E 9 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N VAL E 13 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ILE E 62 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N VAL E 50 " --> pdb=" O ILE E 62 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE E 44 " --> pdb=" O HIS E 34 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N GLN E 33 " --> pdb=" O GLU E 75 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N GLU E 75 " --> pdb=" O GLN E 33 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 84 through 86 Processing sheet with id=AB9, first strand: chain 'E' and resid 95 through 96 removed outlier: 6.399A pdb=" N PHE E 96 " --> pdb=" O PHE E 215 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASP E 252 " --> pdb=" O ALA E 186 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL E 188 " --> pdb=" O ASP E 252 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL E 247 " --> pdb=" O THR E 301 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N ILE E 303 " --> pdb=" O VAL E 247 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU E 249 " --> pdb=" O ILE E 303 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N ALA E 305 " --> pdb=" O LEU E 249 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ILE E 251 " --> pdb=" O ALA E 305 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N TYR E 307 " --> pdb=" O ILE E 251 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ILE E 154 " --> pdb=" O GLN E 304 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ILE E 306 " --> pdb=" O ILE E 154 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LEU E 156 " --> pdb=" O ILE E 306 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N GLY E 155 " --> pdb=" O THR E 329 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 3 through 10 removed outlier: 6.025A pdb=" N VAL F 6 " --> pdb=" O LYS F 17 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N LYS F 17 " --> pdb=" O VAL F 6 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN F 8 " --> pdb=" O ASP F 15 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N VAL F 13 " --> pdb=" O MET F 10 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N THR F 58 " --> pdb=" O HIS F 53 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N HIS F 53 " --> pdb=" O THR F 58 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ARG F 60 " --> pdb=" O ALA F 51 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE F 44 " --> pdb=" O HIS F 34 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N GLN F 33 " --> pdb=" O GLU F 75 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLU F 75 " --> pdb=" O GLN F 33 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 84 through 87 removed outlier: 3.738A pdb=" N ARG F 114 " --> pdb=" O VAL F 87 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 95 through 96 removed outlier: 6.445A pdb=" N PHE F 96 " --> pdb=" O PHE F 215 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N GLN F 217 " --> pdb=" O PHE F 96 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL F 184 " --> pdb=" O PHE F 250 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE F 303 " --> pdb=" O LEU F 249 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE F 251 " --> pdb=" O ILE F 303 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA F 305 " --> pdb=" O ILE F 251 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILE F 154 " --> pdb=" O GLN F 304 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N ILE F 306 " --> pdb=" O ILE F 154 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LEU F 156 " --> pdb=" O ILE F 306 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LYS F 153 " --> pdb=" O ALA F 327 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N THR F 329 " --> pdb=" O LYS F 153 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N GLY F 155 " --> pdb=" O THR F 329 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 134 through 135 removed outlier: 4.419A pdb=" N TYR F 148 " --> pdb=" O LEU F 135 " (cutoff:3.500A) 978 hydrogen bonds defined for protein. 2814 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: 3.29 Time building geometry restraints manager: 1.94 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: 7384 1.34 - 1.46: 2455 1.46 - 1.57: 12373 1.57 - 1.69: 23 1.69 - 1.81: 136 Bond restraints: 22371 Sorted by residual: bond pdb=" O3 PO4 F 503 " pdb=" P PO4 F 503 " ideal model delta sigma weight residual 1.569 1.506 0.063 2.00e-02 2.50e+03 9.90e+00 bond pdb=" O4 PO4 F 503 " pdb=" P PO4 F 503 " ideal model delta sigma weight residual 1.568 1.506 0.062 2.00e-02 2.50e+03 9.67e+00 bond pdb=" O2 PO4 F 503 " pdb=" P PO4 F 503 " ideal model delta sigma weight residual 1.567 1.506 0.061 2.00e-02 2.50e+03 9.32e+00 bond pdb=" O1 PO4 F 503 " pdb=" P PO4 F 503 " ideal model delta sigma weight residual 1.565 1.508 0.057 2.00e-02 2.50e+03 8.21e+00 bond pdb=" CA PRO A 280 " pdb=" C PRO A 280 " ideal model delta sigma weight residual 1.517 1.505 0.012 6.70e-03 2.23e+04 3.43e+00 ... (remaining 22366 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.38: 29106 1.38 - 2.77: 1033 2.77 - 4.15: 157 4.15 - 5.53: 41 5.53 - 6.92: 8 Bond angle restraints: 30345 Sorted by residual: angle pdb=" C ALA F 274 " pdb=" CA ALA F 274 " pdb=" CB ALA F 274 " ideal model delta sigma weight residual 116.54 110.46 6.08 1.15e+00 7.56e-01 2.79e+01 angle pdb=" C TYR B 329 " pdb=" N ILE B 330 " pdb=" CA ILE B 330 " ideal model delta sigma weight residual 120.33 124.43 -4.10 8.00e-01 1.56e+00 2.62e+01 angle pdb=" C GLN E 217 " pdb=" N MET E 218 " pdb=" CA MET E 218 " ideal model delta sigma weight residual 120.38 124.79 -4.41 1.37e+00 5.33e-01 1.04e+01 angle pdb=" N GLY A 360 " pdb=" CA GLY A 360 " pdb=" C GLY A 360 " ideal model delta sigma weight residual 112.64 116.41 -3.77 1.21e+00 6.83e-01 9.70e+00 angle pdb=" N ILE E 292 " pdb=" CA ILE E 292 " pdb=" C ILE E 292 " ideal model delta sigma weight residual 106.21 109.39 -3.18 1.07e+00 8.73e-01 8.84e+00 ... (remaining 30340 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 12490 17.65 - 35.30: 891 35.30 - 52.95: 199 52.95 - 70.60: 54 70.60 - 88.25: 26 Dihedral angle restraints: 13660 sinusoidal: 5602 harmonic: 8058 Sorted by residual: dihedral pdb=" CA PRO C 145 " pdb=" C PRO C 145 " pdb=" N LEU C 146 " pdb=" CA LEU C 146 " ideal model delta harmonic sigma weight residual 180.00 155.71 24.29 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" CA ASP D 45 " pdb=" C ASP D 45 " pdb=" N LEU D 46 " pdb=" CA LEU D 46 " ideal model delta harmonic sigma weight residual -180.00 -156.72 -23.28 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" C4' ADP F 502 " pdb=" C5' ADP F 502 " pdb=" O5' ADP F 502 " pdb=" PA ADP F 502 " ideal model delta sinusoidal sigma weight residual -180.00 -95.60 -84.40 1 2.00e+01 2.50e-03 2.17e+01 ... (remaining 13657 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1972 0.031 - 0.061: 927 0.061 - 0.091: 350 0.091 - 0.122: 190 0.122 - 0.152: 46 Chirality restraints: 3485 Sorted by residual: chirality pdb=" CA ILE D 71 " pdb=" N ILE D 71 " pdb=" C ILE D 71 " pdb=" CB ILE D 71 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.81e-01 chirality pdb=" CA ILE B 38 " pdb=" N ILE B 38 " pdb=" C ILE B 38 " pdb=" CB ILE B 38 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.74e-01 chirality pdb=" CA PRO E 222 " pdb=" N PRO E 222 " pdb=" C PRO E 222 " pdb=" CB PRO E 222 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.14 2.00e-01 2.50e+01 5.22e-01 ... (remaining 3482 not shown) Planarity restraints: 3962 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA D 81 " 0.040 5.00e-02 4.00e+02 6.09e-02 5.93e+00 pdb=" N PRO D 82 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO D 82 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 82 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER B 177 " 0.010 2.00e-02 2.50e+03 2.07e-02 4.29e+00 pdb=" C SER B 177 " -0.036 2.00e-02 2.50e+03 pdb=" O SER B 177 " 0.013 2.00e-02 2.50e+03 pdb=" N VAL B 178 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG E 120 " -0.032 5.00e-02 4.00e+02 4.85e-02 3.77e+00 pdb=" N PRO E 121 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO E 121 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 121 " -0.027 5.00e-02 4.00e+02 ... (remaining 3959 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.50: 67 2.50 - 3.10: 15712 3.10 - 3.70: 31876 3.70 - 4.30: 47902 4.30 - 4.90: 80090 Nonbonded interactions: 175647 Sorted by model distance: nonbonded pdb="MG MG F 501 " pdb=" O3 PO4 F 503 " model vdw 1.895 2.170 nonbonded pdb="MG MG F 501 " pdb=" O2B ADP F 502 " model vdw 1.933 2.170 nonbonded pdb=" O1G ATP D 500 " pdb="MG MG D 501 " model vdw 1.981 2.170 nonbonded pdb=" OG1 THR D 165 " pdb="MG MG D 501 " model vdw 1.996 2.170 nonbonded pdb=" O LYS B 201 " pdb=" OG1 THR B 204 " model vdw 2.169 3.040 ... (remaining 175642 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 27 through 499 or resid 600 through 601)) selection = (chain 'B' and resid 27 through 601) selection = (chain 'C' and (resid 27 through 499 or resid 600 through 601)) } ncs_group { reference = (chain 'D' and resid 2 through 470) selection = (chain 'E' and resid 2 through 470) selection = (chain 'F' and resid 2 through 470) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 17.440 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6293 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 22371 Z= 0.177 Angle : 0.635 6.916 30345 Z= 0.360 Chirality : 0.045 0.152 3485 Planarity : 0.005 0.061 3962 Dihedral : 13.883 88.245 8510 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.03 % Allowed : 8.19 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.15), residues: 2824 helix: 0.27 (0.15), residues: 1077 sheet: 0.08 (0.23), residues: 461 loop : -0.57 (0.17), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 206 TYR 0.020 0.002 TYR A 248 PHE 0.021 0.002 PHE A 236 HIS 0.009 0.001 HIS F 363 Details of bonding type rmsd covalent geometry : bond 0.00363 (22371) covalent geometry : angle 0.63479 (30345) hydrogen bonds : bond 0.17961 ( 968) hydrogen bonds : angle 7.45694 ( 2814) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5648 Ramachandran restraints generated. 2824 Oldfield, 0 Emsley, 2824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5648 Ramachandran restraints generated. 2824 Oldfield, 0 Emsley, 2824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 567 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 375 MET cc_start: 0.6720 (ttp) cc_final: 0.6055 (tpp) REVERT: E 235 MET cc_start: 0.6801 (mtt) cc_final: 0.6509 (mtp) REVERT: F 240 ARG cc_start: 0.6194 (OUTLIER) cc_final: 0.5963 (ptt90) outliers start: 47 outliers final: 12 residues processed: 598 average time/residue: 0.5843 time to fit residues: 395.4095 Evaluate side-chains 344 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 331 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain F residue 240 ARG Chi-restraints excluded: chain F residue 411 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.0970 chunk 111 optimal weight: 9.9990 overall best weight: 1.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 ASN A 467 ASN B 172 GLN B 230 GLN B 322 GLN B 483 ASN C 255 HIS C 358 ASN C 422 GLN C 426 GLN C 433 GLN C 474 HIS D 34 HIS D 174 ASN D 259 GLN D 289 GLN D 324 HIS D 330 ASN D 381 GLN D 401 HIS E 259 GLN E 304 GLN E 412 GLN E 447 HIS F 33 GLN F 38 ASN ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 243 GLN F 245 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.207320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.178193 restraints weight = 24152.442| |-----------------------------------------------------------------------------| r_work (start): 0.4385 rms_B_bonded: 2.12 r_work: 0.4272 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.4128 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.4128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6788 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 22371 Z= 0.150 Angle : 0.642 12.289 30345 Z= 0.336 Chirality : 0.046 0.179 3485 Planarity : 0.005 0.056 3962 Dihedral : 9.130 89.887 3283 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 4.48 % Allowed : 17.46 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.15), residues: 2824 helix: 0.72 (0.15), residues: 1083 sheet: 0.31 (0.23), residues: 471 loop : -0.63 (0.17), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 171 TYR 0.020 0.002 TYR F 199 PHE 0.024 0.002 PHE D 437 HIS 0.005 0.001 HIS B 470 Details of bonding type rmsd covalent geometry : bond 0.00333 (22371) covalent geometry : angle 0.64175 (30345) hydrogen bonds : bond 0.05027 ( 968) hydrogen bonds : angle 5.46242 ( 2814) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5648 Ramachandran restraints generated. 2824 Oldfield, 0 Emsley, 2824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5648 Ramachandran restraints generated. 2824 Oldfield, 0 Emsley, 2824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 360 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 300 ARG cc_start: 0.7915 (mmm-85) cc_final: 0.7660 (mtm180) REVERT: B 377 LYS cc_start: 0.7683 (tttp) cc_final: 0.7425 (mttt) REVERT: C 62 MET cc_start: 0.6386 (ttp) cc_final: 0.6110 (ptm) REVERT: C 190 ASN cc_start: 0.6584 (OUTLIER) cc_final: 0.5943 (p0) REVERT: C 210 GLU cc_start: 0.5928 (mm-30) cc_final: 0.5590 (pt0) REVERT: C 300 ARG cc_start: 0.7312 (OUTLIER) cc_final: 0.6313 (mtp85) REVERT: C 375 MET cc_start: 0.6914 (ttp) cc_final: 0.6062 (tpp) REVERT: D 10 MET cc_start: 0.6885 (mtm) cc_final: 0.6548 (mtp) REVERT: D 271 MET cc_start: 0.7877 (OUTLIER) cc_final: 0.7491 (mtm) REVERT: D 345 ASP cc_start: 0.6735 (t0) cc_final: 0.6386 (t70) REVERT: D 446 ASP cc_start: 0.5951 (p0) cc_final: 0.5690 (p0) REVERT: E 133 GLU cc_start: 0.5492 (pm20) cc_final: 0.5041 (mm-30) REVERT: E 285 MET cc_start: 0.7324 (ttm) cc_final: 0.7101 (ttm) REVERT: E 334 LYS cc_start: 0.7177 (mmtt) cc_final: 0.6915 (ttpt) REVERT: F 5 ARG cc_start: 0.7245 (OUTLIER) cc_final: 0.6485 (mtm180) REVERT: F 37 ARG cc_start: 0.7368 (OUTLIER) cc_final: 0.7127 (mpt-90) REVERT: F 218 MET cc_start: 0.7348 (mtt) cc_final: 0.7146 (mtt) REVERT: F 284 GLU cc_start: 0.7223 (pt0) cc_final: 0.6793 (mm-30) REVERT: F 398 LEU cc_start: 0.8711 (tp) cc_final: 0.8479 (tm) REVERT: F 406 ILE cc_start: 0.7693 (mt) cc_final: 0.7372 (mp) REVERT: F 460 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7760 (mm-30) outliers start: 104 outliers final: 34 residues processed: 421 average time/residue: 0.5422 time to fit residues: 261.6316 Evaluate side-chains 328 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 288 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 137 MET Chi-restraints excluded: chain C residue 190 ASN Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 300 ARG Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 235 MET Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 271 MET Chi-restraints excluded: chain D residue 384 ILE Chi-restraints excluded: chain D residue 458 ARG Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 362 GLU Chi-restraints excluded: chain E residue 428 VAL Chi-restraints excluded: chain F residue 5 ARG Chi-restraints excluded: chain F residue 37 ARG Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain F residue 240 ARG Chi-restraints excluded: chain F residue 283 THR Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 411 SER Chi-restraints excluded: chain F residue 460 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 215 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 chunk 109 optimal weight: 8.9990 chunk 77 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 chunk 182 optimal weight: 5.9990 chunk 150 optimal weight: 8.9990 chunk 258 optimal weight: 6.9990 chunk 138 optimal weight: 20.0000 chunk 118 optimal weight: 5.9990 chunk 103 optimal weight: 0.1980 overall best weight: 3.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 GLN A 358 ASN A 371 GLN A 467 ASN B 143 HIS B 333 ASN B 483 ASN ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 433 GLN C 474 HIS D 259 GLN D 401 HIS E 33 GLN E 34 HIS E 38 ASN E 363 HIS E 412 GLN E 447 HIS F 34 HIS F 38 ASN F 174 ASN F 259 GLN F 363 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.196382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.166717 restraints weight = 24913.125| |-----------------------------------------------------------------------------| r_work (start): 0.4284 rms_B_bonded: 2.14 r_work: 0.4164 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.4019 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.4019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 22371 Z= 0.207 Angle : 0.704 9.000 30345 Z= 0.369 Chirality : 0.049 0.239 3485 Planarity : 0.006 0.050 3962 Dihedral : 9.168 89.962 3276 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 7.20 % Allowed : 18.06 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.15), residues: 2824 helix: 0.39 (0.15), residues: 1087 sheet: 0.21 (0.23), residues: 479 loop : -0.98 (0.17), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 171 TYR 0.020 0.002 TYR F 238 PHE 0.028 0.002 PHE F 414 HIS 0.013 0.002 HIS C 470 Details of bonding type rmsd covalent geometry : bond 0.00484 (22371) covalent geometry : angle 0.70435 (30345) hydrogen bonds : bond 0.05660 ( 968) hydrogen bonds : angle 5.36483 ( 2814) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5648 Ramachandran restraints generated. 2824 Oldfield, 0 Emsley, 2824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5648 Ramachandran restraints generated. 2824 Oldfield, 0 Emsley, 2824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 321 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 ASP cc_start: 0.7734 (OUTLIER) cc_final: 0.7348 (m-30) REVERT: B 300 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7759 (mtm180) REVERT: C 62 MET cc_start: 0.6406 (OUTLIER) cc_final: 0.6154 (ptm) REVERT: C 118 LEU cc_start: 0.7958 (mt) cc_final: 0.7731 (mp) REVERT: C 137 MET cc_start: 0.4135 (OUTLIER) cc_final: 0.3840 (mtt) REVERT: C 190 ASN cc_start: 0.6769 (OUTLIER) cc_final: 0.6154 (p0) REVERT: C 210 GLU cc_start: 0.6002 (mm-30) cc_final: 0.5736 (pt0) REVERT: C 300 ARG cc_start: 0.7316 (OUTLIER) cc_final: 0.6329 (mtp85) REVERT: C 375 MET cc_start: 0.6972 (ttp) cc_final: 0.6281 (tpp) REVERT: D 196 ASN cc_start: 0.6377 (OUTLIER) cc_final: 0.5920 (m110) REVERT: D 271 MET cc_start: 0.7745 (mtp) cc_final: 0.7516 (mtm) REVERT: D 322 PHE cc_start: 0.7817 (OUTLIER) cc_final: 0.6953 (m-80) REVERT: D 345 ASP cc_start: 0.6938 (t0) cc_final: 0.6693 (t70) REVERT: D 351 SER cc_start: 0.6161 (m) cc_final: 0.5411 (t) REVERT: D 352 ARG cc_start: 0.6981 (OUTLIER) cc_final: 0.6753 (mtm180) REVERT: D 402 ARG cc_start: 0.6518 (OUTLIER) cc_final: 0.6106 (mtp180) REVERT: D 413 ASN cc_start: 0.7071 (p0) cc_final: 0.6793 (p0) REVERT: E 128 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7808 (mm) REVERT: E 133 GLU cc_start: 0.5481 (pm20) cc_final: 0.5023 (pm20) REVERT: E 143 ASP cc_start: 0.7222 (m-30) cc_final: 0.7003 (m-30) REVERT: E 204 ASP cc_start: 0.7578 (t70) cc_final: 0.6862 (m-30) REVERT: E 334 LYS cc_start: 0.7408 (mmtt) cc_final: 0.7056 (ttpt) REVERT: E 469 MET cc_start: 0.4969 (mtt) cc_final: 0.4744 (mtt) REVERT: F 5 ARG cc_start: 0.7198 (OUTLIER) cc_final: 0.6478 (mtm180) REVERT: F 148 TYR cc_start: 0.5843 (m-80) cc_final: 0.5364 (m-80) REVERT: F 226 MET cc_start: 0.6925 (OUTLIER) cc_final: 0.6705 (mtm) REVERT: F 284 GLU cc_start: 0.7242 (pt0) cc_final: 0.6619 (mm-30) REVERT: F 285 MET cc_start: 0.7721 (OUTLIER) cc_final: 0.7454 (ttt) REVERT: F 334 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7825 (tptp) REVERT: F 338 MET cc_start: 0.8022 (tpp) cc_final: 0.7667 (tpp) REVERT: F 352 ARG cc_start: 0.6062 (OUTLIER) cc_final: 0.5597 (ptt180) REVERT: F 398 LEU cc_start: 0.8754 (tp) cc_final: 0.8511 (tm) REVERT: F 438 LYS cc_start: 0.8386 (ttmt) cc_final: 0.7982 (tttm) REVERT: F 460 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7855 (mm-30) outliers start: 167 outliers final: 69 residues processed: 436 average time/residue: 0.5626 time to fit residues: 282.4275 Evaluate side-chains 349 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 263 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 397 GLN Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 300 ARG Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 451 GLU Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 137 MET Chi-restraints excluded: chain C residue 190 ASN Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 236 PHE Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 300 ARG Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 322 PHE Chi-restraints excluded: chain D residue 352 ARG Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 384 ILE Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 402 ARG Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 33 GLN Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 220 GLU Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 362 GLU Chi-restraints excluded: chain E residue 428 VAL Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain F residue 5 ARG Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain F residue 226 MET Chi-restraints excluded: chain F residue 240 ARG Chi-restraints excluded: chain F residue 283 THR Chi-restraints excluded: chain F residue 285 MET Chi-restraints excluded: chain F residue 322 PHE Chi-restraints excluded: chain F residue 334 LYS Chi-restraints excluded: chain F residue 352 ARG Chi-restraints excluded: chain F residue 386 ILE Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 392 LEU Chi-restraints excluded: chain F residue 451 ASP Chi-restraints excluded: chain F residue 460 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 49 optimal weight: 4.9990 chunk 206 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 chunk 155 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 126 optimal weight: 9.9990 chunk 277 optimal weight: 0.0870 chunk 278 optimal weight: 2.9990 chunk 256 optimal weight: 0.9990 chunk 62 optimal weight: 6.9990 overall best weight: 2.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN A 65 ASN A 341 GLN A 467 ASN A 469 GLN B 483 ASN ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 433 GLN E 33 GLN F 38 ASN F 401 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.200381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.171181 restraints weight = 24443.485| |-----------------------------------------------------------------------------| r_work (start): 0.4308 rms_B_bonded: 2.14 r_work: 0.4183 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.4040 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.4040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6910 moved from start: 0.3980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 22371 Z= 0.144 Angle : 0.610 10.476 30345 Z= 0.319 Chirality : 0.046 0.200 3485 Planarity : 0.005 0.052 3962 Dihedral : 8.643 87.339 3275 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 5.78 % Allowed : 21.25 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.15), residues: 2824 helix: 0.68 (0.15), residues: 1088 sheet: 0.23 (0.23), residues: 476 loop : -0.97 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 89 TYR 0.015 0.001 TYR D 364 PHE 0.015 0.002 PHE F 414 HIS 0.010 0.001 HIS C 470 Details of bonding type rmsd covalent geometry : bond 0.00336 (22371) covalent geometry : angle 0.61044 (30345) hydrogen bonds : bond 0.04625 ( 968) hydrogen bonds : angle 5.10500 ( 2814) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5648 Ramachandran restraints generated. 2824 Oldfield, 0 Emsley, 2824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5648 Ramachandran restraints generated. 2824 Oldfield, 0 Emsley, 2824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 286 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ARG cc_start: 0.6100 (OUTLIER) cc_final: 0.5898 (mtm110) REVERT: A 137 MET cc_start: 0.3263 (OUTLIER) cc_final: 0.3046 (mtt) REVERT: A 347 ASP cc_start: 0.7546 (OUTLIER) cc_final: 0.7307 (m-30) REVERT: A 448 ILE cc_start: 0.6763 (OUTLIER) cc_final: 0.6500 (pp) REVERT: B 300 ARG cc_start: 0.7925 (mmm-85) cc_final: 0.7696 (mtm180) REVERT: C 62 MET cc_start: 0.6390 (OUTLIER) cc_final: 0.6142 (ptm) REVERT: C 118 LEU cc_start: 0.7961 (mt) cc_final: 0.7752 (mp) REVERT: C 190 ASN cc_start: 0.6884 (OUTLIER) cc_final: 0.6229 (p0) REVERT: C 210 GLU cc_start: 0.5779 (mm-30) cc_final: 0.5522 (pt0) REVERT: C 299 GLU cc_start: 0.6319 (OUTLIER) cc_final: 0.6117 (tt0) REVERT: C 300 ARG cc_start: 0.7212 (OUTLIER) cc_final: 0.6194 (mtp85) REVERT: C 361 LEU cc_start: 0.8401 (tt) cc_final: 0.8015 (mp) REVERT: C 375 MET cc_start: 0.6964 (ttp) cc_final: 0.6081 (tpp) REVERT: D 10 MET cc_start: 0.7127 (mtm) cc_final: 0.6799 (mtp) REVERT: D 115 ARG cc_start: 0.6719 (ptp-110) cc_final: 0.6037 (ptp-170) REVERT: D 196 ASN cc_start: 0.6372 (OUTLIER) cc_final: 0.5879 (m110) REVERT: D 337 GLU cc_start: 0.6950 (OUTLIER) cc_final: 0.5762 (mp0) REVERT: D 345 ASP cc_start: 0.6788 (t0) cc_final: 0.6541 (t70) REVERT: D 402 ARG cc_start: 0.6551 (OUTLIER) cc_final: 0.6116 (mtp180) REVERT: D 413 ASN cc_start: 0.6993 (p0) cc_final: 0.6699 (p0) REVERT: E 128 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7888 (mm) REVERT: E 133 GLU cc_start: 0.5387 (pm20) cc_final: 0.5171 (pm20) REVERT: E 204 ASP cc_start: 0.7468 (t70) cc_final: 0.6863 (m-30) REVERT: E 256 ARG cc_start: 0.7612 (OUTLIER) cc_final: 0.7192 (mmt180) REVERT: E 315 ASP cc_start: 0.7232 (t0) cc_final: 0.6809 (t0) REVERT: E 334 LYS cc_start: 0.7361 (mmtt) cc_final: 0.6983 (ttpt) REVERT: E 357 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.6962 (pp20) REVERT: F 5 ARG cc_start: 0.7135 (OUTLIER) cc_final: 0.6422 (mtm180) REVERT: F 268 LEU cc_start: 0.6046 (OUTLIER) cc_final: 0.5825 (mm) REVERT: F 284 GLU cc_start: 0.7140 (pt0) cc_final: 0.6548 (mm-30) REVERT: F 315 ASP cc_start: 0.5621 (OUTLIER) cc_final: 0.5404 (m-30) REVERT: F 334 LYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7879 (tptp) REVERT: F 338 MET cc_start: 0.7952 (tpp) cc_final: 0.7566 (tpp) REVERT: F 340 ILE cc_start: 0.7195 (OUTLIER) cc_final: 0.6449 (mp) REVERT: F 352 ARG cc_start: 0.6102 (OUTLIER) cc_final: 0.5661 (ptt180) REVERT: F 406 ILE cc_start: 0.7593 (mp) cc_final: 0.7363 (mp) REVERT: F 431 LYS cc_start: 0.7513 (OUTLIER) cc_final: 0.7133 (mppt) REVERT: F 438 LYS cc_start: 0.8362 (ttmt) cc_final: 0.7956 (tttm) outliers start: 134 outliers final: 61 residues processed: 372 average time/residue: 0.5637 time to fit residues: 241.1013 Evaluate side-chains 344 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 262 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ARG Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 397 GLN Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 451 GLU Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 190 ASN Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 236 PHE Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain C residue 300 ARG Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 322 PHE Chi-restraints excluded: chain D residue 332 GLU Chi-restraints excluded: chain D residue 337 GLU Chi-restraints excluded: chain D residue 384 ILE Chi-restraints excluded: chain D residue 402 ARG Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 256 ARG Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 357 GLU Chi-restraints excluded: chain E residue 362 GLU Chi-restraints excluded: chain E residue 428 VAL Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain F residue 5 ARG Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain F residue 240 ARG Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain F residue 315 ASP Chi-restraints excluded: chain F residue 322 PHE Chi-restraints excluded: chain F residue 334 LYS Chi-restraints excluded: chain F residue 340 ILE Chi-restraints excluded: chain F residue 352 ARG Chi-restraints excluded: chain F residue 379 GLU Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 392 LEU Chi-restraints excluded: chain F residue 431 LYS Chi-restraints excluded: chain F residue 451 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 277 optimal weight: 8.9990 chunk 218 optimal weight: 1.9990 chunk 161 optimal weight: 6.9990 chunk 147 optimal weight: 0.3980 chunk 225 optimal weight: 1.9990 chunk 251 optimal weight: 9.9990 chunk 70 optimal weight: 5.9990 chunk 163 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 259 optimal weight: 6.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN A 341 GLN ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 467 ASN B 483 ASN C 172 GLN ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 433 GLN C 474 HIS D 179 HIS D 304 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.202180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.173088 restraints weight = 24146.104| |-----------------------------------------------------------------------------| r_work (start): 0.4325 rms_B_bonded: 2.13 r_work: 0.4202 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.4059 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.4059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6883 moved from start: 0.4207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22371 Z= 0.124 Angle : 0.574 11.501 30345 Z= 0.299 Chirality : 0.044 0.171 3485 Planarity : 0.005 0.051 3962 Dihedral : 8.293 88.795 3275 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 5.86 % Allowed : 21.85 % Favored : 72.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.15), residues: 2824 helix: 0.90 (0.15), residues: 1091 sheet: 0.25 (0.23), residues: 488 loop : -0.98 (0.17), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 89 TYR 0.023 0.001 TYR F 148 PHE 0.040 0.001 PHE F 409 HIS 0.012 0.001 HIS C 474 Details of bonding type rmsd covalent geometry : bond 0.00281 (22371) covalent geometry : angle 0.57441 (30345) hydrogen bonds : bond 0.04168 ( 968) hydrogen bonds : angle 4.91959 ( 2814) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5648 Ramachandran restraints generated. 2824 Oldfield, 0 Emsley, 2824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5648 Ramachandran restraints generated. 2824 Oldfield, 0 Emsley, 2824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 301 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 448 ILE cc_start: 0.6734 (OUTLIER) cc_final: 0.6466 (pp) REVERT: B 53 VAL cc_start: 0.6109 (OUTLIER) cc_final: 0.5769 (m) REVERT: B 60 MET cc_start: 0.6310 (OUTLIER) cc_final: 0.5713 (mmt) REVERT: B 277 LEU cc_start: 0.6205 (mm) cc_final: 0.5713 (mm) REVERT: B 300 ARG cc_start: 0.7899 (mmm-85) cc_final: 0.7664 (mtm180) REVERT: B 384 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7714 (tp) REVERT: C 118 LEU cc_start: 0.7972 (mt) cc_final: 0.7740 (mp) REVERT: C 125 GLU cc_start: 0.5027 (pm20) cc_final: 0.4778 (pm20) REVERT: C 190 ASN cc_start: 0.6842 (OUTLIER) cc_final: 0.6324 (p0) REVERT: C 210 GLU cc_start: 0.5851 (mm-30) cc_final: 0.5637 (pt0) REVERT: C 300 ARG cc_start: 0.7184 (OUTLIER) cc_final: 0.6148 (mtp85) REVERT: C 375 MET cc_start: 0.6874 (ttp) cc_final: 0.5990 (tpp) REVERT: D 10 MET cc_start: 0.7130 (mtm) cc_final: 0.6810 (mtp) REVERT: D 115 ARG cc_start: 0.6656 (ptp-110) cc_final: 0.5903 (ptp-170) REVERT: D 337 GLU cc_start: 0.7001 (OUTLIER) cc_final: 0.6103 (mp0) REVERT: D 345 ASP cc_start: 0.6641 (t0) cc_final: 0.6429 (t70) REVERT: D 351 SER cc_start: 0.6323 (m) cc_final: 0.5559 (t) REVERT: D 402 ARG cc_start: 0.6574 (OUTLIER) cc_final: 0.6106 (mtp180) REVERT: D 413 ASN cc_start: 0.7024 (p0) cc_final: 0.6659 (p0) REVERT: E 128 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7930 (mm) REVERT: E 133 GLU cc_start: 0.5356 (pm20) cc_final: 0.5139 (pm20) REVERT: E 199 TYR cc_start: 0.6105 (t80) cc_final: 0.5864 (t80) REVERT: E 204 ASP cc_start: 0.7413 (t70) cc_final: 0.6870 (m-30) REVERT: E 213 MET cc_start: 0.6915 (mtm) cc_final: 0.6658 (mtt) REVERT: E 256 ARG cc_start: 0.7531 (OUTLIER) cc_final: 0.7082 (mmt180) REVERT: E 315 ASP cc_start: 0.7096 (t0) cc_final: 0.6668 (t0) REVERT: E 357 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.6932 (pp20) REVERT: E 469 MET cc_start: 0.4908 (mtt) cc_final: 0.4672 (mtt) REVERT: F 5 ARG cc_start: 0.7059 (OUTLIER) cc_final: 0.6341 (mtm180) REVERT: F 38 ASN cc_start: 0.6432 (m-40) cc_final: 0.6220 (m110) REVERT: F 284 GLU cc_start: 0.7085 (pt0) cc_final: 0.6360 (mm-30) REVERT: F 334 LYS cc_start: 0.8129 (tmtm) cc_final: 0.7872 (tptp) REVERT: F 352 ARG cc_start: 0.6128 (OUTLIER) cc_final: 0.5680 (ptt180) REVERT: F 406 ILE cc_start: 0.7649 (mp) cc_final: 0.7428 (mp) REVERT: F 431 LYS cc_start: 0.7439 (OUTLIER) cc_final: 0.7142 (mppt) REVERT: F 438 LYS cc_start: 0.8297 (ttmt) cc_final: 0.7915 (tttm) outliers start: 136 outliers final: 62 residues processed: 384 average time/residue: 0.5042 time to fit residues: 223.2656 Evaluate side-chains 340 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 264 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 451 GLU Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 190 ASN Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 300 ARG Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 322 PHE Chi-restraints excluded: chain D residue 332 GLU Chi-restraints excluded: chain D residue 337 GLU Chi-restraints excluded: chain D residue 402 ARG Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 256 ARG Chi-restraints excluded: chain E residue 357 GLU Chi-restraints excluded: chain E residue 362 GLU Chi-restraints excluded: chain E residue 428 VAL Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain F residue 5 ARG Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain F residue 219 ASN Chi-restraints excluded: chain F residue 240 ARG Chi-restraints excluded: chain F residue 322 PHE Chi-restraints excluded: chain F residue 352 ARG Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 379 GLU Chi-restraints excluded: chain F residue 392 LEU Chi-restraints excluded: chain F residue 431 LYS Chi-restraints excluded: chain F residue 440 ILE Chi-restraints excluded: chain F residue 451 ASP Chi-restraints excluded: chain F residue 455 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 52 optimal weight: 9.9990 chunk 277 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 179 optimal weight: 0.9980 chunk 205 optimal weight: 8.9990 chunk 254 optimal weight: 4.9990 chunk 256 optimal weight: 8.9990 chunk 82 optimal weight: 0.9990 chunk 39 optimal weight: 7.9990 chunk 154 optimal weight: 8.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 GLN ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 467 ASN B 215 HIS ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 433 GLN D 179 HIS D 407 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.197317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.168030 restraints weight = 24565.418| |-----------------------------------------------------------------------------| r_work (start): 0.4274 rms_B_bonded: 2.11 r_work: 0.4149 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.4006 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.4006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.4495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 22371 Z= 0.184 Angle : 0.665 11.446 30345 Z= 0.344 Chirality : 0.047 0.214 3485 Planarity : 0.005 0.052 3962 Dihedral : 8.420 88.970 3274 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 6.42 % Allowed : 22.76 % Favored : 70.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.15), residues: 2824 helix: 0.62 (0.15), residues: 1090 sheet: 0.16 (0.23), residues: 474 loop : -1.09 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 171 TYR 0.019 0.002 TYR F 148 PHE 0.029 0.002 PHE F 409 HIS 0.009 0.001 HIS F 363 Details of bonding type rmsd covalent geometry : bond 0.00439 (22371) covalent geometry : angle 0.66535 (30345) hydrogen bonds : bond 0.05016 ( 968) hydrogen bonds : angle 5.02382 ( 2814) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5648 Ramachandran restraints generated. 2824 Oldfield, 0 Emsley, 2824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5648 Ramachandran restraints generated. 2824 Oldfield, 0 Emsley, 2824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 279 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ARG cc_start: 0.6205 (OUTLIER) cc_final: 0.5882 (mtm110) REVERT: A 132 ARG cc_start: 0.6856 (mtt-85) cc_final: 0.6598 (ptm-80) REVERT: A 278 ARG cc_start: 0.7017 (OUTLIER) cc_final: 0.5529 (mtm-85) REVERT: B 300 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.7778 (mtm180) REVERT: B 345 GLN cc_start: 0.6942 (OUTLIER) cc_final: 0.6573 (mt0) REVERT: B 384 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7661 (tp) REVERT: B 483 ASN cc_start: 0.7845 (m-40) cc_final: 0.7265 (t0) REVERT: C 118 LEU cc_start: 0.7996 (mt) cc_final: 0.7779 (mp) REVERT: C 190 ASN cc_start: 0.6907 (OUTLIER) cc_final: 0.6339 (p0) REVERT: C 210 GLU cc_start: 0.5766 (mm-30) cc_final: 0.5553 (pt0) REVERT: C 375 MET cc_start: 0.6920 (ttp) cc_final: 0.5988 (tpp) REVERT: C 392 LEU cc_start: 0.6232 (OUTLIER) cc_final: 0.5463 (tp) REVERT: D 10 MET cc_start: 0.7235 (mtm) cc_final: 0.6930 (mtp) REVERT: D 115 ARG cc_start: 0.6592 (ptp-110) cc_final: 0.5948 (ptp-170) REVERT: D 190 GLU cc_start: 0.4028 (OUTLIER) cc_final: 0.3810 (tp30) REVERT: D 271 MET cc_start: 0.7750 (mtp) cc_final: 0.7487 (mtm) REVERT: D 337 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.5906 (mp0) REVERT: D 351 SER cc_start: 0.6339 (m) cc_final: 0.5560 (t) REVERT: D 402 ARG cc_start: 0.6450 (OUTLIER) cc_final: 0.5971 (mtp180) REVERT: D 413 ASN cc_start: 0.7290 (p0) cc_final: 0.6812 (p0) REVERT: D 437 PHE cc_start: 0.7098 (OUTLIER) cc_final: 0.6753 (m-10) REVERT: E 128 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7927 (mm) REVERT: E 204 ASP cc_start: 0.7439 (t70) cc_final: 0.6940 (m-30) REVERT: E 213 MET cc_start: 0.6899 (mtm) cc_final: 0.6623 (mtt) REVERT: E 256 ARG cc_start: 0.7678 (OUTLIER) cc_final: 0.7263 (mmt180) REVERT: E 315 ASP cc_start: 0.7275 (t70) cc_final: 0.6848 (t0) REVERT: E 334 LYS cc_start: 0.7407 (mmtt) cc_final: 0.7038 (ttpt) REVERT: F 5 ARG cc_start: 0.7218 (OUTLIER) cc_final: 0.6468 (mtm180) REVERT: F 226 MET cc_start: 0.7062 (OUTLIER) cc_final: 0.6705 (mtm) REVERT: F 284 GLU cc_start: 0.7127 (pt0) cc_final: 0.6482 (mm-30) REVERT: F 334 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7882 (tptp) REVERT: F 338 MET cc_start: 0.7792 (tpp) cc_final: 0.7267 (tpt) REVERT: F 340 ILE cc_start: 0.7202 (OUTLIER) cc_final: 0.6532 (mp) REVERT: F 352 ARG cc_start: 0.6203 (OUTLIER) cc_final: 0.5810 (ptt180) REVERT: F 406 ILE cc_start: 0.7727 (OUTLIER) cc_final: 0.7525 (mp) REVERT: F 431 LYS cc_start: 0.7326 (OUTLIER) cc_final: 0.7010 (mppt) REVERT: F 438 LYS cc_start: 0.8276 (ttmt) cc_final: 0.8047 (ttmt) outliers start: 149 outliers final: 78 residues processed: 381 average time/residue: 0.5136 time to fit residues: 225.7741 Evaluate side-chains 355 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 257 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ARG Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 278 ARG Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 300 ARG Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 345 GLN Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 451 GLU Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 190 ASN Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 322 PHE Chi-restraints excluded: chain D residue 332 GLU Chi-restraints excluded: chain D residue 337 GLU Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 402 ARG Chi-restraints excluded: chain D residue 437 PHE Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 256 ARG Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 362 GLU Chi-restraints excluded: chain E residue 396 ASP Chi-restraints excluded: chain E residue 428 VAL Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain F residue 5 ARG Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 219 ASN Chi-restraints excluded: chain F residue 226 MET Chi-restraints excluded: chain F residue 240 ARG Chi-restraints excluded: chain F residue 322 PHE Chi-restraints excluded: chain F residue 334 LYS Chi-restraints excluded: chain F residue 340 ILE Chi-restraints excluded: chain F residue 352 ARG Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 379 GLU Chi-restraints excluded: chain F residue 392 LEU Chi-restraints excluded: chain F residue 406 ILE Chi-restraints excluded: chain F residue 431 LYS Chi-restraints excluded: chain F residue 451 ASP Chi-restraints excluded: chain F residue 455 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 126 optimal weight: 9.9990 chunk 177 optimal weight: 5.9990 chunk 174 optimal weight: 9.9990 chunk 134 optimal weight: 0.6980 chunk 26 optimal weight: 6.9990 chunk 71 optimal weight: 7.9990 chunk 114 optimal weight: 1.9990 chunk 205 optimal weight: 6.9990 chunk 170 optimal weight: 3.9990 chunk 218 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 GLN ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 467 ASN B 322 GLN C 172 GLN ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 HIS D 173 HIS F 38 ASN F 259 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.199080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.169725 restraints weight = 24485.502| |-----------------------------------------------------------------------------| r_work (start): 0.4301 rms_B_bonded: 2.15 r_work: 0.4185 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.4046 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.4046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.4685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 22371 Z= 0.146 Angle : 0.630 12.289 30345 Z= 0.324 Chirality : 0.045 0.193 3485 Planarity : 0.005 0.052 3962 Dihedral : 8.186 86.071 3273 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 5.65 % Allowed : 24.09 % Favored : 70.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.15), residues: 2824 helix: 0.72 (0.15), residues: 1091 sheet: 0.19 (0.23), residues: 472 loop : -1.07 (0.17), residues: 1261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 171 TYR 0.016 0.002 TYR E 27 PHE 0.033 0.002 PHE A 494 HIS 0.015 0.001 HIS C 474 Details of bonding type rmsd covalent geometry : bond 0.00341 (22371) covalent geometry : angle 0.63038 (30345) hydrogen bonds : bond 0.04442 ( 968) hydrogen bonds : angle 4.92628 ( 2814) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5648 Ramachandran restraints generated. 2824 Oldfield, 0 Emsley, 2824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5648 Ramachandran restraints generated. 2824 Oldfield, 0 Emsley, 2824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 276 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ARG cc_start: 0.6174 (OUTLIER) cc_final: 0.5830 (mtm110) REVERT: A 132 ARG cc_start: 0.6798 (mtt-85) cc_final: 0.6568 (ptm-80) REVERT: A 278 ARG cc_start: 0.6964 (OUTLIER) cc_final: 0.6690 (mmt-90) REVERT: B 210 GLU cc_start: 0.7548 (tm-30) cc_final: 0.7022 (mm-30) REVERT: B 300 ARG cc_start: 0.7950 (mmm-85) cc_final: 0.7702 (mtm180) REVERT: B 345 GLN cc_start: 0.6940 (OUTLIER) cc_final: 0.6540 (mt0) REVERT: B 384 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7664 (tp) REVERT: B 403 ASP cc_start: 0.7459 (t70) cc_final: 0.6918 (t0) REVERT: C 118 LEU cc_start: 0.7996 (mt) cc_final: 0.7776 (mp) REVERT: C 129 ILE cc_start: 0.5839 (OUTLIER) cc_final: 0.5633 (mt) REVERT: C 137 MET cc_start: 0.4298 (mtt) cc_final: 0.4091 (mpp) REVERT: C 190 ASN cc_start: 0.6952 (OUTLIER) cc_final: 0.6426 (p0) REVERT: C 210 GLU cc_start: 0.5757 (mm-30) cc_final: 0.5525 (pt0) REVERT: C 357 ILE cc_start: 0.6084 (OUTLIER) cc_final: 0.5841 (pp) REVERT: C 375 MET cc_start: 0.6971 (ttp) cc_final: 0.6054 (tpp) REVERT: C 392 LEU cc_start: 0.6284 (OUTLIER) cc_final: 0.5501 (tp) REVERT: C 465 ASP cc_start: 0.6003 (t0) cc_final: 0.5637 (t0) REVERT: D 10 MET cc_start: 0.7225 (mtm) cc_final: 0.6905 (mtp) REVERT: D 115 ARG cc_start: 0.6614 (ptp-110) cc_final: 0.5874 (ptp-170) REVERT: D 337 GLU cc_start: 0.7069 (OUTLIER) cc_final: 0.6276 (mp0) REVERT: D 351 SER cc_start: 0.6246 (m) cc_final: 0.5435 (t) REVERT: D 402 ARG cc_start: 0.6553 (OUTLIER) cc_final: 0.6071 (mtp180) REVERT: D 413 ASN cc_start: 0.7321 (p0) cc_final: 0.6850 (p0) REVERT: D 437 PHE cc_start: 0.7100 (OUTLIER) cc_final: 0.6770 (m-10) REVERT: D 459 ILE cc_start: 0.6432 (OUTLIER) cc_final: 0.6084 (tt) REVERT: E 128 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7835 (mm) REVERT: E 204 ASP cc_start: 0.7402 (t70) cc_final: 0.6869 (m-30) REVERT: E 213 MET cc_start: 0.6711 (mtm) cc_final: 0.6491 (mtt) REVERT: E 256 ARG cc_start: 0.7580 (OUTLIER) cc_final: 0.7165 (mmt180) REVERT: E 315 ASP cc_start: 0.7068 (t70) cc_final: 0.6706 (t0) REVERT: E 334 LYS cc_start: 0.7376 (mmtt) cc_final: 0.6932 (ttpt) REVERT: E 469 MET cc_start: 0.5001 (mtt) cc_final: 0.4744 (mtt) REVERT: F 5 ARG cc_start: 0.7100 (OUTLIER) cc_final: 0.6323 (mtm180) REVERT: F 226 MET cc_start: 0.7043 (OUTLIER) cc_final: 0.6667 (mtm) REVERT: F 284 GLU cc_start: 0.7130 (pt0) cc_final: 0.6410 (mm-30) REVERT: F 338 MET cc_start: 0.7908 (tpp) cc_final: 0.7551 (tpt) REVERT: F 352 ARG cc_start: 0.6183 (OUTLIER) cc_final: 0.5833 (ptt180) REVERT: F 431 LYS cc_start: 0.7242 (OUTLIER) cc_final: 0.6996 (mppt) REVERT: F 438 LYS cc_start: 0.8208 (ttmt) cc_final: 0.7956 (ttmt) outliers start: 131 outliers final: 74 residues processed: 363 average time/residue: 0.6119 time to fit residues: 255.2571 Evaluate side-chains 349 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 257 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ARG Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 278 ARG Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 345 GLN Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 451 GLU Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 190 ASN Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 461 TYR Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 322 PHE Chi-restraints excluded: chain D residue 332 GLU Chi-restraints excluded: chain D residue 337 GLU Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain D residue 402 ARG Chi-restraints excluded: chain D residue 437 PHE Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 256 ARG Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 362 GLU Chi-restraints excluded: chain E residue 428 VAL Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain F residue 5 ARG Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 219 ASN Chi-restraints excluded: chain F residue 226 MET Chi-restraints excluded: chain F residue 240 ARG Chi-restraints excluded: chain F residue 322 PHE Chi-restraints excluded: chain F residue 352 ARG Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 379 GLU Chi-restraints excluded: chain F residue 392 LEU Chi-restraints excluded: chain F residue 431 LYS Chi-restraints excluded: chain F residue 451 ASP Chi-restraints excluded: chain F residue 455 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 215 optimal weight: 0.9980 chunk 124 optimal weight: 0.6980 chunk 276 optimal weight: 6.9990 chunk 34 optimal weight: 0.7980 chunk 201 optimal weight: 0.8980 chunk 80 optimal weight: 7.9990 chunk 140 optimal weight: 9.9990 chunk 122 optimal weight: 8.9990 chunk 203 optimal weight: 9.9990 chunk 118 optimal weight: 2.9990 chunk 260 optimal weight: 10.0000 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 GLN ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 ASN ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 324 HIS E 413 ASN F 259 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.201021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.171862 restraints weight = 24243.012| |-----------------------------------------------------------------------------| r_work (start): 0.4322 rms_B_bonded: 2.15 r_work: 0.4204 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.4063 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.4063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6901 moved from start: 0.4799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 22371 Z= 0.126 Angle : 0.611 13.127 30345 Z= 0.314 Chirality : 0.045 0.207 3485 Planarity : 0.005 0.051 3962 Dihedral : 7.921 81.429 3272 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 4.91 % Allowed : 25.30 % Favored : 69.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.14 (0.15), residues: 2824 helix: 0.85 (0.15), residues: 1092 sheet: 0.21 (0.23), residues: 469 loop : -1.03 (0.17), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 171 TYR 0.015 0.001 TYR C 461 PHE 0.030 0.001 PHE A 494 HIS 0.008 0.001 HIS C 470 Details of bonding type rmsd covalent geometry : bond 0.00287 (22371) covalent geometry : angle 0.61107 (30345) hydrogen bonds : bond 0.04084 ( 968) hydrogen bonds : angle 4.84679 ( 2814) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5648 Ramachandran restraints generated. 2824 Oldfield, 0 Emsley, 2824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5648 Ramachandran restraints generated. 2824 Oldfield, 0 Emsley, 2824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 271 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 ARG cc_start: 0.6796 (mtt-85) cc_final: 0.6570 (ptm-80) REVERT: A 278 ARG cc_start: 0.6939 (OUTLIER) cc_final: 0.6656 (mmt-90) REVERT: B 60 MET cc_start: 0.6365 (OUTLIER) cc_final: 0.5786 (mmt) REVERT: B 300 ARG cc_start: 0.7933 (mmm-85) cc_final: 0.7698 (mtm180) REVERT: B 403 ASP cc_start: 0.7465 (t70) cc_final: 0.6943 (t0) REVERT: B 483 ASN cc_start: 0.7837 (m-40) cc_final: 0.7266 (t0) REVERT: C 118 LEU cc_start: 0.8004 (mt) cc_final: 0.7720 (mp) REVERT: C 190 ASN cc_start: 0.6988 (OUTLIER) cc_final: 0.6456 (p0) REVERT: C 210 GLU cc_start: 0.5807 (mm-30) cc_final: 0.5592 (pt0) REVERT: C 375 MET cc_start: 0.6957 (ttp) cc_final: 0.6063 (tpp) REVERT: C 392 LEU cc_start: 0.6274 (OUTLIER) cc_final: 0.5519 (tp) REVERT: D 10 MET cc_start: 0.7174 (mtm) cc_final: 0.6864 (mtp) REVERT: D 45 ASP cc_start: 0.6478 (p0) cc_final: 0.5710 (t0) REVERT: D 115 ARG cc_start: 0.6603 (ptp-110) cc_final: 0.5861 (ptp-170) REVERT: D 337 GLU cc_start: 0.7025 (OUTLIER) cc_final: 0.6249 (mp0) REVERT: D 351 SER cc_start: 0.6260 (m) cc_final: 0.5428 (t) REVERT: D 387 LEU cc_start: 0.7266 (mp) cc_final: 0.6811 (pp) REVERT: D 402 ARG cc_start: 0.6424 (OUTLIER) cc_final: 0.5963 (mtp180) REVERT: D 413 ASN cc_start: 0.7320 (p0) cc_final: 0.6839 (p0) REVERT: D 437 PHE cc_start: 0.7057 (OUTLIER) cc_final: 0.6744 (m-10) REVERT: D 459 ILE cc_start: 0.6330 (OUTLIER) cc_final: 0.6017 (tt) REVERT: E 3 ARG cc_start: 0.6878 (OUTLIER) cc_final: 0.6569 (mmm-85) REVERT: E 204 ASP cc_start: 0.7435 (t70) cc_final: 0.6945 (m-30) REVERT: E 213 MET cc_start: 0.6631 (mtm) cc_final: 0.6429 (mtt) REVERT: E 256 ARG cc_start: 0.7557 (OUTLIER) cc_final: 0.7112 (mmt180) REVERT: E 315 ASP cc_start: 0.6990 (t70) cc_final: 0.6601 (t0) REVERT: E 324 HIS cc_start: 0.6963 (m-70) cc_final: 0.6755 (m-70) REVERT: E 413 ASN cc_start: 0.7834 (OUTLIER) cc_final: 0.7477 (p0) REVERT: E 423 GLN cc_start: 0.6427 (OUTLIER) cc_final: 0.6157 (pm20) REVERT: E 469 MET cc_start: 0.4961 (mtt) cc_final: 0.4735 (mtt) REVERT: F 5 ARG cc_start: 0.7077 (OUTLIER) cc_final: 0.6306 (mtm180) REVERT: F 218 MET cc_start: 0.7305 (mtt) cc_final: 0.6088 (mtt) REVERT: F 226 MET cc_start: 0.7031 (OUTLIER) cc_final: 0.6819 (mmm) REVERT: F 284 GLU cc_start: 0.7036 (pt0) cc_final: 0.6344 (mm-30) REVERT: F 338 MET cc_start: 0.7796 (tpp) cc_final: 0.7536 (tpt) REVERT: F 352 ARG cc_start: 0.6197 (OUTLIER) cc_final: 0.5846 (ptt180) REVERT: F 438 LYS cc_start: 0.8171 (ttmt) cc_final: 0.7923 (ttmt) outliers start: 114 outliers final: 63 residues processed: 349 average time/residue: 0.5942 time to fit residues: 240.4657 Evaluate side-chains 331 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 253 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 278 ARG Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 451 GLU Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 190 ASN Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 322 PHE Chi-restraints excluded: chain D residue 332 GLU Chi-restraints excluded: chain D residue 337 GLU Chi-restraints excluded: chain D residue 402 ARG Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 437 PHE Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain E residue 3 ARG Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 256 ARG Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 362 GLU Chi-restraints excluded: chain E residue 413 ASN Chi-restraints excluded: chain E residue 423 GLN Chi-restraints excluded: chain E residue 428 VAL Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain F residue 5 ARG Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 219 ASN Chi-restraints excluded: chain F residue 226 MET Chi-restraints excluded: chain F residue 240 ARG Chi-restraints excluded: chain F residue 322 PHE Chi-restraints excluded: chain F residue 352 ARG Chi-restraints excluded: chain F residue 379 GLU Chi-restraints excluded: chain F residue 392 LEU Chi-restraints excluded: chain F residue 451 ASP Chi-restraints excluded: chain F residue 455 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 10 optimal weight: 9.9990 chunk 199 optimal weight: 7.9990 chunk 4 optimal weight: 0.9980 chunk 161 optimal weight: 3.9990 chunk 189 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 44 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 113 optimal weight: 2.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 HIS ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 HIS F 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.200612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.171127 restraints weight = 24353.176| |-----------------------------------------------------------------------------| r_work (start): 0.4313 rms_B_bonded: 2.20 r_work: 0.4198 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.4057 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.4057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.4925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 22371 Z= 0.135 Angle : 0.619 13.994 30345 Z= 0.319 Chirality : 0.045 0.218 3485 Planarity : 0.005 0.050 3962 Dihedral : 7.782 81.306 3272 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 4.35 % Allowed : 25.91 % Favored : 69.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.15), residues: 2824 helix: 0.87 (0.15), residues: 1090 sheet: 0.15 (0.23), residues: 486 loop : -1.01 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 171 TYR 0.023 0.001 TYR E 27 PHE 0.028 0.002 PHE A 494 HIS 0.017 0.001 HIS C 474 Details of bonding type rmsd covalent geometry : bond 0.00312 (22371) covalent geometry : angle 0.61921 (30345) hydrogen bonds : bond 0.04160 ( 968) hydrogen bonds : angle 4.83022 ( 2814) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5648 Ramachandran restraints generated. 2824 Oldfield, 0 Emsley, 2824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5648 Ramachandran restraints generated. 2824 Oldfield, 0 Emsley, 2824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 266 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 ARG cc_start: 0.6817 (mtt-85) cc_final: 0.6582 (ptm-80) REVERT: A 278 ARG cc_start: 0.6925 (OUTLIER) cc_final: 0.6582 (mmt-90) REVERT: A 320 GLU cc_start: 0.6285 (tp30) cc_final: 0.6077 (tm-30) REVERT: B 60 MET cc_start: 0.6412 (OUTLIER) cc_final: 0.5826 (mmt) REVERT: B 130 GLU cc_start: 0.6726 (mm-30) cc_final: 0.5948 (pp20) REVERT: B 277 LEU cc_start: 0.6299 (mm) cc_final: 0.5732 (mm) REVERT: B 300 ARG cc_start: 0.7918 (mmm-85) cc_final: 0.7681 (mtm180) REVERT: B 345 GLN cc_start: 0.6932 (OUTLIER) cc_final: 0.6582 (mt0) REVERT: B 384 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7654 (tp) REVERT: B 403 ASP cc_start: 0.7477 (t70) cc_final: 0.6995 (t0) REVERT: B 483 ASN cc_start: 0.7867 (m-40) cc_final: 0.7297 (t0) REVERT: C 118 LEU cc_start: 0.7962 (mt) cc_final: 0.7662 (mp) REVERT: C 210 GLU cc_start: 0.5780 (mm-30) cc_final: 0.5558 (pt0) REVERT: C 251 TYR cc_start: 0.6504 (m-10) cc_final: 0.6028 (m-80) REVERT: C 375 MET cc_start: 0.6950 (ttp) cc_final: 0.6077 (tpp) REVERT: C 392 LEU cc_start: 0.6290 (OUTLIER) cc_final: 0.5582 (tm) REVERT: C 465 ASP cc_start: 0.5968 (t0) cc_final: 0.5618 (t0) REVERT: D 10 MET cc_start: 0.7184 (mtm) cc_final: 0.6858 (mtp) REVERT: D 45 ASP cc_start: 0.6474 (p0) cc_final: 0.5663 (t0) REVERT: D 115 ARG cc_start: 0.6612 (ptp-110) cc_final: 0.5870 (ptp-170) REVERT: D 254 ILE cc_start: 0.5832 (OUTLIER) cc_final: 0.5523 (pp) REVERT: D 337 GLU cc_start: 0.7000 (OUTLIER) cc_final: 0.6142 (mp0) REVERT: D 351 SER cc_start: 0.6273 (m) cc_final: 0.5453 (t) REVERT: D 387 LEU cc_start: 0.7303 (mp) cc_final: 0.6738 (pp) REVERT: D 402 ARG cc_start: 0.6398 (OUTLIER) cc_final: 0.5947 (mtp180) REVERT: D 413 ASN cc_start: 0.7336 (p0) cc_final: 0.6850 (p0) REVERT: D 437 PHE cc_start: 0.7014 (OUTLIER) cc_final: 0.6714 (m-10) REVERT: D 459 ILE cc_start: 0.6377 (OUTLIER) cc_final: 0.6061 (tt) REVERT: E 3 ARG cc_start: 0.6854 (OUTLIER) cc_final: 0.6514 (mmm-85) REVERT: E 204 ASP cc_start: 0.7421 (t70) cc_final: 0.6924 (m-30) REVERT: E 213 MET cc_start: 0.6688 (mtm) cc_final: 0.6469 (mtt) REVERT: E 256 ARG cc_start: 0.7544 (OUTLIER) cc_final: 0.7083 (mmt180) REVERT: E 315 ASP cc_start: 0.7023 (t70) cc_final: 0.6616 (t0) REVERT: E 324 HIS cc_start: 0.7001 (m-70) cc_final: 0.6771 (m-70) REVERT: E 469 MET cc_start: 0.4916 (mtt) cc_final: 0.4715 (mtt) REVERT: F 5 ARG cc_start: 0.7057 (OUTLIER) cc_final: 0.6267 (mtm180) REVERT: F 213 MET cc_start: 0.6956 (mtt) cc_final: 0.6690 (mtt) REVERT: F 218 MET cc_start: 0.7346 (mtt) cc_final: 0.6150 (mtt) REVERT: F 284 GLU cc_start: 0.7035 (pt0) cc_final: 0.6292 (mm-30) REVERT: F 338 MET cc_start: 0.7799 (tpp) cc_final: 0.7533 (tpt) REVERT: F 352 ARG cc_start: 0.6230 (OUTLIER) cc_final: 0.5906 (ptt180) REVERT: F 438 LYS cc_start: 0.8227 (ttmt) cc_final: 0.7982 (ttmt) outliers start: 101 outliers final: 69 residues processed: 338 average time/residue: 0.6591 time to fit residues: 256.6569 Evaluate side-chains 340 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 257 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 278 ARG Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 345 GLN Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 451 GLU Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 474 HIS Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 322 PHE Chi-restraints excluded: chain D residue 332 GLU Chi-restraints excluded: chain D residue 337 GLU Chi-restraints excluded: chain D residue 402 ARG Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 437 PHE Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain E residue 3 ARG Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 256 ARG Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 362 GLU Chi-restraints excluded: chain E residue 428 VAL Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain F residue 5 ARG Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 219 ASN Chi-restraints excluded: chain F residue 240 ARG Chi-restraints excluded: chain F residue 322 PHE Chi-restraints excluded: chain F residue 352 ARG Chi-restraints excluded: chain F residue 379 GLU Chi-restraints excluded: chain F residue 451 ASP Chi-restraints excluded: chain F residue 455 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 37 optimal weight: 5.9990 chunk 172 optimal weight: 0.2980 chunk 124 optimal weight: 0.0970 chunk 270 optimal weight: 0.5980 chunk 207 optimal weight: 8.9990 chunk 243 optimal weight: 0.9990 chunk 210 optimal weight: 0.9990 chunk 187 optimal weight: 8.9990 chunk 262 optimal weight: 6.9990 chunk 156 optimal weight: 7.9990 chunk 52 optimal weight: 5.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 333 ASN B 426 GLN ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 HIS F 259 GLN F 375 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4636 r_free = 0.4636 target = 0.204520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.175273 restraints weight = 24098.948| |-----------------------------------------------------------------------------| r_work (start): 0.4354 rms_B_bonded: 2.20 r_work: 0.4240 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.4101 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.4101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6822 moved from start: 0.5046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 22371 Z= 0.115 Angle : 0.596 14.332 30345 Z= 0.307 Chirality : 0.044 0.204 3485 Planarity : 0.005 0.053 3962 Dihedral : 7.395 81.117 3272 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.59 % Allowed : 27.76 % Favored : 69.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.16), residues: 2824 helix: 1.08 (0.16), residues: 1091 sheet: 0.32 (0.24), residues: 463 loop : -0.88 (0.17), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 89 TYR 0.022 0.001 TYR E 27 PHE 0.026 0.001 PHE A 494 HIS 0.036 0.001 HIS C 474 Details of bonding type rmsd covalent geometry : bond 0.00251 (22371) covalent geometry : angle 0.59642 (30345) hydrogen bonds : bond 0.03630 ( 968) hydrogen bonds : angle 4.70427 ( 2814) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5648 Ramachandran restraints generated. 2824 Oldfield, 0 Emsley, 2824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5648 Ramachandran restraints generated. 2824 Oldfield, 0 Emsley, 2824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 272 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 ARG cc_start: 0.6818 (mtt-85) cc_final: 0.6555 (ptm-80) REVERT: A 278 ARG cc_start: 0.6887 (OUTLIER) cc_final: 0.5278 (mtm-85) REVERT: A 320 GLU cc_start: 0.6297 (tp30) cc_final: 0.6077 (tm-30) REVERT: B 60 MET cc_start: 0.6340 (OUTLIER) cc_final: 0.5859 (mmt) REVERT: B 130 GLU cc_start: 0.6626 (mm-30) cc_final: 0.5922 (pp20) REVERT: B 245 MET cc_start: 0.4147 (ptp) cc_final: 0.3937 (pmm) REVERT: B 300 ARG cc_start: 0.7837 (mmm-85) cc_final: 0.7623 (mtm180) REVERT: B 384 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7712 (tp) REVERT: B 403 ASP cc_start: 0.7456 (t70) cc_final: 0.7025 (t0) REVERT: B 483 ASN cc_start: 0.7814 (m-40) cc_final: 0.7259 (t0) REVERT: C 118 LEU cc_start: 0.7885 (mt) cc_final: 0.7547 (mp) REVERT: C 125 GLU cc_start: 0.5424 (pm20) cc_final: 0.4526 (pm20) REVERT: C 210 GLU cc_start: 0.5680 (mm-30) cc_final: 0.5455 (pt0) REVERT: C 251 TYR cc_start: 0.6503 (m-10) cc_final: 0.6119 (m-80) REVERT: C 375 MET cc_start: 0.6921 (ttp) cc_final: 0.6063 (tpp) REVERT: C 392 LEU cc_start: 0.6313 (OUTLIER) cc_final: 0.5638 (tm) REVERT: D 10 MET cc_start: 0.7082 (mtm) cc_final: 0.6793 (mtp) REVERT: D 45 ASP cc_start: 0.6232 (p0) cc_final: 0.5586 (t0) REVERT: D 115 ARG cc_start: 0.6546 (ptp-110) cc_final: 0.5815 (ptp-170) REVERT: D 254 ILE cc_start: 0.5839 (OUTLIER) cc_final: 0.5498 (pp) REVERT: D 313 TYR cc_start: 0.6744 (m-80) cc_final: 0.6516 (m-80) REVERT: D 337 GLU cc_start: 0.6913 (OUTLIER) cc_final: 0.6085 (mp0) REVERT: D 402 ARG cc_start: 0.6494 (OUTLIER) cc_final: 0.6058 (mtp180) REVERT: D 413 ASN cc_start: 0.7229 (p0) cc_final: 0.6784 (p0) REVERT: D 437 PHE cc_start: 0.6873 (OUTLIER) cc_final: 0.6631 (m-10) REVERT: D 459 ILE cc_start: 0.6262 (OUTLIER) cc_final: 0.5976 (tt) REVERT: E 3 ARG cc_start: 0.6843 (ptp-110) cc_final: 0.6474 (mmt90) REVERT: E 204 ASP cc_start: 0.7359 (t70) cc_final: 0.6827 (m-30) REVERT: E 256 ARG cc_start: 0.7480 (OUTLIER) cc_final: 0.7149 (mmt180) REVERT: E 315 ASP cc_start: 0.6951 (t70) cc_final: 0.6570 (t0) REVERT: E 324 HIS cc_start: 0.6948 (m-70) cc_final: 0.6730 (m-70) REVERT: E 413 ASN cc_start: 0.7730 (p0) cc_final: 0.7395 (p0) REVERT: F 5 ARG cc_start: 0.7000 (OUTLIER) cc_final: 0.6271 (mtm180) REVERT: F 13 VAL cc_start: 0.7874 (t) cc_final: 0.7604 (m) REVERT: F 218 MET cc_start: 0.7211 (mtt) cc_final: 0.6124 (mtt) REVERT: F 284 GLU cc_start: 0.6864 (pt0) cc_final: 0.6081 (mm-30) REVERT: F 352 ARG cc_start: 0.6145 (OUTLIER) cc_final: 0.5859 (ptt180) REVERT: F 438 LYS cc_start: 0.8233 (ttmt) cc_final: 0.8002 (ttmt) outliers start: 60 outliers final: 33 residues processed: 312 average time/residue: 0.6522 time to fit residues: 233.5591 Evaluate side-chains 297 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 252 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 278 ARG Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 322 PHE Chi-restraints excluded: chain D residue 332 GLU Chi-restraints excluded: chain D residue 337 GLU Chi-restraints excluded: chain D residue 402 ARG Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 437 PHE Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 256 ARG Chi-restraints excluded: chain E residue 428 VAL Chi-restraints excluded: chain F residue 5 ARG Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 322 PHE Chi-restraints excluded: chain F residue 352 ARG Chi-restraints excluded: chain F residue 455 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 121 optimal weight: 10.0000 chunk 179 optimal weight: 4.9990 chunk 144 optimal weight: 0.0870 chunk 239 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 112 optimal weight: 0.5980 chunk 223 optimal weight: 0.0570 chunk 137 optimal weight: 10.0000 chunk 90 optimal weight: 2.9990 chunk 27 optimal weight: 9.9990 chunk 252 optimal weight: 8.9990 overall best weight: 1.3480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 ASN C 185 ASN ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.202629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.173342 restraints weight = 24177.698| |-----------------------------------------------------------------------------| r_work (start): 0.4340 rms_B_bonded: 2.20 r_work: 0.4228 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.4090 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.4090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6854 moved from start: 0.5114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 22371 Z= 0.125 Angle : 0.613 14.742 30345 Z= 0.312 Chirality : 0.045 0.202 3485 Planarity : 0.005 0.051 3962 Dihedral : 7.269 81.111 3268 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.54 % Allowed : 28.15 % Favored : 69.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.16), residues: 2824 helix: 1.03 (0.16), residues: 1093 sheet: 0.24 (0.24), residues: 468 loop : -0.89 (0.17), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 89 TYR 0.012 0.001 TYR F 148 PHE 0.029 0.001 PHE B 395 HIS 0.008 0.001 HIS C 470 Details of bonding type rmsd covalent geometry : bond 0.00284 (22371) covalent geometry : angle 0.61273 (30345) hydrogen bonds : bond 0.03844 ( 968) hydrogen bonds : angle 4.70768 ( 2814) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7377.24 seconds wall clock time: 126 minutes 17.96 seconds (7577.96 seconds total)