Starting phenix.real_space_refine on Thu Jun 19 00:26:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8spx_40689/06_2025/8spx_40689.cif Found real_map, /net/cci-nas-00/data/ceres_data/8spx_40689/06_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_40689/06_2025/8spx_40689.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8spx_40689/06_2025/8spx_40689.map" model { file = "/net/cci-nas-00/data/ceres_data/8spx_40689/06_2025/8spx_40689.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8spx_40689/06_2025/8spx_40689.cif" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.029 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 14.65, per 1000 atoms: 0.67 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: 6.40 Conformation dependent library (CDL) restraints added in 3.1 seconds 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: 3.07 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: 8.60 Time building geometry restraints manager: 7.54 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 499 or resid 600 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: 0.820 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: 0.030 Extract box with map and model: 1.020 Check model and map are aligned: 0.190 Set scattering table: 0.200 Process input model: 56.450 Find NCS groups from input model: 1.460 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:15.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.610 ------------------------------------------------------------------------------- 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 : 4.76 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (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 HIS 0.009 0.001 HIS F 363 PHE 0.021 0.002 PHE A 236 TYR 0.020 0.002 TYR A 248 ARG 0.004 0.001 ARG C 206 Details of bonding type rmsd hydrogen bonds : bond 0.17961 ( 968) hydrogen bonds : angle 7.45694 ( 2814) covalent geometry : bond 0.00363 (22371) covalent geometry : angle 0.63479 (30345) *********************** 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 : 2.586 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: 0.6047 (tpp) REVERT: E 235 MET cc_start: 0.6801 (mtt) cc_final: 0.6508 (mtp) REVERT: F 240 ARG cc_start: 0.6194 (OUTLIER) cc_final: 0.5963 (ptt90) outliers start: 47 outliers final: 13 residues processed: 598 average time/residue: 1.3318 time to fit residues: 906.3817 Evaluate side-chains 344 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 330 time to evaluate : 2.498 ------------------------------------------------------------------------------- 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 252 ASP 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 238 optimal weight: 0.6980 chunk 213 optimal weight: 6.9990 chunk 118 optimal weight: 1.9990 chunk 73 optimal weight: 8.9990 chunk 144 optimal weight: 0.0570 chunk 114 optimal weight: 4.9990 chunk 221 optimal weight: 0.3980 chunk 85 optimal weight: 10.0000 chunk 134 optimal weight: 10.0000 chunk 164 optimal weight: 8.9990 chunk 256 optimal weight: 0.7980 overall best weight: 0.7900 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 GLN C 426 GLN C 433 GLN C 474 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 F 243 GLN F 245 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4698 r_free = 0.4698 target = 0.211619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.182511 restraints weight = 23971.406| |-----------------------------------------------------------------------------| r_work (start): 0.4425 rms_B_bonded: 2.18 r_work: 0.4309 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.4309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6597 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22371 Z= 0.137 Angle : 0.620 11.947 30345 Z= 0.325 Chirality : 0.045 0.207 3485 Planarity : 0.005 0.053 3962 Dihedral : 9.057 88.052 3285 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.97 % Allowed : 17.54 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.15), residues: 2824 helix: 0.89 (0.15), residues: 1080 sheet: 0.37 (0.23), residues: 475 loop : -0.52 (0.17), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 470 PHE 0.026 0.002 PHE D 437 TYR 0.021 0.002 TYR F 199 ARG 0.008 0.001 ARG B 140 Details of bonding type rmsd hydrogen bonds : bond 0.04708 ( 968) hydrogen bonds : angle 5.43819 ( 2814) covalent geometry : bond 0.00283 (22371) covalent geometry : angle 0.61982 (30345) *********************** 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 458 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 366 time to evaluate : 2.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 469 GLN cc_start: 0.7541 (tp40) cc_final: 0.7268 (tp-100) REVERT: B 300 ARG cc_start: 0.7764 (mmm-85) cc_final: 0.7471 (mtm180) REVERT: B 377 LYS cc_start: 0.7473 (tttp) cc_final: 0.7269 (mttt) REVERT: C 62 MET cc_start: 0.6113 (ttp) cc_final: 0.5831 (ptm) REVERT: C 190 ASN cc_start: 0.6512 (OUTLIER) cc_final: 0.5901 (p0) REVERT: C 210 GLU cc_start: 0.5779 (mm-30) cc_final: 0.5473 (pt0) REVERT: C 300 ARG cc_start: 0.7218 (OUTLIER) cc_final: 0.6174 (mtp85) REVERT: C 354 ARG cc_start: 0.6956 (mtt90) cc_final: 0.6491 (mmm160) REVERT: C 375 MET cc_start: 0.6918 (ttp) cc_final: 0.6106 (tpp) REVERT: C 470 HIS cc_start: 0.7517 (p-80) cc_final: 0.7275 (p-80) REVERT: D 10 MET cc_start: 0.6541 (mtm) cc_final: 0.6250 (mtp) REVERT: D 44 ILE cc_start: 0.6633 (OUTLIER) cc_final: 0.6167 (mt) REVERT: D 271 MET cc_start: 0.7706 (OUTLIER) cc_final: 0.7342 (mtm) REVERT: D 345 ASP cc_start: 0.6518 (t0) cc_final: 0.6253 (t70) REVERT: D 446 ASP cc_start: 0.6007 (p0) cc_final: 0.5718 (p0) REVERT: E 133 GLU cc_start: 0.5389 (pm20) cc_final: 0.4972 (mm-30) REVERT: E 235 MET cc_start: 0.6642 (mtt) cc_final: 0.6295 (mtp) REVERT: E 357 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.6794 (pp20) REVERT: F 37 ARG cc_start: 0.7294 (OUTLIER) cc_final: 0.7085 (mpt-90) REVERT: F 218 MET cc_start: 0.7246 (mtt) cc_final: 0.7033 (mtt) REVERT: F 240 ARG cc_start: 0.6649 (OUTLIER) cc_final: 0.6411 (ttp80) REVERT: F 284 GLU cc_start: 0.7013 (pt0) cc_final: 0.6682 (mm-30) REVERT: F 398 LEU cc_start: 0.8720 (tp) cc_final: 0.8499 (tm) REVERT: F 406 ILE cc_start: 0.7588 (mt) cc_final: 0.7283 (mp) REVERT: F 438 LYS cc_start: 0.8257 (ttmt) cc_final: 0.7952 (tttm) REVERT: F 460 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7655 (mm-30) outliers start: 92 outliers final: 29 residues processed: 423 average time/residue: 1.2761 time to fit residues: 617.6378 Evaluate side-chains 329 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 292 time to evaluate : 2.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL 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 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 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 300 ARG Chi-restraints excluded: chain C residue 467 ASN Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 145 LEU 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 E residue 9 VAL Chi-restraints excluded: chain E residue 337 GLU Chi-restraints excluded: chain E residue 357 GLU Chi-restraints excluded: chain E residue 362 GLU Chi-restraints excluded: chain F residue 37 ARG Chi-restraints excluded: chain F residue 99 LEU 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 379 GLU 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 99 optimal weight: 10.0000 chunk 176 optimal weight: 3.9990 chunk 257 optimal weight: 0.9990 chunk 116 optimal weight: 4.9990 chunk 14 optimal weight: 9.9990 chunk 279 optimal weight: 8.9990 chunk 84 optimal weight: 5.9990 chunk 7 optimal weight: 0.5980 chunk 191 optimal weight: 9.9990 chunk 123 optimal weight: 10.0000 chunk 194 optimal weight: 1.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 GLN A 467 ASN B 143 HIS B 483 ASN C 426 GLN C 433 GLN C 474 HIS D 34 HIS D 179 HIS D 401 HIS E 34 HIS E 38 ASN E 412 GLN E 447 HIS F 34 HIS F 38 ASN ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 259 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.202812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.173645 restraints weight = 24215.124| |-----------------------------------------------------------------------------| r_work (start): 0.4335 rms_B_bonded: 2.13 r_work: 0.4212 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.4068 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.4068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6859 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22371 Z= 0.164 Angle : 0.640 8.975 30345 Z= 0.333 Chirality : 0.047 0.218 3485 Planarity : 0.005 0.047 3962 Dihedral : 8.913 89.624 3276 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 6.12 % Allowed : 18.06 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.15), residues: 2824 helix: 0.75 (0.15), residues: 1092 sheet: 0.23 (0.23), residues: 482 loop : -0.76 (0.17), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS C 474 PHE 0.025 0.002 PHE F 414 TYR 0.020 0.002 TYR D 364 ARG 0.010 0.001 ARG C 171 Details of bonding type rmsd hydrogen bonds : bond 0.04973 ( 968) hydrogen bonds : angle 5.18594 ( 2814) covalent geometry : bond 0.00379 (22371) covalent geometry : angle 0.63978 (30345) *********************** 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 459 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 317 time to evaluate : 3.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 ASP cc_start: 0.7641 (OUTLIER) cc_final: 0.7310 (m-30) REVERT: B 300 ARG cc_start: 0.7914 (mmm-85) cc_final: 0.7675 (mtm180) REVERT: C 62 MET cc_start: 0.6315 (OUTLIER) cc_final: 0.6042 (ptm) REVERT: C 95 MET cc_start: 0.7495 (tpt) cc_final: 0.7158 (ttm) REVERT: C 190 ASN cc_start: 0.6541 (OUTLIER) cc_final: 0.5904 (p0) REVERT: C 210 GLU cc_start: 0.5829 (mm-30) cc_final: 0.5562 (pt0) REVERT: C 300 ARG cc_start: 0.7360 (OUTLIER) cc_final: 0.6306 (mtp85) REVERT: C 375 MET cc_start: 0.6956 (ttp) cc_final: 0.6232 (tpp) REVERT: D 5 ARG cc_start: 0.6769 (mmt180) cc_final: 0.6495 (mmm160) REVERT: D 196 ASN cc_start: 0.6273 (OUTLIER) cc_final: 0.5942 (m110) REVERT: D 271 MET cc_start: 0.7805 (mtp) cc_final: 0.7571 (mtm) REVERT: D 313 TYR cc_start: 0.6712 (m-80) cc_final: 0.6400 (m-80) REVERT: D 322 PHE cc_start: 0.7717 (OUTLIER) cc_final: 0.6977 (m-80) REVERT: D 345 ASP cc_start: 0.6661 (t0) cc_final: 0.6394 (t70) REVERT: D 364 TYR cc_start: 0.5614 (t80) cc_final: 0.5401 (t80) REVERT: D 402 ARG cc_start: 0.6429 (OUTLIER) cc_final: 0.6039 (mtp180) REVERT: D 458 ARG cc_start: 0.6790 (OUTLIER) cc_final: 0.5614 (tpp80) REVERT: E 128 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7857 (mm) REVERT: E 133 GLU cc_start: 0.5472 (pm20) cc_final: 0.5100 (pm20) REVERT: E 357 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.6847 (pp20) REVERT: E 397 LYS cc_start: 0.6207 (OUTLIER) cc_final: 0.5944 (ptmt) REVERT: E 413 ASN cc_start: 0.7677 (p0) cc_final: 0.7355 (p0) REVERT: E 469 MET cc_start: 0.4738 (mtt) cc_final: 0.4430 (mtt) REVERT: F 5 ARG cc_start: 0.7203 (OUTLIER) cc_final: 0.6486 (mtm180) REVERT: F 284 GLU cc_start: 0.7184 (pt0) cc_final: 0.6671 (mm-30) REVERT: F 334 LYS cc_start: 0.7960 (tmtm) cc_final: 0.7625 (tptp) REVERT: F 352 ARG cc_start: 0.6054 (OUTLIER) cc_final: 0.5727 (ptt180) REVERT: F 398 LEU cc_start: 0.8688 (tp) cc_final: 0.8446 (tm) REVERT: F 438 LYS cc_start: 0.8210 (ttmt) cc_final: 0.7941 (tttm) REVERT: F 460 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7806 (mm-30) outliers start: 142 outliers final: 53 residues processed: 412 average time/residue: 1.8861 time to fit residues: 897.3944 Evaluate side-chains 333 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 266 time to evaluate : 2.540 ------------------------------------------------------------------------------- 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 A residue 319 VAL Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain B residue 53 VAL 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 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 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 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 196 ASN Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 231 THR 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 384 ILE Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 402 ARG Chi-restraints excluded: chain D residue 458 ARG Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 337 GLU Chi-restraints excluded: chain E residue 338 MET Chi-restraints excluded: chain E residue 357 GLU Chi-restraints excluded: chain E residue 362 GLU Chi-restraints excluded: chain E residue 397 LYS 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 240 ARG Chi-restraints excluded: chain F residue 283 THR Chi-restraints excluded: chain F residue 352 ARG Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 392 LEU Chi-restraints excluded: chain F residue 411 SER 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 204 optimal weight: 2.9990 chunk 223 optimal weight: 5.9990 chunk 248 optimal weight: 10.0000 chunk 182 optimal weight: 10.0000 chunk 130 optimal weight: 9.9990 chunk 189 optimal weight: 6.9990 chunk 3 optimal weight: 0.6980 chunk 224 optimal weight: 0.0970 chunk 218 optimal weight: 9.9990 chunk 227 optimal weight: 7.9990 chunk 7 optimal weight: 0.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 GLN B 483 ASN C 426 GLN C 433 GLN ** C 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 HIS D 179 HIS D 401 HIS D 407 GLN E 363 HIS E 447 HIS F 174 ASN F 401 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.202181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.172945 restraints weight = 24484.704| |-----------------------------------------------------------------------------| r_work (start): 0.4329 rms_B_bonded: 2.14 r_work: 0.4206 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.4063 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.4063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6877 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 22371 Z= 0.148 Angle : 0.608 10.698 30345 Z= 0.315 Chirality : 0.046 0.215 3485 Planarity : 0.005 0.050 3962 Dihedral : 8.673 89.240 3276 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 5.82 % Allowed : 20.26 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.15), residues: 2824 helix: 0.82 (0.15), residues: 1089 sheet: 0.31 (0.23), residues: 488 loop : -0.84 (0.17), residues: 1247 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.016 0.001 HIS C 470 PHE 0.036 0.002 PHE F 409 TYR 0.015 0.002 TYR A 260 ARG 0.010 0.001 ARG C 171 Details of bonding type rmsd hydrogen bonds : bond 0.04536 ( 968) hydrogen bonds : angle 4.99429 ( 2814) covalent geometry : bond 0.00354 (22371) covalent geometry : angle 0.60789 (30345) *********************** 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 433 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 298 time to evaluate : 3.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.7504 (tm-30) cc_final: 0.7162 (tm-30) REVERT: A 347 ASP cc_start: 0.7629 (OUTLIER) cc_final: 0.7354 (m-30) REVERT: B 300 ARG cc_start: 0.7931 (OUTLIER) cc_final: 0.7676 (mtm180) REVERT: B 314 THR cc_start: 0.7264 (OUTLIER) cc_final: 0.6888 (t) REVERT: B 403 ASP cc_start: 0.7510 (t70) cc_final: 0.7013 (t0) REVERT: B 416 THR cc_start: 0.7904 (m) cc_final: 0.7704 (m) REVERT: C 62 MET cc_start: 0.6329 (OUTLIER) cc_final: 0.6059 (ptm) REVERT: C 137 MET cc_start: 0.4087 (OUTLIER) cc_final: 0.3816 (mtt) REVERT: C 190 ASN cc_start: 0.6560 (OUTLIER) cc_final: 0.5943 (p0) REVERT: C 210 GLU cc_start: 0.5789 (mm-30) cc_final: 0.5523 (pt0) REVERT: C 300 ARG cc_start: 0.7241 (OUTLIER) cc_final: 0.6258 (mtp85) REVERT: C 361 LEU cc_start: 0.8407 (tt) cc_final: 0.7873 (mp) REVERT: C 375 MET cc_start: 0.6823 (ttp) cc_final: 0.6021 (tpp) REVERT: C 452 ASP cc_start: 0.6937 (m-30) cc_final: 0.6289 (t0) REVERT: D 5 ARG cc_start: 0.6769 (mmt180) cc_final: 0.6498 (mmm160) REVERT: D 196 ASN cc_start: 0.6333 (OUTLIER) cc_final: 0.5905 (m110) REVERT: D 322 PHE cc_start: 0.7702 (OUTLIER) cc_final: 0.6900 (m-80) REVERT: D 337 GLU cc_start: 0.6959 (OUTLIER) cc_final: 0.6034 (mp0) REVERT: D 345 ASP cc_start: 0.6610 (t0) cc_final: 0.6334 (t70) REVERT: D 351 SER cc_start: 0.6144 (m) cc_final: 0.5435 (t) REVERT: D 402 ARG cc_start: 0.6520 (OUTLIER) cc_final: 0.6105 (mtp180) REVERT: D 458 ARG cc_start: 0.6734 (OUTLIER) cc_final: 0.5537 (tpp80) REVERT: E 128 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7903 (mm) REVERT: E 133 GLU cc_start: 0.5385 (pm20) cc_final: 0.5033 (pm20) REVERT: E 204 ASP cc_start: 0.7407 (t70) cc_final: 0.6793 (m-30) REVERT: E 213 MET cc_start: 0.6941 (mtm) cc_final: 0.6687 (mtt) REVERT: E 256 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.7200 (mmt180) REVERT: E 397 LYS cc_start: 0.6260 (OUTLIER) cc_final: 0.5930 (ptmt) REVERT: E 413 ASN cc_start: 0.7684 (p0) cc_final: 0.7258 (p0) REVERT: F 5 ARG cc_start: 0.7153 (OUTLIER) cc_final: 0.6423 (mtm180) REVERT: F 38 ASN cc_start: 0.6309 (m-40) cc_final: 0.6093 (m110) REVERT: F 284 GLU cc_start: 0.7130 (pt0) cc_final: 0.6553 (mm-30) REVERT: F 334 LYS cc_start: 0.8047 (OUTLIER) cc_final: 0.7719 (tptp) REVERT: F 352 ARG cc_start: 0.6015 (OUTLIER) cc_final: 0.5709 (ptt180) REVERT: F 406 ILE cc_start: 0.7543 (mp) cc_final: 0.7332 (mp) REVERT: F 431 LYS cc_start: 0.7532 (OUTLIER) cc_final: 0.7045 (mppt) REVERT: F 438 LYS cc_start: 0.8291 (ttmt) cc_final: 0.7983 (tttm) REVERT: F 442 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7658 (mt-10) outliers start: 135 outliers final: 62 residues processed: 386 average time/residue: 1.7496 time to fit residues: 784.6479 Evaluate side-chains 350 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 269 time to evaluate : 3.230 ------------------------------------------------------------------------------- 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 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 397 GLN Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 435 LEU 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 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 300 ARG Chi-restraints excluded: chain B residue 314 THR 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 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 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 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 337 GLU Chi-restraints excluded: chain D residue 384 ILE Chi-restraints excluded: chain D residue 402 ARG Chi-restraints excluded: chain D residue 458 ARG Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 67 THR 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 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 397 LYS 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 214 VAL 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 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 30 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 141 optimal weight: 0.7980 chunk 236 optimal weight: 6.9990 chunk 264 optimal weight: 0.5980 chunk 102 optimal weight: 0.9980 chunk 240 optimal weight: 9.9990 chunk 27 optimal weight: 6.9990 chunk 111 optimal weight: 10.0000 chunk 72 optimal weight: 8.9990 chunk 153 optimal weight: 0.0370 overall best weight: 0.6258 ------------------------------------------------------------------------------- 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 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 467 ASN C 172 GLN ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 358 ASN C 426 GLN C 433 GLN C 474 HIS D 179 HIS D 401 HIS F 375 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4652 r_free = 0.4652 target = 0.206637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.177332 restraints weight = 24006.540| |-----------------------------------------------------------------------------| r_work (start): 0.4378 rms_B_bonded: 2.13 r_work: 0.4257 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.4113 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.4113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6805 moved from start: 0.4075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 22371 Z= 0.110 Angle : 0.557 11.241 30345 Z= 0.288 Chirality : 0.044 0.177 3485 Planarity : 0.005 0.050 3962 Dihedral : 8.010 87.651 3275 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.18 % Allowed : 22.72 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.15), residues: 2824 helix: 1.14 (0.15), residues: 1089 sheet: 0.30 (0.23), residues: 491 loop : -0.76 (0.17), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.001 HIS C 470 PHE 0.039 0.001 PHE F 409 TYR 0.023 0.001 TYR C 461 ARG 0.012 0.000 ARG B 89 Details of bonding type rmsd hydrogen bonds : bond 0.03761 ( 968) hydrogen bonds : angle 4.77639 ( 2814) covalent geometry : bond 0.00238 (22371) covalent geometry : angle 0.55702 (30345) *********************** 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 397 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 300 time to evaluate : 2.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.7460 (tm-30) cc_final: 0.7212 (tm-30) REVERT: B 245 MET cc_start: 0.4342 (ptp) cc_final: 0.4008 (pmm) REVERT: B 403 ASP cc_start: 0.7443 (t70) cc_final: 0.6960 (t0) REVERT: C 190 ASN cc_start: 0.6515 (OUTLIER) cc_final: 0.5970 (p0) REVERT: C 210 GLU cc_start: 0.5748 (mm-30) cc_final: 0.5505 (pt0) REVERT: C 300 ARG cc_start: 0.7251 (OUTLIER) cc_final: 0.6235 (mtp85) REVERT: C 375 MET cc_start: 0.6842 (ttp) cc_final: 0.6015 (tpp) REVERT: C 452 ASP cc_start: 0.6962 (m-30) cc_final: 0.6357 (t0) REVERT: D 45 ASP cc_start: 0.6044 (p0) cc_final: 0.5517 (t0) REVERT: D 196 ASN cc_start: 0.6267 (OUTLIER) cc_final: 0.5888 (m110) REVERT: D 271 MET cc_start: 0.7668 (mtp) cc_final: 0.7299 (mtm) REVERT: D 322 PHE cc_start: 0.7656 (OUTLIER) cc_final: 0.7088 (m-80) REVERT: D 337 GLU cc_start: 0.6830 (OUTLIER) cc_final: 0.6067 (mp0) REVERT: D 345 ASP cc_start: 0.6562 (t0) cc_final: 0.6316 (t70) REVERT: D 399 VAL cc_start: 0.6426 (p) cc_final: 0.6042 (m) REVERT: D 402 ARG cc_start: 0.6543 (OUTLIER) cc_final: 0.6131 (mtp180) REVERT: D 458 ARG cc_start: 0.6632 (OUTLIER) cc_final: 0.5387 (tpp80) REVERT: E 128 LEU cc_start: 0.8216 (mm) cc_final: 0.7875 (mm) REVERT: E 213 MET cc_start: 0.6759 (mtm) cc_final: 0.6494 (mtt) REVERT: E 256 ARG cc_start: 0.7614 (OUTLIER) cc_final: 0.7372 (mpt90) REVERT: E 397 LYS cc_start: 0.6192 (OUTLIER) cc_final: 0.5929 (ptmt) REVERT: E 413 ASN cc_start: 0.7573 (p0) cc_final: 0.7195 (p0) REVERT: E 469 MET cc_start: 0.4645 (mtt) cc_final: 0.4409 (mtt) REVERT: F 5 ARG cc_start: 0.7084 (OUTLIER) cc_final: 0.6375 (mtm180) REVERT: F 37 ARG cc_start: 0.7449 (mpp80) cc_final: 0.7219 (mpp80) REVERT: F 218 MET cc_start: 0.7338 (mtt) cc_final: 0.7050 (mtt) REVERT: F 284 GLU cc_start: 0.7042 (pt0) cc_final: 0.6402 (mm-30) REVERT: F 334 LYS cc_start: 0.8023 (OUTLIER) cc_final: 0.7756 (tptp) REVERT: F 338 MET cc_start: 0.7460 (mmm) cc_final: 0.7210 (tpt) REVERT: F 406 ILE cc_start: 0.7659 (mp) cc_final: 0.7456 (mp) REVERT: F 431 LYS cc_start: 0.7505 (OUTLIER) cc_final: 0.7102 (mppt) outliers start: 97 outliers final: 33 residues processed: 359 average time/residue: 1.7015 time to fit residues: 700.7809 Evaluate side-chains 303 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 258 time to evaluate : 3.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 121 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 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 236 PHE 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 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 322 PHE 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 D residue 458 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 397 LYS Chi-restraints excluded: chain E residue 428 VAL Chi-restraints excluded: chain F residue 5 ARG 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 219 ASN 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 56 optimal weight: 0.2980 chunk 88 optimal weight: 7.9990 chunk 241 optimal weight: 7.9990 chunk 174 optimal weight: 7.9990 chunk 104 optimal weight: 9.9990 chunk 268 optimal weight: 8.9990 chunk 125 optimal weight: 10.0000 chunk 180 optimal weight: 5.9990 chunk 276 optimal weight: 0.6980 chunk 120 optimal weight: 7.9990 chunk 207 optimal weight: 9.9990 overall best weight: 4.5986 ------------------------------------------------------------------------------- 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 C 433 GLN D 179 HIS ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 GLN E 447 HIS F 38 ASN F 259 GLN F 363 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.196603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.167126 restraints weight = 24812.795| |-----------------------------------------------------------------------------| r_work (start): 0.4265 rms_B_bonded: 2.13 r_work: 0.4143 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.4000 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.4000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.4389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 22371 Z= 0.235 Angle : 0.718 11.748 30345 Z= 0.372 Chirality : 0.049 0.211 3485 Planarity : 0.006 0.051 3962 Dihedral : 8.444 85.852 3274 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 6.21 % Allowed : 22.11 % Favored : 71.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.15), residues: 2824 helix: 0.57 (0.15), residues: 1084 sheet: 0.15 (0.23), residues: 465 loop : -1.06 (0.17), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.002 HIS C 470 PHE 0.029 0.002 PHE A 494 TYR 0.021 0.003 TYR B 286 ARG 0.011 0.001 ARG B 89 Details of bonding type rmsd hydrogen bonds : bond 0.05463 ( 968) hydrogen bonds : angle 5.07077 ( 2814) covalent geometry : bond 0.00571 (22371) covalent geometry : angle 0.71802 (30345) *********************** 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 424 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 280 time to evaluate : 2.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ARG cc_start: 0.6189 (OUTLIER) cc_final: 0.5860 (mtm110) REVERT: B 60 MET cc_start: 0.6450 (OUTLIER) cc_final: 0.5806 (mmt) REVERT: B 300 ARG cc_start: 0.7963 (mmt90) cc_final: 0.7613 (mtm180) REVERT: B 384 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7730 (tp) REVERT: B 403 ASP cc_start: 0.7508 (t70) cc_final: 0.6976 (t0) REVERT: C 190 ASN cc_start: 0.6505 (OUTLIER) cc_final: 0.5862 (p0) REVERT: C 210 GLU cc_start: 0.5808 (mm-30) cc_final: 0.5559 (pt0) REVERT: C 300 ARG cc_start: 0.7270 (OUTLIER) cc_final: 0.6233 (mtp85) REVERT: C 375 MET cc_start: 0.6912 (ttp) cc_final: 0.6008 (tpp) REVERT: C 392 LEU cc_start: 0.6259 (OUTLIER) cc_final: 0.5459 (tp) REVERT: C 452 ASP cc_start: 0.7046 (m-30) cc_final: 0.6419 (t0) REVERT: D 5 ARG cc_start: 0.6760 (mmt180) cc_final: 0.6159 (mpp80) REVERT: D 271 MET cc_start: 0.7786 (mtp) cc_final: 0.7555 (mtm) REVERT: D 337 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.6253 (mp0) REVERT: D 351 SER cc_start: 0.6371 (m) cc_final: 0.5643 (t) REVERT: D 402 ARG cc_start: 0.6485 (OUTLIER) cc_final: 0.6015 (mtp180) REVERT: E 52 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7172 (mp) REVERT: E 128 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7824 (mm) REVERT: E 133 GLU cc_start: 0.5576 (pm20) cc_final: 0.5371 (pm20) REVERT: E 204 ASP cc_start: 0.7423 (t70) cc_final: 0.6881 (m-30) REVERT: E 213 MET cc_start: 0.6897 (mtm) cc_final: 0.6610 (mtt) REVERT: E 256 ARG cc_start: 0.7734 (OUTLIER) cc_final: 0.7335 (mmt180) REVERT: E 397 LYS cc_start: 0.6207 (OUTLIER) cc_final: 0.5878 (ptmt) REVERT: E 413 ASN cc_start: 0.7850 (p0) cc_final: 0.7469 (p0) REVERT: F 5 ARG cc_start: 0.7170 (OUTLIER) cc_final: 0.6403 (mtm180) REVERT: F 284 GLU cc_start: 0.7213 (pt0) cc_final: 0.6540 (mm-30) REVERT: F 334 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7815 (tptp) REVERT: F 352 ARG cc_start: 0.6142 (OUTLIER) cc_final: 0.5716 (ptt180) REVERT: F 406 ILE cc_start: 0.7766 (OUTLIER) cc_final: 0.7564 (mp) REVERT: F 431 LYS cc_start: 0.7585 (OUTLIER) cc_final: 0.7183 (mppt) outliers start: 144 outliers final: 63 residues processed: 379 average time/residue: 1.3394 time to fit residues: 585.7172 Evaluate side-chains 332 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 252 time to evaluate : 2.508 ------------------------------------------------------------------------------- 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 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 406 THR 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 203 SER Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 314 THR 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 31 VAL Chi-restraints excluded: chain C residue 62 MET 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 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 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 231 THR Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 258 THR 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 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 52 LEU Chi-restraints excluded: chain E residue 67 THR 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 338 MET Chi-restraints excluded: chain E residue 397 LYS 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 66 SER 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 334 LYS Chi-restraints excluded: chain F residue 352 ARG Chi-restraints excluded: chain F residue 386 ILE 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 32 optimal weight: 10.0000 chunk 222 optimal weight: 6.9990 chunk 217 optimal weight: 4.9990 chunk 219 optimal weight: 0.8980 chunk 192 optimal weight: 0.9980 chunk 266 optimal weight: 0.6980 chunk 75 optimal weight: 9.9990 chunk 115 optimal weight: 3.9990 chunk 157 optimal weight: 0.9990 chunk 184 optimal weight: 1.9990 chunk 41 optimal weight: 7.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 186 GLN C 433 GLN C 474 HIS D 179 HIS D 304 GLN E 324 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4613 r_free = 0.4613 target = 0.202379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.172826 restraints weight = 24284.892| |-----------------------------------------------------------------------------| r_work (start): 0.4339 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: 0.6859 moved from start: 0.4618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 22371 Z= 0.125 Angle : 0.602 11.878 30345 Z= 0.311 Chirality : 0.044 0.173 3485 Planarity : 0.005 0.053 3962 Dihedral : 7.914 83.519 3273 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 4.53 % Allowed : 24.61 % Favored : 70.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.15), residues: 2824 helix: 0.95 (0.15), residues: 1086 sheet: 0.21 (0.23), residues: 480 loop : -1.01 (0.17), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.015 0.001 HIS C 474 PHE 0.028 0.001 PHE A 494 TYR 0.019 0.001 TYR F 148 ARG 0.016 0.001 ARG C 93 Details of bonding type rmsd hydrogen bonds : bond 0.04055 ( 968) hydrogen bonds : angle 4.80107 ( 2814) covalent geometry : bond 0.00283 (22371) covalent geometry : angle 0.60179 (30345) *********************** 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 382 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 277 time to evaluate : 2.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 60 MET cc_start: 0.6479 (OUTLIER) cc_final: 0.5851 (mmt) REVERT: B 93 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.7829 (mtp180) REVERT: B 245 MET cc_start: 0.4328 (ptp) cc_final: 0.4014 (pmm) REVERT: B 300 ARG cc_start: 0.7828 (mmt90) cc_final: 0.7523 (mtm180) REVERT: B 384 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7785 (tp) REVERT: B 403 ASP cc_start: 0.7480 (t70) cc_final: 0.6969 (t0) REVERT: B 483 ASN cc_start: 0.7865 (m-40) cc_final: 0.7275 (t0) REVERT: C 210 GLU cc_start: 0.5689 (mm-30) cc_final: 0.5435 (pt0) REVERT: C 300 ARG cc_start: 0.7052 (OUTLIER) cc_final: 0.5976 (mtp85) REVERT: C 375 MET cc_start: 0.6841 (ttp) cc_final: 0.5907 (tpp) REVERT: C 392 LEU cc_start: 0.6220 (OUTLIER) cc_final: 0.5416 (tt) REVERT: C 435 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7989 (mm) REVERT: C 452 ASP cc_start: 0.7012 (m-30) cc_final: 0.6543 (t0) REVERT: D 10 MET cc_start: 0.7048 (mtm) cc_final: 0.6715 (mtp) REVERT: D 45 ASP cc_start: 0.6110 (p0) cc_final: 0.5536 (t0) REVERT: D 115 ARG cc_start: 0.6622 (ptp-110) cc_final: 0.5951 (ptp-170) REVERT: D 337 GLU cc_start: 0.6944 (OUTLIER) cc_final: 0.6046 (mp0) REVERT: D 351 SER cc_start: 0.6415 (m) cc_final: 0.5615 (t) REVERT: D 402 ARG cc_start: 0.6414 (OUTLIER) cc_final: 0.6026 (mtp180) REVERT: D 437 PHE cc_start: 0.7047 (OUTLIER) cc_final: 0.6749 (m-10) REVERT: D 459 ILE cc_start: 0.6264 (OUTLIER) cc_final: 0.5947 (tt) REVERT: E 3 ARG cc_start: 0.6850 (OUTLIER) cc_final: 0.6544 (mmm-85) REVERT: E 204 ASP cc_start: 0.7361 (t70) cc_final: 0.6832 (m-30) REVERT: E 213 MET cc_start: 0.6717 (mtm) cc_final: 0.6517 (mtt) REVERT: E 256 ARG cc_start: 0.7587 (OUTLIER) cc_final: 0.7354 (mpt90) REVERT: E 397 LYS cc_start: 0.6009 (OUTLIER) cc_final: 0.5773 (ptmt) REVERT: E 413 ASN cc_start: 0.7780 (p0) cc_final: 0.7433 (p0) REVERT: E 469 MET cc_start: 0.4655 (mtt) cc_final: 0.4427 (mtt) REVERT: F 5 ARG cc_start: 0.7038 (OUTLIER) cc_final: 0.6245 (mtm180) REVERT: F 284 GLU cc_start: 0.7087 (pt0) cc_final: 0.6444 (mm-30) REVERT: F 334 LYS cc_start: 0.8093 (OUTLIER) cc_final: 0.7874 (tptp) REVERT: F 338 MET cc_start: 0.7644 (mmm) cc_final: 0.7152 (tpt) REVERT: F 352 ARG cc_start: 0.6055 (OUTLIER) cc_final: 0.5646 (ptt180) REVERT: F 431 LYS cc_start: 0.7438 (OUTLIER) cc_final: 0.7127 (mppt) outliers start: 105 outliers final: 48 residues processed: 343 average time/residue: 1.2787 time to fit residues: 504.1571 Evaluate side-chains 322 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 257 time to evaluate : 2.678 ------------------------------------------------------------------------------- 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 227 SER Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 397 GLN Chi-restraints excluded: chain A residue 406 THR 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 93 ARG 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 264 SER 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 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 202 GLU Chi-restraints excluded: chain C residue 236 PHE 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 C residue 392 LEU Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 90 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 322 PHE Chi-restraints excluded: chain D residue 332 GLU Chi-restraints excluded: chain D residue 337 GLU Chi-restraints excluded: chain D residue 370 VAL 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 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 397 LYS 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 334 LYS Chi-restraints excluded: chain F residue 352 ARG Chi-restraints excluded: chain F residue 392 LEU Chi-restraints excluded: chain F residue 431 LYS 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 238 optimal weight: 9.9990 chunk 32 optimal weight: 20.0000 chunk 142 optimal weight: 3.9990 chunk 69 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 179 optimal weight: 7.9990 chunk 3 optimal weight: 8.9990 chunk 124 optimal weight: 0.8980 chunk 230 optimal weight: 4.9990 chunk 216 optimal weight: 6.9990 chunk 234 optimal weight: 9.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- 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 C 433 GLN D 179 HIS ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 324 HIS E 447 HIS F 38 ASN F 173 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.196736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.167429 restraints weight = 24784.142| |-----------------------------------------------------------------------------| r_work (start): 0.4265 rms_B_bonded: 2.18 r_work: 0.4154 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.4015 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.4015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 moved from start: 0.4856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 22371 Z= 0.212 Angle : 0.707 11.045 30345 Z= 0.367 Chirality : 0.048 0.199 3485 Planarity : 0.006 0.053 3962 Dihedral : 8.374 82.159 3273 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 5.09 % Allowed : 24.70 % Favored : 70.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.15), residues: 2824 helix: 0.46 (0.15), residues: 1094 sheet: 0.05 (0.23), residues: 460 loop : -1.21 (0.16), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.002 HIS C 470 PHE 0.025 0.002 PHE A 494 TYR 0.029 0.002 TYR D 148 ARG 0.012 0.001 ARG C 171 Details of bonding type rmsd hydrogen bonds : bond 0.05347 ( 968) hydrogen bonds : angle 5.04095 ( 2814) covalent geometry : bond 0.00512 (22371) covalent geometry : angle 0.70733 (30345) *********************** 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 397 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 279 time to evaluate : 2.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ARG cc_start: 0.6198 (OUTLIER) cc_final: 0.5852 (mtm110) REVERT: A 278 ARG cc_start: 0.6985 (OUTLIER) cc_final: 0.5387 (mtm-85) REVERT: B 60 MET cc_start: 0.6350 (OUTLIER) cc_final: 0.5747 (mmt) REVERT: B 210 GLU cc_start: 0.7636 (tm-30) cc_final: 0.7089 (mm-30) REVERT: B 300 ARG cc_start: 0.7889 (mmt90) cc_final: 0.7539 (mtm180) REVERT: B 384 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7670 (tp) REVERT: B 403 ASP cc_start: 0.7499 (t70) cc_final: 0.6947 (t0) REVERT: B 409 LYS cc_start: 0.5879 (OUTLIER) cc_final: 0.4621 (ttpp) REVERT: C 210 GLU cc_start: 0.5842 (mm-30) cc_final: 0.5618 (pt0) REVERT: C 251 TYR cc_start: 0.6611 (m-10) cc_final: 0.6072 (m-80) REVERT: C 300 ARG cc_start: 0.7173 (OUTLIER) cc_final: 0.6050 (mtp85) REVERT: C 357 ILE cc_start: 0.5977 (OUTLIER) cc_final: 0.5486 (pp) REVERT: C 375 MET cc_start: 0.6915 (ttp) cc_final: 0.6038 (tpp) REVERT: C 392 LEU cc_start: 0.6237 (OUTLIER) cc_final: 0.5469 (tp) REVERT: C 452 ASP cc_start: 0.7018 (m-30) cc_final: 0.6618 (p0) REVERT: D 10 MET cc_start: 0.7217 (mtm) cc_final: 0.6908 (mtp) REVERT: D 115 ARG cc_start: 0.6696 (ptp-110) cc_final: 0.6347 (ptp-170) REVERT: D 271 MET cc_start: 0.7715 (mtp) cc_final: 0.7460 (mtm) REVERT: D 337 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6274 (mp0) REVERT: D 351 SER cc_start: 0.6370 (m) cc_final: 0.5638 (t) REVERT: D 387 LEU cc_start: 0.7386 (mp) cc_final: 0.6820 (pp) REVERT: D 402 ARG cc_start: 0.6537 (OUTLIER) cc_final: 0.6057 (mtp180) REVERT: D 459 ILE cc_start: 0.6485 (OUTLIER) cc_final: 0.6133 (tt) REVERT: E 3 ARG cc_start: 0.6978 (OUTLIER) cc_final: 0.6757 (ptp-110) REVERT: E 52 LEU cc_start: 0.7725 (OUTLIER) cc_final: 0.7058 (mp) REVERT: E 133 GLU cc_start: 0.5554 (pm20) cc_final: 0.5220 (pm20) REVERT: E 204 ASP cc_start: 0.7519 (t70) cc_final: 0.6969 (m-30) REVERT: E 213 MET cc_start: 0.6834 (mtm) cc_final: 0.6570 (mtt) REVERT: E 256 ARG cc_start: 0.7666 (OUTLIER) cc_final: 0.7253 (mmt180) REVERT: E 397 LYS cc_start: 0.6032 (pptt) cc_final: 0.5759 (ptpt) REVERT: E 469 MET cc_start: 0.5070 (mtt) cc_final: 0.4852 (mtt) REVERT: F 5 ARG cc_start: 0.7137 (OUTLIER) cc_final: 0.6380 (mtm180) REVERT: F 213 MET cc_start: 0.7323 (OUTLIER) cc_final: 0.7081 (mtt) REVERT: F 218 MET cc_start: 0.7630 (mtt) cc_final: 0.7058 (mtt) REVERT: F 284 GLU cc_start: 0.7204 (pt0) cc_final: 0.6504 (mm-30) REVERT: F 334 LYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7914 (tptp) REVERT: F 338 MET cc_start: 0.7723 (mmm) cc_final: 0.7292 (tpt) REVERT: F 352 ARG cc_start: 0.6214 (OUTLIER) cc_final: 0.5851 (ptt180) REVERT: F 431 LYS cc_start: 0.7469 (OUTLIER) cc_final: 0.7154 (mppt) REVERT: F 438 LYS cc_start: 0.8460 (ttmt) cc_final: 0.8139 (ttmt) outliers start: 118 outliers final: 60 residues processed: 355 average time/residue: 1.3323 time to fit residues: 542.8481 Evaluate side-chains 338 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 259 time to evaluate : 2.382 ------------------------------------------------------------------------------- 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 204 THR Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 278 ARG Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 397 GLN Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 491 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 74 VAL Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 95 MET 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 200 GLN Chi-restraints excluded: chain B residue 224 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 409 LYS 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 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 198 ILE Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 300 ARG 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 D residue 32 ILE Chi-restraints excluded: chain D residue 90 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 370 VAL Chi-restraints excluded: chain D residue 402 ARG 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 52 LEU Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 103 ILE 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 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 62 ILE Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 213 MET 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 334 LYS Chi-restraints excluded: chain F residue 352 ARG Chi-restraints excluded: chain F residue 370 VAL 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 456 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 170 optimal weight: 4.9990 chunk 126 optimal weight: 9.9990 chunk 264 optimal weight: 7.9990 chunk 164 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 chunk 219 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 225 optimal weight: 0.9990 chunk 259 optimal weight: 0.0670 overall best weight: 0.7924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 333 ASN C 433 GLN C 474 HIS D 173 HIS ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 173 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.202891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.173377 restraints weight = 24233.761| |-----------------------------------------------------------------------------| r_work (start): 0.4343 rms_B_bonded: 2.19 r_work: 0.4233 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.4094 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.4094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6852 moved from start: 0.4989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 22371 Z= 0.119 Angle : 0.599 11.757 30345 Z= 0.311 Chirality : 0.044 0.200 3485 Planarity : 0.005 0.055 3962 Dihedral : 7.660 81.692 3272 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.62 % Allowed : 26.34 % Favored : 70.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.15), residues: 2824 helix: 0.94 (0.16), residues: 1090 sheet: 0.16 (0.23), residues: 461 loop : -1.06 (0.17), residues: 1273 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.016 0.001 HIS C 474 PHE 0.026 0.001 PHE A 494 TYR 0.021 0.001 TYR D 148 ARG 0.011 0.001 ARG C 171 Details of bonding type rmsd hydrogen bonds : bond 0.03805 ( 968) hydrogen bonds : angle 4.75213 ( 2814) covalent geometry : bond 0.00264 (22371) covalent geometry : angle 0.59924 (30345) *********************** 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 365 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 281 time to evaluate : 2.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 ARG cc_start: 0.6916 (OUTLIER) cc_final: 0.6643 (mmt-90) REVERT: A 472 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7582 (mp) REVERT: B 60 MET cc_start: 0.6354 (OUTLIER) cc_final: 0.5869 (mmt) REVERT: B 93 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7827 (mtp180) REVERT: B 130 GLU cc_start: 0.6642 (mm-30) cc_final: 0.5913 (pp20) REVERT: B 245 MET cc_start: 0.4203 (ptp) cc_final: 0.3953 (pmm) REVERT: B 300 ARG cc_start: 0.7810 (mmt90) cc_final: 0.7526 (mtm180) REVERT: B 314 THR cc_start: 0.7130 (OUTLIER) cc_final: 0.6736 (t) REVERT: B 403 ASP cc_start: 0.7505 (t70) cc_final: 0.7032 (t0) REVERT: B 483 ASN cc_start: 0.7905 (m-40) cc_final: 0.7303 (t0) REVERT: C 125 GLU cc_start: 0.5187 (pm20) cc_final: 0.4932 (pm20) REVERT: C 137 MET cc_start: 0.4268 (mtt) cc_final: 0.4062 (mpp) REVERT: C 210 GLU cc_start: 0.5760 (mm-30) cc_final: 0.5482 (pt0) REVERT: C 251 TYR cc_start: 0.6383 (m-10) cc_final: 0.5917 (m-80) REVERT: C 300 ARG cc_start: 0.7047 (OUTLIER) cc_final: 0.6779 (mtm-85) REVERT: C 375 MET cc_start: 0.6941 (ttp) cc_final: 0.6016 (tpp) REVERT: C 392 LEU cc_start: 0.6272 (OUTLIER) cc_final: 0.5579 (tm) REVERT: C 435 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7975 (mm) REVERT: C 452 ASP cc_start: 0.6950 (m-30) cc_final: 0.6509 (p0) REVERT: D 10 MET cc_start: 0.7150 (mtm) cc_final: 0.6810 (mtp) REVERT: D 45 ASP cc_start: 0.6316 (p0) cc_final: 0.5707 (t0) REVERT: D 115 ARG cc_start: 0.6581 (ptp-110) cc_final: 0.6329 (ptp-170) REVERT: D 337 GLU cc_start: 0.6925 (OUTLIER) cc_final: 0.6096 (mp0) REVERT: D 351 SER cc_start: 0.6370 (m) cc_final: 0.5552 (t) REVERT: D 402 ARG cc_start: 0.6422 (OUTLIER) cc_final: 0.5961 (mtp180) REVERT: D 459 ILE cc_start: 0.6267 (OUTLIER) cc_final: 0.5974 (tt) REVERT: E 3 ARG cc_start: 0.6975 (ptp-110) cc_final: 0.6573 (mmm-85) REVERT: E 204 ASP cc_start: 0.7375 (t70) cc_final: 0.6945 (m-30) REVERT: E 213 MET cc_start: 0.6742 (mtm) cc_final: 0.6513 (mtt) REVERT: E 256 ARG cc_start: 0.7515 (OUTLIER) cc_final: 0.7169 (mmt180) REVERT: E 397 LYS cc_start: 0.5990 (OUTLIER) cc_final: 0.5755 (ptmt) REVERT: E 413 ASN cc_start: 0.7726 (p0) cc_final: 0.7486 (p0) REVERT: F 5 ARG cc_start: 0.7004 (OUTLIER) cc_final: 0.6317 (mtm180) REVERT: F 284 GLU cc_start: 0.6953 (pt0) cc_final: 0.6250 (mm-30) REVERT: F 338 MET cc_start: 0.7708 (mmm) cc_final: 0.7294 (tpt) REVERT: F 352 ARG cc_start: 0.6132 (OUTLIER) cc_final: 0.5773 (ptt180) REVERT: F 392 LEU cc_start: 0.5074 (OUTLIER) cc_final: 0.4873 (pp) REVERT: F 431 LYS cc_start: 0.7416 (OUTLIER) cc_final: 0.7188 (mppt) REVERT: F 438 LYS cc_start: 0.8325 (ttmt) cc_final: 0.8034 (ttmt) outliers start: 84 outliers final: 46 residues processed: 334 average time/residue: 1.2742 time to fit residues: 486.4342 Evaluate side-chains 319 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 256 time to evaluate : 2.532 ------------------------------------------------------------------------------- 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 278 ARG Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 397 GLN Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 472 LEU 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 93 ARG 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 224 VAL Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 319 VAL 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 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 C residue 392 LEU Chi-restraints excluded: chain C residue 435 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 228 VAL Chi-restraints excluded: chain D residue 248 LEU 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 370 VAL Chi-restraints excluded: chain D residue 402 ARG 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 67 THR Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 256 ARG Chi-restraints excluded: chain E residue 397 LYS 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 66 SER 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 75 optimal weight: 7.9990 chunk 150 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 240 optimal weight: 10.0000 chunk 279 optimal weight: 6.9990 chunk 217 optimal weight: 9.9990 chunk 280 optimal weight: 7.9990 chunk 85 optimal weight: 0.9990 chunk 255 optimal weight: 0.0770 chunk 243 optimal weight: 0.8980 chunk 271 optimal weight: 8.9990 overall best weight: 1.7944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 HIS C 433 GLN C 474 HIS ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 324 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.200940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.171425 restraints weight = 24374.138| |-----------------------------------------------------------------------------| r_work (start): 0.4321 rms_B_bonded: 2.18 r_work: 0.4211 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.4072 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.4072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 moved from start: 0.5067 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= 0.138 Angle : 0.625 11.674 30345 Z= 0.323 Chirality : 0.046 0.398 3485 Planarity : 0.005 0.059 3962 Dihedral : 7.621 81.387 3272 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.28 % Allowed : 26.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.15), residues: 2824 helix: 0.87 (0.15), residues: 1096 sheet: 0.10 (0.23), residues: 470 loop : -1.06 (0.17), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.032 0.001 HIS C 474 PHE 0.024 0.001 PHE A 494 TYR 0.023 0.002 TYR E 27 ARG 0.012 0.001 ARG C 171 Details of bonding type rmsd hydrogen bonds : bond 0.04171 ( 968) hydrogen bonds : angle 4.75914 ( 2814) covalent geometry : bond 0.00322 (22371) covalent geometry : angle 0.62494 (30345) ********************** 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 348 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 272 time to evaluate : 2.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 ARG cc_start: 0.6945 (OUTLIER) cc_final: 0.6482 (mmt-90) REVERT: B 60 MET cc_start: 0.6402 (OUTLIER) cc_final: 0.5907 (mmt) REVERT: B 130 GLU cc_start: 0.6663 (mm-30) cc_final: 0.5931 (pp20) REVERT: B 300 ARG cc_start: 0.7859 (mmt90) cc_final: 0.7546 (mtm180) REVERT: B 403 ASP cc_start: 0.7483 (t70) cc_final: 0.7026 (t0) REVERT: C 137 MET cc_start: 0.4409 (mtt) cc_final: 0.4197 (mpp) REVERT: C 210 GLU cc_start: 0.5761 (mm-30) cc_final: 0.5499 (pt0) REVERT: C 251 TYR cc_start: 0.6536 (m-10) cc_final: 0.6080 (m-80) REVERT: C 300 ARG cc_start: 0.7084 (OUTLIER) cc_final: 0.6831 (mtm110) REVERT: C 375 MET cc_start: 0.7033 (ttp) cc_final: 0.6139 (tpp) REVERT: C 392 LEU cc_start: 0.6324 (OUTLIER) cc_final: 0.5650 (tm) REVERT: C 435 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7997 (mm) REVERT: C 452 ASP cc_start: 0.6961 (m-30) cc_final: 0.6589 (p0) REVERT: C 465 ASP cc_start: 0.5683 (t0) cc_final: 0.5314 (t0) REVERT: D 10 MET cc_start: 0.7172 (mtm) cc_final: 0.6844 (mtp) REVERT: D 45 ASP cc_start: 0.6342 (p0) cc_final: 0.5671 (t0) REVERT: D 115 ARG cc_start: 0.6607 (ptp-110) cc_final: 0.6346 (ptp-170) REVERT: D 337 GLU cc_start: 0.7090 (OUTLIER) cc_final: 0.6188 (mp0) REVERT: D 338 MET cc_start: 0.6953 (mtp) cc_final: 0.6729 (mpp) REVERT: D 351 SER cc_start: 0.6488 (m) cc_final: 0.5679 (t) REVERT: D 402 ARG cc_start: 0.6370 (OUTLIER) cc_final: 0.6004 (mtp180) REVERT: D 437 PHE cc_start: 0.7045 (OUTLIER) cc_final: 0.6740 (m-10) REVERT: D 459 ILE cc_start: 0.6329 (OUTLIER) cc_final: 0.5993 (tt) REVERT: E 3 ARG cc_start: 0.6915 (ptp-110) cc_final: 0.6550 (mmt90) REVERT: E 133 GLU cc_start: 0.5475 (pm20) cc_final: 0.5114 (mp0) REVERT: E 204 ASP cc_start: 0.7431 (t70) cc_final: 0.6983 (m-30) REVERT: E 213 MET cc_start: 0.6833 (mtm) cc_final: 0.6595 (mtt) REVERT: E 256 ARG cc_start: 0.7611 (OUTLIER) cc_final: 0.7289 (mmt180) REVERT: E 413 ASN cc_start: 0.7743 (p0) cc_final: 0.7455 (p0) REVERT: F 218 MET cc_start: 0.7433 (mtt) cc_final: 0.6401 (mtt) REVERT: F 284 GLU cc_start: 0.7017 (pt0) cc_final: 0.6303 (mm-30) REVERT: F 338 MET cc_start: 0.7616 (mmm) cc_final: 0.7241 (tpt) REVERT: F 352 ARG cc_start: 0.6165 (OUTLIER) cc_final: 0.5826 (ptt180) REVERT: F 431 LYS cc_start: 0.7456 (OUTLIER) cc_final: 0.7223 (mppt) REVERT: F 438 LYS cc_start: 0.8306 (ttmt) cc_final: 0.7960 (ttmt) outliers start: 76 outliers final: 52 residues processed: 320 average time/residue: 1.2715 time to fit residues: 470.5477 Evaluate side-chains 323 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 259 time to evaluate : 2.463 ------------------------------------------------------------------------------- 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 243 VAL Chi-restraints excluded: chain A residue 278 ARG Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 397 GLN Chi-restraints excluded: chain A residue 406 THR 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 264 SER Chi-restraints excluded: chain B residue 319 VAL 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 115 VAL Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 136 VAL 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 C residue 392 LEU Chi-restraints excluded: chain C residue 435 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 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 370 VAL 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 67 THR Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 256 ARG Chi-restraints excluded: chain E residue 428 VAL Chi-restraints excluded: chain F residue 16 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 431 LYS Chi-restraints excluded: chain F residue 451 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 191 optimal weight: 10.0000 chunk 82 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 188 optimal weight: 0.0770 chunk 80 optimal weight: 7.9990 chunk 95 optimal weight: 10.0000 chunk 97 optimal weight: 4.9990 chunk 259 optimal weight: 9.9990 chunk 216 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 142 optimal weight: 10.0000 overall best weight: 2.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 433 GLN C 474 HIS ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 173 HIS F 259 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.198094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.168624 restraints weight = 24524.623| |-----------------------------------------------------------------------------| r_work (start): 0.4291 rms_B_bonded: 2.18 r_work: 0.4180 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.4040 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.4040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6942 moved from start: 0.5169 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= 0.172 Angle : 0.668 11.787 30345 Z= 0.347 Chirality : 0.047 0.409 3485 Planarity : 0.005 0.051 3962 Dihedral : 7.782 81.307 3272 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.62 % Allowed : 26.98 % Favored : 69.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.15), residues: 2824 helix: 0.67 (0.15), residues: 1093 sheet: 0.01 (0.23), residues: 473 loop : -1.09 (0.17), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.046 0.002 HIS C 474 PHE 0.022 0.002 PHE A 494 TYR 0.027 0.002 TYR E 27 ARG 0.011 0.001 ARG C 171 Details of bonding type rmsd hydrogen bonds : bond 0.04719 ( 968) hydrogen bonds : angle 4.86787 ( 2814) covalent geometry : bond 0.00409 (22371) covalent geometry : angle 0.66792 (30345) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17552.60 seconds wall clock time: 308 minutes 37.41 seconds (18517.41 seconds total)