Starting phenix.real_space_refine on Tue Aug 26 16:12:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vol_21268/08_2025/6vol_21268.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vol_21268/08_2025/6vol_21268.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6vol_21268/08_2025/6vol_21268.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vol_21268/08_2025/6vol_21268.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vol_21268/08_2025/6vol_21268.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vol_21268/08_2025/6vol_21268.map" } resolution = 4.06 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 16 5.49 5 S 129 5.16 5 C 24741 2.51 5 N 6646 2.21 5 O 7459 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 160 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38991 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 3818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3818 Classifications: {'peptide': 497} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 478} Chain: "B" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3851 Classifications: {'peptide': 501} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 482} Chain: "C" Number of atoms: 3843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3843 Classifications: {'peptide': 500} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 481} Chain: "D" Number of atoms: 3627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3627 Classifications: {'peptide': 479} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 24, 'TRANS': 452} Chain: "E" Number of atoms: 3636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3636 Classifications: {'peptide': 480} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 24, 'TRANS': 453} Chain: "F" Number of atoms: 3619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3619 Classifications: {'peptide': 478} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 24, 'TRANS': 451} Chain: "d" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1383 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 4, 'TRANS': 174} Chain: "g" Number of atoms: 2497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2497 Classifications: {'peptide': 321} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 308} Chain: "e" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1010 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "I" Number of atoms: 1213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1213 Classifications: {'peptide': 150} Link IDs: {'TRANS': 149} Chain: "J" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1041 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 3, 'TRANS': 129} Chain: "a" Number of atoms: 1629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1629 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 14, 'TRANS': 195} Chain: "M" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "N" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "O" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "P" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "Q" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "R" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "S" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "T" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "U" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "V" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "W" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "X" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "Y" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "Z" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 61 Unusual residues: {'ATP': 1, 'TTX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.86, per 1000 atoms: 0.20 Number of scatterers: 38991 At special positions: 0 Unit cell: (225.342, 138.996, 154.791, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 129 16.00 P 16 15.00 O 7459 8.00 N 6646 7.00 C 24741 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: 3.49 Conformation dependent library (CDL) restraints added in 1.8 seconds Enol-peptide restraints added in 953.7 nanoseconds 10226 Ramachandran restraints generated. 5113 Oldfield, 0 Emsley, 5113 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9386 Finding SS restraints... Secondary structure from input PDB file: 185 helices and 30 sheets defined 61.7% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 10 through 25 removed outlier: 3.817A pdb=" N TYR A 20 " --> pdb=" O ARG A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 105 removed outlier: 3.528A pdb=" N LEU A 105 " --> pdb=" O GLU A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 158 Processing helix chain 'A' and resid 175 through 187 Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 218 through 221 Processing helix chain 'A' and resid 232 through 253 Proline residue: A 240 - end of helix removed outlier: 3.663A pdb=" N PHE A 250 " --> pdb=" O LEU A 246 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ARG A 253 " --> pdb=" O TYR A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 277 Processing helix chain 'A' and resid 290 through 300 removed outlier: 3.829A pdb=" N HIS A 295 " --> pdb=" O VAL A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 337 Processing helix chain 'A' and resid 346 through 353 Processing helix chain 'A' and resid 367 through 372 removed outlier: 3.540A pdb=" N ALA A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN A 372 " --> pdb=" O GLY A 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 367 through 372' Processing helix chain 'A' and resid 373 through 395 removed outlier: 4.551A pdb=" N LYS A 382 " --> pdb=" O LYS A 378 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU A 383 " --> pdb=" O VAL A 379 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU A 385 " --> pdb=" O GLY A 381 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU A 392 " --> pdb=" O ALA A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 401 removed outlier: 3.932A pdb=" N SER A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 422 Processing helix chain 'A' and resid 430 through 443 removed outlier: 3.591A pdb=" N ASN A 443 " --> pdb=" O TYR A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 468 removed outlier: 4.360A pdb=" N ARG A 455 " --> pdb=" O LEU A 451 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LYS A 456 " --> pdb=" O ASP A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 479 Processing helix chain 'A' and resid 483 through 501 Processing helix chain 'B' and resid 11 through 19 Processing helix chain 'B' and resid 57 through 59 No H-bonds generated for 'chain 'B' and resid 57 through 59' Processing helix chain 'B' and resid 101 through 105 removed outlier: 3.733A pdb=" N TYR B 104 " --> pdb=" O SER B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 158 Processing helix chain 'B' and resid 175 through 187 Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 218 through 220 No H-bonds generated for 'chain 'B' and resid 218 through 220' Processing helix chain 'B' and resid 232 through 253 Proline residue: B 240 - end of helix removed outlier: 3.691A pdb=" N PHE B 250 " --> pdb=" O LEU B 246 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG B 253 " --> pdb=" O TYR B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 278 Processing helix chain 'B' and resid 283 through 287 removed outlier: 3.895A pdb=" N ALA B 286 " --> pdb=" O GLY B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 289 No H-bonds generated for 'chain 'B' and resid 288 through 289' Processing helix chain 'B' and resid 290 through 301 Processing helix chain 'B' and resid 329 through 339 Processing helix chain 'B' and resid 346 through 352 Processing helix chain 'B' and resid 367 through 371 removed outlier: 3.788A pdb=" N ALA B 370 " --> pdb=" O VAL B 367 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA B 371 " --> pdb=" O GLY B 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 367 through 371' Processing helix chain 'B' and resid 373 through 394 removed outlier: 4.526A pdb=" N LYS B 382 " --> pdb=" O LYS B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 397 No H-bonds generated for 'chain 'B' and resid 395 through 397' Processing helix chain 'B' and resid 399 through 403 removed outlier: 4.063A pdb=" N LEU B 403 " --> pdb=" O ALA B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 421 removed outlier: 3.524A pdb=" N GLU B 419 " --> pdb=" O GLN B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 444 Processing helix chain 'B' and resid 453 through 469 Processing helix chain 'B' and resid 470 through 480 removed outlier: 3.657A pdb=" N GLU B 474 " --> pdb=" O PRO B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 504 Processing helix chain 'C' and resid 6 through 20 removed outlier: 4.051A pdb=" N SER C 10 " --> pdb=" O ALA C 6 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY C 19 " --> pdb=" O GLU C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 105 removed outlier: 3.601A pdb=" N TYR C 104 " --> pdb=" O SER C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 157 Processing helix chain 'C' and resid 175 through 186 Processing helix chain 'C' and resid 187 through 190 removed outlier: 3.561A pdb=" N GLN C 190 " --> pdb=" O GLN C 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 187 through 190' Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 232 through 253 Proline residue: C 240 - end of helix removed outlier: 3.781A pdb=" N PHE C 250 " --> pdb=" O LEU C 246 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG C 253 " --> pdb=" O TYR C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 278 removed outlier: 3.904A pdb=" N GLN C 267 " --> pdb=" O ASP C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 287 Processing helix chain 'C' and resid 288 through 289 No H-bonds generated for 'chain 'C' and resid 288 through 289' Processing helix chain 'C' and resid 290 through 300 removed outlier: 3.542A pdb=" N LEU C 298 " --> pdb=" O LEU C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 310 Processing helix chain 'C' and resid 322 through 326 removed outlier: 3.796A pdb=" N GLY C 325 " --> pdb=" O THR C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 339 Processing helix chain 'C' and resid 346 through 352 Processing helix chain 'C' and resid 359 through 363 removed outlier: 3.621A pdb=" N ILE C 362 " --> pdb=" O ASN C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 372 removed outlier: 3.651A pdb=" N ALA C 370 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 381 Processing helix chain 'C' and resid 382 through 397 Processing helix chain 'C' and resid 404 through 421 Processing helix chain 'C' and resid 430 through 443 Processing helix chain 'C' and resid 453 through 469 Processing helix chain 'C' and resid 469 through 479 removed outlier: 4.584A pdb=" N GLN C 473 " --> pdb=" O LYS C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 504 Processing helix chain 'D' and resid 103 through 107 removed outlier: 3.561A pdb=" N THR D 106 " --> pdb=" O GLY D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 142 removed outlier: 3.846A pdb=" N LEU D 142 " --> pdb=" O PHE D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 159 Processing helix chain 'D' and resid 177 through 192 Processing helix chain 'D' and resid 205 through 219 Processing helix chain 'D' and resid 242 through 263 removed outlier: 3.632A pdb=" N ARG D 246 " --> pdb=" O PRO D 242 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N MET D 247 " --> pdb=" O PRO D 243 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N GLY D 250 " --> pdb=" O ARG D 246 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LEU D 251 " --> pdb=" O MET D 247 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N PHE D 260 " --> pdb=" O MET D 256 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG D 261 " --> pdb=" O ALA D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 290 Processing helix chain 'D' and resid 301 through 311 removed outlier: 3.716A pdb=" N LEU D 309 " --> pdb=" O GLU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 333 removed outlier: 3.960A pdb=" N ASP D 332 " --> pdb=" O VAL D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 344 Processing helix chain 'D' and resid 353 through 359 removed outlier: 4.076A pdb=" N ALA D 357 " --> pdb=" O SER D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 381 Processing helix chain 'D' and resid 381 through 402 Processing helix chain 'D' and resid 403 through 409 removed outlier: 3.860A pdb=" N ILE D 407 " --> pdb=" O ASP D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 431 Processing helix chain 'D' and resid 438 through 443 Processing helix chain 'D' and resid 450 through 463 Processing helix chain 'D' and resid 470 through 475 Processing helix chain 'D' and resid 479 through 496 removed outlier: 4.758A pdb=" N LEU D 496 " --> pdb=" O MET D 492 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 107 Processing helix chain 'E' and resid 153 through 160 Processing helix chain 'E' and resid 177 through 193 removed outlier: 5.365A pdb=" N LYS E 191 " --> pdb=" O ASN E 187 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ALA E 192 " --> pdb=" O ASN E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 219 Processing helix chain 'E' and resid 242 through 264 removed outlier: 3.682A pdb=" N ARG E 246 " --> pdb=" O PRO E 242 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N GLY E 250 " --> pdb=" O ARG E 246 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N LEU E 251 " --> pdb=" O MET E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 290 removed outlier: 3.925A pdb=" N VAL E 279 " --> pdb=" O ILE E 275 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA E 287 " --> pdb=" O SER E 283 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N LEU E 288 " --> pdb=" O GLU E 284 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY E 290 " --> pdb=" O SER E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 311 Processing helix chain 'E' and resid 330 through 333 Processing helix chain 'E' and resid 336 through 346 removed outlier: 4.316A pdb=" N ALA E 344 " --> pdb=" O ALA E 340 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N HIS E 345 " --> pdb=" O THR E 341 " (cutoff:3.500A) Processing helix chain 'E' and resid 353 through 359 Processing helix chain 'E' and resid 376 through 381 Processing helix chain 'E' and resid 381 through 409 removed outlier: 5.206A pdb=" N ASP E 403 " --> pdb=" O LYS E 399 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ILE E 404 " --> pdb=" O GLU E 400 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 431 Processing helix chain 'E' and resid 438 through 443 Processing helix chain 'E' and resid 450 through 464 Processing helix chain 'E' and resid 470 through 475 Processing helix chain 'E' and resid 479 through 496 removed outlier: 3.590A pdb=" N LYS E 495 " --> pdb=" O GLU E 491 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 107 Processing helix chain 'F' and resid 153 through 160 removed outlier: 3.686A pdb=" N ALA F 160 " --> pdb=" O VAL F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 193 removed outlier: 4.362A pdb=" N LYS F 191 " --> pdb=" O ASN F 187 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ALA F 192 " --> pdb=" O ASN F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 219 Processing helix chain 'F' and resid 248 through 265 Processing helix chain 'F' and resid 274 through 290 removed outlier: 3.923A pdb=" N PHE F 278 " --> pdb=" O ASN F 274 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU F 288 " --> pdb=" O GLU F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 311 removed outlier: 3.607A pdb=" N LEU F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 333 Processing helix chain 'F' and resid 336 through 343 Processing helix chain 'F' and resid 353 through 360 removed outlier: 3.974A pdb=" N ALA F 357 " --> pdb=" O SER F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 376 through 381 Processing helix chain 'F' and resid 381 through 408 removed outlier: 4.477A pdb=" N ASP F 403 " --> pdb=" O LYS F 399 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N ILE F 404 " --> pdb=" O GLU F 400 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE F 407 " --> pdb=" O ASP F 403 " (cutoff:3.500A) Processing helix chain 'F' and resid 409 through 413 removed outlier: 3.634A pdb=" N GLU F 412 " --> pdb=" O GLY F 409 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU F 413 " --> pdb=" O LEU F 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 409 through 413' Processing helix chain 'F' and resid 414 through 431 Processing helix chain 'F' and resid 450 through 464 removed outlier: 3.913A pdb=" N ARG F 456 " --> pdb=" O ALA F 452 " (cutoff:3.500A) Processing helix chain 'F' and resid 465 through 469 removed outlier: 4.324A pdb=" N SER F 468 " --> pdb=" O GLU F 465 " (cutoff:3.500A) Processing helix chain 'F' and resid 471 through 475 Processing helix chain 'F' and resid 479 through 493 Processing helix chain 'd' and resid 73 through 90 Processing helix chain 'd' and resid 91 through 108 removed outlier: 3.572A pdb=" N ASP d 98 " --> pdb=" O ALA d 94 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ARG d 104 " --> pdb=" O GLU d 100 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLU d 108 " --> pdb=" O ARG d 104 " (cutoff:3.500A) Processing helix chain 'd' and resid 108 through 117 removed outlier: 3.801A pdb=" N TYR d 112 " --> pdb=" O GLU d 108 " (cutoff:3.500A) Processing helix chain 'd' and resid 121 through 137 Processing helix chain 'd' and resid 139 through 153 Processing helix chain 'd' and resid 154 through 156 No H-bonds generated for 'chain 'd' and resid 154 through 156' Processing helix chain 'd' and resid 157 through 174 removed outlier: 4.005A pdb=" N GLU d 166 " --> pdb=" O LEU d 162 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASP d 167 " --> pdb=" O ASN d 163 " (cutoff:3.500A) Processing helix chain 'd' and resid 187 through 203 Processing helix chain 'd' and resid 237 through 248 removed outlier: 4.067A pdb=" N GLN d 247 " --> pdb=" O GLU d 243 " (cutoff:3.500A) Processing helix chain 'g' and resid 44 through 100 removed outlier: 3.704A pdb=" N VAL g 80 " --> pdb=" O GLN g 76 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASN g 81 " --> pdb=" O GLU g 77 " (cutoff:3.500A) Proline residue: g 84 - end of helix removed outlier: 3.514A pdb=" N MET g 96 " --> pdb=" O VAL g 92 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASN g 97 " --> pdb=" O LEU g 93 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU g 98 " --> pdb=" O TYR g 94 " (cutoff:3.500A) Processing helix chain 'g' and resid 132 through 152 removed outlier: 3.619A pdb=" N LEU g 137 " --> pdb=" O PHE g 133 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU g 142 " --> pdb=" O LEU g 138 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LYS g 150 " --> pdb=" O ALA g 146 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LEU g 151 " --> pdb=" O GLU g 147 " (cutoff:3.500A) Processing helix chain 'g' and resid 162 through 171 Processing helix chain 'g' and resid 188 through 204 removed outlier: 4.085A pdb=" N SER g 204 " --> pdb=" O SER g 200 " (cutoff:3.500A) Processing helix chain 'g' and resid 241 through 245 Processing helix chain 'g' and resid 287 through 363 Proline residue: g 297 - end of helix removed outlier: 4.406A pdb=" N ASP g 328 " --> pdb=" O SER g 324 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY g 359 " --> pdb=" O GLU g 355 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA g 360 " --> pdb=" O ILE g 356 " (cutoff:3.500A) Processing helix chain 'e' and resid 85 through 87 No H-bonds generated for 'chain 'e' and resid 85 through 87' Processing helix chain 'e' and resid 88 through 106 Processing helix chain 'e' and resid 108 through 130 Processing helix chain 'I' and resid 34 through 157 removed outlier: 3.937A pdb=" N GLU I 106 " --> pdb=" O GLU I 102 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N LYS I 107 " --> pdb=" O ILE I 103 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N MET I 108 " --> pdb=" O GLU I 104 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ASN I 109 " --> pdb=" O ARG I 105 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN I 123 " --> pdb=" O GLU I 119 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N TYR I 124 " --> pdb=" O GLN I 120 " (cutoff:3.500A) Processing helix chain 'I' and resid 158 through 182 Processing helix chain 'J' and resid 89 through 110 Processing helix chain 'J' and resid 110 through 213 Processing helix chain 'a' and resid 36 through 60 removed outlier: 4.706A pdb=" N THR a 42 " --> pdb=" O GLN a 38 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL a 45 " --> pdb=" O ILE a 41 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA a 55 " --> pdb=" O LEU a 51 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALA a 57 " --> pdb=" O SER a 53 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N VAL a 58 " --> pdb=" O ALA a 54 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N SER a 60 " --> pdb=" O ILE a 56 " (cutoff:3.500A) Processing helix chain 'a' and resid 68 through 87 removed outlier: 3.601A pdb=" N PHE a 72 " --> pdb=" O GLY a 68 " (cutoff:3.500A) Processing helix chain 'a' and resid 91 through 93 No H-bonds generated for 'chain 'a' and resid 91 through 93' Processing helix chain 'a' and resid 94 through 114 removed outlier: 4.076A pdb=" N MET a 101 " --> pdb=" O PHE a 97 " (cutoff:3.500A) Processing helix chain 'a' and resid 129 through 132 removed outlier: 3.505A pdb=" N ASN a 132 " --> pdb=" O ALA a 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 129 through 132' Processing helix chain 'a' and resid 133 through 155 removed outlier: 4.272A pdb=" N THR a 137 " --> pdb=" O ASP a 133 " (cutoff:3.500A) Processing helix chain 'a' and resid 171 through 208 Proline residue: a 183 - end of helix removed outlier: 4.231A pdb=" N LEU a 190 " --> pdb=" O LEU a 186 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ASN a 193 " --> pdb=" O ARG a 189 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N VAL a 202 " --> pdb=" O GLU a 198 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU a 207 " --> pdb=" O VAL a 203 " (cutoff:3.500A) Processing helix chain 'a' and resid 213 through 244 removed outlier: 4.506A pdb=" N GLY a 225 " --> pdb=" O LEU a 221 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE a 226 " --> pdb=" O PHE a 222 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 21 removed outlier: 3.882A pdb=" N VAL M 17 " --> pdb=" O ALA M 13 " (cutoff:3.500A) Processing helix chain 'M' and resid 21 through 42 removed outlier: 4.310A pdb=" N GLY M 25 " --> pdb=" O SER M 21 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N VAL M 26 " --> pdb=" O ILE M 22 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 76 removed outlier: 3.751A pdb=" N THR M 52 " --> pdb=" O LYS M 48 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU M 63 " --> pdb=" O PHE M 59 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR M 64 " --> pdb=" O MET M 60 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY M 67 " --> pdb=" O LEU M 63 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 21 removed outlier: 4.747A pdb=" N VAL N 17 " --> pdb=" O ALA N 13 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLY N 18 " --> pdb=" O GLY N 14 " (cutoff:3.500A) Processing helix chain 'N' and resid 22 through 42 removed outlier: 3.533A pdb=" N VAL N 26 " --> pdb=" O ILE N 22 " (cutoff:3.500A) Processing helix chain 'N' and resid 45 through 76 removed outlier: 4.544A pdb=" N THR N 52 " --> pdb=" O LYS N 48 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU N 63 " --> pdb=" O PHE N 59 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY N 67 " --> pdb=" O LEU N 63 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 20 Processing helix chain 'O' and resid 21 through 42 removed outlier: 3.667A pdb=" N VAL O 26 " --> pdb=" O ILE O 22 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLY O 29 " --> pdb=" O GLY O 25 " (cutoff:3.500A) Processing helix chain 'O' and resid 45 through 76 removed outlier: 4.545A pdb=" N GLY O 51 " --> pdb=" O GLY O 47 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR O 52 " --> pdb=" O LYS O 48 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU O 63 " --> pdb=" O PHE O 59 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N THR O 64 " --> pdb=" O MET O 60 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLY O 67 " --> pdb=" O LEU O 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 4 through 21 removed outlier: 4.085A pdb=" N VAL P 17 " --> pdb=" O ALA P 13 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER P 21 " --> pdb=" O VAL P 17 " (cutoff:3.500A) Processing helix chain 'P' and resid 21 through 40 removed outlier: 3.539A pdb=" N VAL P 26 " --> pdb=" O ILE P 22 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLY P 29 " --> pdb=" O GLY P 25 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA P 40 " --> pdb=" O VAL P 36 " (cutoff:3.500A) Processing helix chain 'P' and resid 45 through 76 removed outlier: 3.856A pdb=" N THR P 64 " --> pdb=" O MET P 60 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLY P 67 " --> pdb=" O LEU P 63 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 39 Proline residue: Q 24 - end of helix Processing helix chain 'Q' and resid 40 through 44 Proline residue: Q 43 - end of helix No H-bonds generated for 'chain 'Q' and resid 40 through 44' Processing helix chain 'Q' and resid 45 through 76 removed outlier: 3.998A pdb=" N THR Q 52 " --> pdb=" O LYS Q 48 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU Q 63 " --> pdb=" O PHE Q 59 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR Q 64 " --> pdb=" O MET Q 60 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 42 removed outlier: 3.872A pdb=" N SER R 9 " --> pdb=" O ILE R 5 " (cutoff:3.500A) Proline residue: R 24 - end of helix Processing helix chain 'R' and resid 45 through 76 removed outlier: 3.638A pdb=" N ARG R 50 " --> pdb=" O GLU R 46 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N GLY R 51 " --> pdb=" O GLY R 47 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N THR R 52 " --> pdb=" O LYS R 48 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU R 63 " --> pdb=" O PHE R 59 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR R 64 " --> pdb=" O MET R 60 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLY R 67 " --> pdb=" O LEU R 63 " (cutoff:3.500A) Processing helix chain 'S' and resid 4 through 42 Proline residue: S 24 - end of helix Processing helix chain 'S' and resid 45 through 76 removed outlier: 3.756A pdb=" N THR S 52 " --> pdb=" O LYS S 48 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LEU S 63 " --> pdb=" O PHE S 59 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR S 64 " --> pdb=" O MET S 60 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY S 67 " --> pdb=" O LEU S 63 " (cutoff:3.500A) Processing helix chain 'T' and resid 4 through 42 Proline residue: T 24 - end of helix Processing helix chain 'T' and resid 45 through 76 removed outlier: 3.500A pdb=" N GLY T 51 " --> pdb=" O GLY T 47 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LEU T 63 " --> pdb=" O PHE T 59 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N THR T 64 " --> pdb=" O MET T 60 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY T 67 " --> pdb=" O LEU T 63 " (cutoff:3.500A) Processing helix chain 'U' and resid 4 through 42 removed outlier: 4.025A pdb=" N VAL U 10 " --> pdb=" O ALA U 6 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ILE U 11 " --> pdb=" O ALA U 7 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA U 12 " --> pdb=" O ALA U 8 " (cutoff:3.500A) Proline residue: U 24 - end of helix Processing helix chain 'U' and resid 45 through 76 removed outlier: 3.764A pdb=" N THR U 52 " --> pdb=" O LYS U 48 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LEU U 63 " --> pdb=" O PHE U 59 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N THR U 64 " --> pdb=" O MET U 60 " (cutoff:3.500A) Processing helix chain 'V' and resid 4 through 40 removed outlier: 4.150A pdb=" N VAL V 10 " --> pdb=" O ALA V 6 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ILE V 11 " --> pdb=" O ALA V 7 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA V 12 " --> pdb=" O ALA V 8 " (cutoff:3.500A) Proline residue: V 24 - end of helix removed outlier: 3.857A pdb=" N ALA V 40 " --> pdb=" O VAL V 36 " (cutoff:3.500A) Processing helix chain 'V' and resid 41 through 44 removed outlier: 6.949A pdb=" N GLU V 44 " --> pdb=" O ARG V 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 41 through 44' Processing helix chain 'V' and resid 45 through 76 removed outlier: 3.693A pdb=" N GLY V 51 " --> pdb=" O GLY V 47 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR V 52 " --> pdb=" O LYS V 48 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU V 63 " --> pdb=" O PHE V 59 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR V 64 " --> pdb=" O MET V 60 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY V 67 " --> pdb=" O LEU V 63 " (cutoff:3.500A) Processing helix chain 'W' and resid 4 through 42 removed outlier: 3.514A pdb=" N VAL W 10 " --> pdb=" O ALA W 6 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE W 11 " --> pdb=" O ALA W 7 " (cutoff:3.500A) Proline residue: W 24 - end of helix Processing helix chain 'W' and resid 45 through 76 removed outlier: 3.960A pdb=" N GLY W 51 " --> pdb=" O GLY W 47 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N THR W 52 " --> pdb=" O LYS W 48 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU W 63 " --> pdb=" O PHE W 59 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N THR W 64 " --> pdb=" O MET W 60 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY W 67 " --> pdb=" O LEU W 63 " (cutoff:3.500A) Processing helix chain 'X' and resid 4 through 42 removed outlier: 4.098A pdb=" N VAL X 10 " --> pdb=" O ALA X 6 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE X 11 " --> pdb=" O ALA X 7 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA X 12 " --> pdb=" O ALA X 8 " (cutoff:3.500A) Proline residue: X 24 - end of helix Processing helix chain 'X' and resid 45 through 76 removed outlier: 4.368A pdb=" N GLY X 51 " --> pdb=" O GLY X 47 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR X 52 " --> pdb=" O LYS X 48 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LEU X 63 " --> pdb=" O PHE X 59 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N THR X 64 " --> pdb=" O MET X 60 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLY X 67 " --> pdb=" O LEU X 63 " (cutoff:3.500A) Processing helix chain 'Y' and resid 4 through 42 removed outlier: 3.503A pdb=" N VAL Y 10 " --> pdb=" O ALA Y 6 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ILE Y 11 " --> pdb=" O ALA Y 7 " (cutoff:3.500A) Proline residue: Y 24 - end of helix removed outlier: 3.775A pdb=" N GLN Y 42 " --> pdb=" O GLY Y 38 " (cutoff:3.500A) Processing helix chain 'Y' and resid 44 through 76 removed outlier: 4.621A pdb=" N LYS Y 48 " --> pdb=" O GLU Y 44 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N GLY Y 51 " --> pdb=" O GLY Y 47 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N THR Y 52 " --> pdb=" O LYS Y 48 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU Y 63 " --> pdb=" O PHE Y 59 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR Y 64 " --> pdb=" O MET Y 60 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLY Y 67 " --> pdb=" O LEU Y 63 " (cutoff:3.500A) Processing helix chain 'Z' and resid 4 through 22 removed outlier: 3.631A pdb=" N VAL Z 10 " --> pdb=" O ALA Z 6 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ILE Z 11 " --> pdb=" O ALA Z 7 " (cutoff:3.500A) Processing helix chain 'Z' and resid 23 through 39 removed outlier: 4.829A pdb=" N GLY Z 29 " --> pdb=" O GLY Z 25 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR Z 30 " --> pdb=" O VAL Z 26 " (cutoff:3.500A) Processing helix chain 'Z' and resid 45 through 76 removed outlier: 3.814A pdb=" N GLY Z 51 " --> pdb=" O GLY Z 47 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR Z 52 " --> pdb=" O LYS Z 48 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU Z 63 " --> pdb=" O PHE Z 59 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N THR Z 64 " --> pdb=" O MET Z 60 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY Z 67 " --> pdb=" O LEU Z 63 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 30 through 36 removed outlier: 4.393A pdb=" N GLU E 90 " --> pdb=" O LYS E 50 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU C 67 " --> pdb=" O ILE E 26 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N ASN C 28 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU C 33 " --> pdb=" O ARG C 41 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ARG C 41 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N VAL C 35 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ILE C 39 " --> pdb=" O VAL C 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 72 through 76 removed outlier: 3.845A pdb=" N GLN A 34 " --> pdb=" O ARG A 41 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY A 30 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL A 89 " --> pdb=" O GLY A 30 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY A 62 " --> pdb=" O VAL A 54 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ASP F 32 " --> pdb=" O ALA F 24 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ILE F 26 " --> pdb=" O VAL F 30 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL F 30 " --> pdb=" O ILE F 26 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ARG F 73 " --> pdb=" O LEU F 68 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N LEU F 68 " --> pdb=" O ARG F 73 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ARG F 75 " --> pdb=" O GLN F 66 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 45 through 49 removed outlier: 6.793A pdb=" N ALA F 46 " --> pdb=" O THR F 94 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR F 94 " --> pdb=" O ALA F 46 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY F 21 " --> pdb=" O VAL F 91 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ALA A 64 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL A 75 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLN A 34 " --> pdb=" O ARG A 41 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ARG D 75 " --> pdb=" O GLN D 66 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N LEU D 68 " --> pdb=" O ARG D 73 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ARG D 73 " --> pdb=" O LEU D 68 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL D 30 " --> pdb=" O ILE D 26 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ILE D 26 " --> pdb=" O VAL D 30 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ASP D 32 " --> pdb=" O ALA D 24 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 71 through 77 removed outlier: 6.933A pdb=" N VAL C 75 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N ALA C 64 " --> pdb=" O VAL C 75 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N MET C 77 " --> pdb=" O GLY C 62 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N GLY C 62 " --> pdb=" O MET C 77 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU C 67 " --> pdb=" O ILE E 26 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N ILE E 23 " --> pdb=" O ALA E 34 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ALA E 34 " --> pdb=" O ILE E 23 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N ARG E 73 " --> pdb=" O LEU E 68 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N LEU E 68 " --> pdb=" O ARG E 73 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ARG E 75 " --> pdb=" O GLN E 66 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL B 32 " --> pdb=" O HIS B 43 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N HIS B 43 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN B 34 " --> pdb=" O ARG B 41 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY B 36 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N VAL B 75 " --> pdb=" O ALA B 64 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N ALA B 64 " --> pdb=" O VAL B 75 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLU D 90 " --> pdb=" O LYS D 50 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 97 through 99 Processing sheet with id=AA6, first strand: chain 'A' and resid 108 through 109 removed outlier: 6.303A pdb=" N ILE A 109 " --> pdb=" O ALA A 226 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 168 through 170 Processing sheet with id=AA8, first strand: chain 'A' and resid 195 through 196 removed outlier: 3.672A pdb=" N THR A 315 " --> pdb=" O THR A 257 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 282 through 283 Processing sheet with id=AB1, first strand: chain 'A' and resid 341 through 342 removed outlier: 3.612A pdb=" N GLN A 342 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 97 through 99 Processing sheet with id=AB3, first strand: chain 'B' and resid 319 through 321 removed outlier: 6.482A pdb=" N LEU B 167 " --> pdb=" O ILE B 343 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 222 through 228 Processing sheet with id=AB5, first strand: chain 'C' and resid 97 through 100 removed outlier: 3.845A pdb=" N GLU C 126 " --> pdb=" O VAL C 100 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 108 through 109 Processing sheet with id=AB7, first strand: chain 'C' and resid 167 through 170 removed outlier: 6.511A pdb=" N LEU C 167 " --> pdb=" O ILE C 343 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N LEU C 345 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ILE C 169 " --> pdb=" O LEU C 345 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'D' and resid 99 through 101 Processing sheet with id=AB9, first strand: chain 'D' and resid 234 through 238 removed outlier: 6.348A pdb=" N VAL D 268 " --> pdb=" O THR D 322 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ILE D 324 " --> pdb=" O VAL D 268 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LEU D 270 " --> pdb=" O ILE D 324 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ALA D 326 " --> pdb=" O LEU D 270 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ILE D 272 " --> pdb=" O ALA D 326 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE D 171 " --> pdb=" O THR D 350 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 99 through 101 Processing sheet with id=AC2, first strand: chain 'E' and resid 148 through 149 removed outlier: 4.527A pdb=" N TYR E 162 " --> pdb=" O PHE E 149 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 232 through 238 removed outlier: 7.296A pdb=" N SER E 197 " --> pdb=" O ALA E 233 " (cutoff:3.500A) removed outlier: 8.654A pdb=" N VAL E 235 " --> pdb=" O SER E 197 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N PHE E 199 " --> pdb=" O VAL E 235 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N GLY E 237 " --> pdb=" O PHE E 199 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N GLY E 201 " --> pdb=" O GLY E 237 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ILE E 168 " --> pdb=" O GLN E 325 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N VAL E 327 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N LEU E 170 " --> pdb=" O VAL E 327 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 99 through 101 Processing sheet with id=AC5, first strand: chain 'F' and resid 148 through 149 removed outlier: 3.788A pdb=" N TYR F 162 " --> pdb=" O PHE F 149 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 232 through 237 removed outlier: 3.998A pdb=" N LEU F 270 " --> pdb=" O THR F 322 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N ILE F 168 " --> pdb=" O GLN F 325 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL F 327 " --> pdb=" O ILE F 168 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N LEU F 170 " --> pdb=" O VAL F 327 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'd' and resid 175 through 182 removed outlier: 6.197A pdb=" N GLU d 176 " --> pdb=" O ARG d 208 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N LYS d 210 " --> pdb=" O GLU d 176 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ALA d 178 " --> pdb=" O LYS d 210 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N VAL d 212 " --> pdb=" O ALA d 178 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL d 180 " --> pdb=" O VAL d 212 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'g' and resid 176 through 180 removed outlier: 10.511A pdb=" N TYR g 155 " --> pdb=" O VAL g 176 " (cutoff:3.500A) removed outlier: 10.566A pdb=" N ARG g 178 " --> pdb=" O TYR g 155 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N ILE g 157 " --> pdb=" O ARG g 178 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N PHE g 180 " --> pdb=" O ILE g 157 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N SER g 159 " --> pdb=" O PHE g 180 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL g 118 " --> pdb=" O THR g 156 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N ILE g 158 " --> pdb=" O VAL g 118 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU g 120 " --> pdb=" O ILE g 158 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N ILE g 160 " --> pdb=" O LEU g 120 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N VAL g 122 " --> pdb=" O ILE g 160 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N GLU g 211 " --> pdb=" O LYS g 117 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ALA g 119 " --> pdb=" O GLU g 211 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N LEU g 213 " --> pdb=" O ALA g 119 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N MET g 121 " --> pdb=" O LEU g 213 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL g 210 " --> pdb=" O LEU g 230 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'g' and resid 255 through 256 Processing sheet with id=AD1, first strand: chain 'g' and resid 283 through 284 removed outlier: 5.535A pdb=" N GLU g 283 " --> pdb=" O ALA e 41 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'e' and resid 30 through 33 removed outlier: 3.515A pdb=" N ILE e 22 " --> pdb=" O VAL e 33 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ILE e 23 " --> pdb=" O ARG e 50 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ARG e 50 " --> pdb=" O ILE e 23 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'e' and resid 60 through 62 2476 hydrogen bonds defined for protein. 7257 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.05 Time building geometry restraints manager: 4.32 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: 11973 1.34 - 1.45: 4674 1.45 - 1.57: 22618 1.57 - 1.69: 26 1.69 - 1.81: 246 Bond restraints: 39537 Sorted by residual: bond pdb=" C4 ATP A 601 " pdb=" C5 ATP A 601 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.23e+01 bond pdb=" C4 ATP F 502 " pdb=" C5 ATP F 502 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.99e+01 bond pdb=" C4 ATP C 601 " pdb=" C5 ATP C 601 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.91e+01 bond pdb=" C4 ATP B 601 " pdb=" C5 ATP B 601 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.74e+01 bond pdb=" C5 ATP C 601 " pdb=" C6 ATP C 601 " ideal model delta sigma weight residual 1.409 1.479 -0.070 1.00e-02 1.00e+04 4.95e+01 ... (remaining 39532 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.36: 53403 4.36 - 8.72: 204 8.72 - 13.08: 8 13.08 - 17.44: 2 17.44 - 21.80: 6 Bond angle restraints: 53623 Sorted by residual: angle pdb=" PB ATP C 601 " pdb=" O3B ATP C 601 " pdb=" PG ATP C 601 " ideal model delta sigma weight residual 139.87 118.07 21.80 1.00e+00 1.00e+00 4.75e+02 angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 119.20 20.67 1.00e+00 1.00e+00 4.27e+02 angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 119.67 20.20 1.00e+00 1.00e+00 4.08e+02 angle pdb=" PA ATP B 601 " pdb=" O3A ATP B 601 " pdb=" PB ATP B 601 " ideal model delta sigma weight residual 136.83 117.26 19.57 1.00e+00 1.00e+00 3.83e+02 angle pdb=" PA ATP C 601 " pdb=" O3A ATP C 601 " pdb=" PB ATP C 601 " ideal model delta sigma weight residual 136.83 118.19 18.64 1.00e+00 1.00e+00 3.48e+02 ... (remaining 53618 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.79: 23444 33.79 - 67.59: 601 67.59 - 101.38: 53 101.38 - 135.17: 3 135.17 - 168.96: 3 Dihedral angle restraints: 24104 sinusoidal: 9452 harmonic: 14652 Sorted by residual: dihedral pdb=" CA ALA F 295 " pdb=" C ALA F 295 " pdb=" N VAL F 296 " pdb=" CA VAL F 296 " ideal model delta harmonic sigma weight residual 180.00 -129.45 -50.55 0 5.00e+00 4.00e-02 1.02e+02 dihedral pdb=" CA ALA D 295 " pdb=" C ALA D 295 " pdb=" N VAL D 296 " pdb=" CA VAL D 296 " ideal model delta harmonic sigma weight residual -180.00 -139.93 -40.07 0 5.00e+00 4.00e-02 6.42e+01 dihedral pdb=" CA TYR B 20 " pdb=" C TYR B 20 " pdb=" N ASN B 21 " pdb=" CA ASN B 21 " ideal model delta harmonic sigma weight residual -180.00 -145.07 -34.93 0 5.00e+00 4.00e-02 4.88e+01 ... (remaining 24101 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 4998 0.053 - 0.105: 1193 0.105 - 0.158: 205 0.158 - 0.211: 14 0.211 - 0.263: 7 Chirality restraints: 6417 Sorted by residual: chirality pdb=" CB ILE e 51 " pdb=" CA ILE e 51 " pdb=" CG1 ILE e 51 " pdb=" CG2 ILE e 51 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA THR J 110 " pdb=" N THR J 110 " pdb=" C THR J 110 " pdb=" CB THR J 110 " both_signs ideal model delta sigma weight residual False 2.53 2.28 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CB ILE A 354 " pdb=" CA ILE A 354 " pdb=" CG1 ILE A 354 " pdb=" CG2 ILE A 354 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 6414 not shown) Planarity restraints: 6914 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C11 TTX F 501 " 0.684 2.00e-02 2.50e+03 6.32e-01 5.99e+03 pdb=" C12 TTX F 501 " -0.071 2.00e-02 2.50e+03 pdb=" C13 TTX F 501 " 0.880 2.00e-02 2.50e+03 pdb=" C9 TTX F 501 " -0.627 2.00e-02 2.50e+03 pdb=" N3 TTX F 501 " 0.005 2.00e-02 2.50e+03 pdb=" O3 TTX F 501 " -0.870 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C15 TTX F 501 " 0.332 2.00e-02 2.50e+03 3.97e-01 2.36e+03 pdb=" C5 TTX F 501 " -0.514 2.00e-02 2.50e+03 pdb=" C6 TTX F 501 " 0.079 2.00e-02 2.50e+03 pdb=" C7 TTX F 501 " -0.576 2.00e-02 2.50e+03 pdb=" N1 TTX F 501 " 0.325 2.00e-02 2.50e+03 pdb=" O1 TTX F 501 " 0.354 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C13 TTX F 501 " -0.544 2.00e-02 2.50e+03 2.72e-01 1.48e+03 pdb=" C14 TTX F 501 " 0.138 2.00e-02 2.50e+03 pdb=" C15 TTX F 501 " 0.094 2.00e-02 2.50e+03 pdb=" C16 TTX F 501 " -0.083 2.00e-02 2.50e+03 pdb=" C17 TTX F 501 " -0.175 2.00e-02 2.50e+03 pdb=" N1 TTX F 501 " 0.236 2.00e-02 2.50e+03 pdb=" N4 TTX F 501 " 0.412 2.00e-02 2.50e+03 pdb=" O4 TTX F 501 " -0.079 2.00e-02 2.50e+03 ... (remaining 6911 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 1087 2.70 - 3.25: 41548 3.25 - 3.80: 64592 3.80 - 4.35: 83213 4.35 - 4.90: 135379 Nonbonded interactions: 325819 Sorted by model distance: nonbonded pdb=" O ALA D 295 " pdb=" N GLY D 297 " model vdw 2.148 3.120 nonbonded pdb=" O ASP A 402 " pdb=" OG1 THR A 407 " model vdw 2.149 3.040 nonbonded pdb=" OH TYR C 196 " pdb=" OD2 ASP C 262 " model vdw 2.174 3.040 nonbonded pdb=" OG1 THR B 149 " pdb=" OG1 THR B 183 " model vdw 2.178 3.040 nonbonded pdb=" O ALA E 295 " pdb=" N GLY E 297 " model vdw 2.204 3.120 ... (remaining 325814 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' selection = (chain 'B' and (resid 7 through 503 or resid 601)) selection = (chain 'C' and (resid 7 through 503 or resid 601)) } ncs_group { reference = (chain 'D' and resid 18 through 494) selection = (chain 'E' and resid 18 through 494) selection = (chain 'F' and resid 18 through 494) } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } 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 group one per residue 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: 6.420 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 33.080 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 39537 Z= 0.275 Angle : 0.890 21.798 53623 Z= 0.556 Chirality : 0.046 0.263 6417 Planarity : 0.011 0.632 6914 Dihedral : 15.393 168.964 14718 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.20 % Favored : 94.66 % Rotamer: Outliers : 0.12 % Allowed : 7.24 % Favored : 92.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.18 (0.10), residues: 5113 helix: -1.50 (0.08), residues: 2855 sheet: -2.79 (0.19), residues: 504 loop : -2.69 (0.13), residues: 1754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 119 TYR 0.051 0.002 TYR J 109 PHE 0.027 0.002 PHE E 343 TRP 0.017 0.002 TRP e 57 HIS 0.004 0.001 HIS F 133 Details of bonding type rmsd covalent geometry : bond 0.00515 (39537) covalent geometry : angle 0.88985 (53623) hydrogen bonds : bond 0.12171 ( 2462) hydrogen bonds : angle 6.05160 ( 7257) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10226 Ramachandran restraints generated. 5113 Oldfield, 0 Emsley, 5113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10226 Ramachandran restraints generated. 5113 Oldfield, 0 Emsley, 5113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 894 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 889 time to evaluate : 1.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7068 (mm-30) REVERT: A 131 GLU cc_start: 0.7808 (tm-30) cc_final: 0.7577 (tm-30) REVERT: A 293 TYR cc_start: 0.8554 (t80) cc_final: 0.8200 (t80) REVERT: A 430 THR cc_start: 0.8169 (p) cc_final: 0.7298 (p) REVERT: B 171 ASP cc_start: 0.5609 (t0) cc_final: 0.5386 (t0) REVERT: C 251 MET cc_start: 0.8566 (ttp) cc_final: 0.8311 (ttm) REVERT: C 321 GLU cc_start: 0.8469 (tm-30) cc_final: 0.7875 (tm-30) REVERT: C 498 MET cc_start: 0.6898 (tpp) cc_final: 0.6100 (ttp) REVERT: D 79 MET cc_start: 0.8218 (mmp) cc_final: 0.8007 (mmp) REVERT: D 239 MET cc_start: 0.7790 (mtt) cc_final: 0.7333 (mtm) REVERT: D 311 GLU cc_start: 0.7297 (mt-10) cc_final: 0.6912 (mm-30) REVERT: D 333 ASP cc_start: 0.8618 (t0) cc_final: 0.8386 (t0) REVERT: E 89 MET cc_start: 0.8262 (mtt) cc_final: 0.8002 (mtt) REVERT: E 254 LEU cc_start: 0.8683 (tp) cc_final: 0.8455 (tp) REVERT: E 273 ASP cc_start: 0.8613 (t70) cc_final: 0.8401 (t0) REVERT: F 254 LEU cc_start: 0.9104 (tp) cc_final: 0.8816 (tp) REVERT: F 301 THR cc_start: 0.9098 (p) cc_final: 0.8602 (t) REVERT: F 311 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7538 (mm-30) REVERT: F 374 MET cc_start: 0.8398 (mmp) cc_final: 0.8098 (mmp) REVERT: F 458 PHE cc_start: 0.7485 (m-80) cc_final: 0.7281 (m-80) REVERT: F 472 GLN cc_start: 0.7269 (mp10) cc_final: 0.6875 (tm-30) REVERT: d 72 ASP cc_start: 0.7950 (t0) cc_final: 0.7599 (t70) REVERT: g 96 MET cc_start: 0.6632 (tpp) cc_final: 0.6404 (mmp) REVERT: e 50 ARG cc_start: 0.6094 (pmt170) cc_final: 0.5430 (ptt180) REVERT: e 63 MET cc_start: 0.5351 (mmt) cc_final: 0.4758 (mmm) REVERT: e 110 ARG cc_start: 0.6919 (mtt180) cc_final: 0.6006 (mtp180) REVERT: I 105 ARG cc_start: 0.6157 (mtm-85) cc_final: 0.5226 (ttp80) REVERT: J 106 LYS cc_start: 0.4054 (ttpp) cc_final: 0.3786 (tptt) REVERT: J 182 GLU cc_start: 0.4770 (mt-10) cc_final: 0.3661 (tp30) REVERT: a 71 PHE cc_start: 0.5424 (t80) cc_final: 0.5134 (t80) REVERT: a 186 LEU cc_start: 0.4360 (tp) cc_final: 0.3898 (tp) REVERT: O 68 LEU cc_start: 0.4504 (tp) cc_final: 0.4131 (tt) REVERT: R 57 LEU cc_start: 0.6571 (mt) cc_final: 0.5912 (mp) REVERT: R 76 PHE cc_start: 0.3083 (m-10) cc_final: 0.1839 (t80) REVERT: S 60 MET cc_start: 0.2314 (tpp) cc_final: 0.1294 (tpp) REVERT: T 48 LYS cc_start: 0.5248 (mtmm) cc_final: 0.4727 (mmtm) REVERT: V 59 PHE cc_start: 0.6085 (m-80) cc_final: 0.5828 (m-80) REVERT: W 30 THR cc_start: 0.7137 (t) cc_final: 0.6850 (m) REVERT: X 49 ILE cc_start: 0.5538 (mt) cc_final: 0.5271 (mm) outliers start: 5 outliers final: 2 residues processed: 893 average time/residue: 0.2322 time to fit residues: 326.7619 Evaluate side-chains 600 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 598 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 432 optimal weight: 0.8980 chunk 197 optimal weight: 0.3980 chunk 388 optimal weight: 0.8980 chunk 455 optimal weight: 4.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 0.7980 chunk 494 optimal weight: 10.0000 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 GLN A 256 HIS A 351 ASN A 423 GLN A 468 ASN A 497 GLN B 34 GLN B 208 GLN B 212 ASN B 256 HIS C 70 ASN C 214 GLN C 256 HIS C 295 HIS C 389 GLN ** C 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 ASN D 57 GLN D 133 HIS D 238 GLN D 264 ASN D 396 GLN E 25 GLN E 72 ASN E 188 ASN E 226 ASN E 238 GLN E 240 ASN ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 389 GLN F 25 GLN F 112 ASN F 223 ASN F 238 GLN d 170 ASN d 240 GLN g 95 ASN g 97 ASN g 134 ASN I 55 ASN I 109 ASN I 120 GLN ** I 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 161 ASN ** I 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 145 ASN J 186 GLN a 86 GLN a 109 ASN a 175 ASN P 28 GLN P 34 GLN ** R 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 34 GLN ** X 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.136729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.117040 restraints weight = 88434.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.115695 restraints weight = 126785.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.115119 restraints weight = 119638.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.114556 restraints weight = 91827.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.114754 restraints weight = 91042.953| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 39537 Z= 0.163 Angle : 0.683 10.572 53623 Z= 0.344 Chirality : 0.044 0.240 6417 Planarity : 0.005 0.062 6914 Dihedral : 7.947 145.020 5700 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.60 % Favored : 95.29 % Rotamer: Outliers : 0.15 % Allowed : 5.69 % Favored : 94.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.74 (0.11), residues: 5113 helix: -0.24 (0.09), residues: 2898 sheet: -2.29 (0.19), residues: 542 loop : -2.24 (0.14), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG U 50 TYR 0.030 0.002 TYR T 66 PHE 0.027 0.001 PHE Q 59 TRP 0.017 0.001 TRP e 57 HIS 0.003 0.001 HIS E 133 Details of bonding type rmsd covalent geometry : bond 0.00356 (39537) covalent geometry : angle 0.68266 (53623) hydrogen bonds : bond 0.05185 ( 2462) hydrogen bonds : angle 5.02417 ( 7257) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10226 Ramachandran restraints generated. 5113 Oldfield, 0 Emsley, 5113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10226 Ramachandran restraints generated. 5113 Oldfield, 0 Emsley, 5113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 798 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 792 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7492 (mm-30) REVERT: B 149 THR cc_start: 0.8468 (t) cc_final: 0.7941 (m) REVERT: B 182 ASP cc_start: 0.6060 (m-30) cc_final: 0.5783 (m-30) REVERT: C 321 GLU cc_start: 0.8395 (tm-30) cc_final: 0.7773 (tm-30) REVERT: C 498 MET cc_start: 0.7126 (tpp) cc_final: 0.6061 (ttp) REVERT: D 79 MET cc_start: 0.8169 (mmp) cc_final: 0.7814 (mmp) REVERT: D 311 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7040 (mm-30) REVERT: E 89 MET cc_start: 0.8485 (mtt) cc_final: 0.8250 (mtt) REVERT: E 223 ASN cc_start: 0.7207 (t0) cc_final: 0.6995 (t0) REVERT: E 313 ILE cc_start: 0.8007 (mt) cc_final: 0.7806 (mt) REVERT: F 18 LYS cc_start: 0.7521 (mttt) cc_final: 0.7215 (mtmm) REVERT: F 254 LEU cc_start: 0.9176 (tp) cc_final: 0.8962 (tp) REVERT: F 292 MET cc_start: 0.8014 (mtt) cc_final: 0.7778 (mtt) REVERT: F 301 THR cc_start: 0.8931 (p) cc_final: 0.8585 (t) REVERT: F 374 MET cc_start: 0.8327 (mmp) cc_final: 0.8085 (mmp) REVERT: F 472 GLN cc_start: 0.7023 (mp10) cc_final: 0.6710 (tm-30) REVERT: e 50 ARG cc_start: 0.5861 (pmt170) cc_final: 0.5421 (ptt180) REVERT: e 110 ARG cc_start: 0.6765 (mtt180) cc_final: 0.5890 (mtp180) REVERT: I 105 ARG cc_start: 0.6508 (mtm-85) cc_final: 0.5358 (ttp80) REVERT: I 121 PHE cc_start: 0.6271 (p90) cc_final: 0.5399 (m-10) REVERT: J 182 GLU cc_start: 0.4920 (mt-10) cc_final: 0.3662 (tp30) REVERT: a 186 LEU cc_start: 0.4980 (tp) cc_final: 0.4253 (tp) REVERT: M 57 LEU cc_start: 0.5017 (mt) cc_final: 0.4751 (mt) REVERT: O 68 LEU cc_start: 0.4258 (tp) cc_final: 0.3906 (tt) REVERT: R 28 GLN cc_start: 0.6934 (mp10) cc_final: 0.6245 (mp10) REVERT: R 61 GLU cc_start: 0.2196 (mp0) cc_final: 0.1785 (mt-10) REVERT: T 48 LYS cc_start: 0.4881 (mtmm) cc_final: 0.4665 (mmtm) REVERT: X 28 GLN cc_start: 0.5313 (tt0) cc_final: 0.4902 (tt0) REVERT: Y 69 VAL cc_start: 0.7271 (p) cc_final: 0.7051 (m) outliers start: 6 outliers final: 1 residues processed: 797 average time/residue: 0.2151 time to fit residues: 278.2626 Evaluate side-chains 602 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 601 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 483 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 172 optimal weight: 1.9990 chunk 150 optimal weight: 4.9990 chunk 140 optimal weight: 0.7980 chunk 247 optimal weight: 0.8980 chunk 130 optimal weight: 0.8980 chunk 274 optimal weight: 2.9990 chunk 318 optimal weight: 1.9990 chunk 143 optimal weight: 0.0570 chunk 184 optimal weight: 0.1980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN A 334 ASN A 389 GLN A 425 GLN B 187 GLN B 201 GLN B 273 GLN ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 GLN C 425 GLN ** C 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 ASN ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 210 ASN ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 240 GLN g 58 GLN ** g 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 228 HIS e 56 GLN e 111 GLN I 120 GLN I 133 GLN ** I 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 28 GLN ** S 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 34 GLN Y 42 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.137584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.117225 restraints weight = 88275.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.115618 restraints weight = 144511.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.115416 restraints weight = 120281.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.114803 restraints weight = 98302.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.115088 restraints weight = 81293.740| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 39537 Z= 0.147 Angle : 0.648 10.580 53623 Z= 0.325 Chirality : 0.043 0.216 6417 Planarity : 0.005 0.056 6914 Dihedral : 7.581 151.885 5700 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.19 % Favored : 95.70 % Rotamer: Outliers : 0.10 % Allowed : 4.59 % Favored : 95.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.11 (0.11), residues: 5113 helix: 0.24 (0.09), residues: 2923 sheet: -1.99 (0.20), residues: 542 loop : -1.94 (0.14), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 378 TYR 0.036 0.002 TYR O 66 PHE 0.036 0.002 PHE a 161 TRP 0.011 0.001 TRP a 117 HIS 0.003 0.001 HIS g 228 Details of bonding type rmsd covalent geometry : bond 0.00321 (39537) covalent geometry : angle 0.64795 (53623) hydrogen bonds : bond 0.04882 ( 2462) hydrogen bonds : angle 4.76425 ( 7257) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10226 Ramachandran restraints generated. 5113 Oldfield, 0 Emsley, 5113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10226 Ramachandran restraints generated. 5113 Oldfield, 0 Emsley, 5113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 777 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 773 time to evaluate : 1.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7562 (mm-30) REVERT: A 307 SER cc_start: 0.7895 (m) cc_final: 0.7623 (p) REVERT: B 149 THR cc_start: 0.8394 (t) cc_final: 0.8032 (m) REVERT: B 182 ASP cc_start: 0.5695 (m-30) cc_final: 0.5385 (m-30) REVERT: B 278 LEU cc_start: 0.8622 (pp) cc_final: 0.8360 (tp) REVERT: C 321 GLU cc_start: 0.8364 (tm-30) cc_final: 0.8000 (tm-30) REVERT: C 498 MET cc_start: 0.6895 (tpp) cc_final: 0.5944 (ttp) REVERT: D 79 MET cc_start: 0.8185 (mmp) cc_final: 0.7800 (mmp) REVERT: D 305 GLU cc_start: 0.6127 (mt-10) cc_final: 0.5919 (mt-10) REVERT: E 223 ASN cc_start: 0.7206 (t0) cc_final: 0.6784 (t0) REVERT: E 313 ILE cc_start: 0.8104 (mt) cc_final: 0.7877 (mt) REVERT: F 247 MET cc_start: 0.6692 (ttp) cc_final: 0.6381 (ttp) REVERT: F 292 MET cc_start: 0.8134 (mtt) cc_final: 0.7893 (mtt) REVERT: F 301 THR cc_start: 0.8904 (p) cc_final: 0.8577 (t) REVERT: F 374 MET cc_start: 0.8397 (mmp) cc_final: 0.8052 (mmp) REVERT: F 488 MET cc_start: 0.5074 (ttm) cc_final: 0.4829 (ttm) REVERT: F 489 ASN cc_start: 0.5582 (t0) cc_final: 0.5314 (t0) REVERT: e 50 ARG cc_start: 0.5604 (pmt170) cc_final: 0.5355 (ptt180) REVERT: e 63 MET cc_start: 0.4889 (mmm) cc_final: 0.4396 (mmm) REVERT: e 110 ARG cc_start: 0.6564 (mtt180) cc_final: 0.5894 (mtp180) REVERT: I 104 GLU cc_start: 0.7593 (mt-10) cc_final: 0.7385 (mt-10) REVERT: I 105 ARG cc_start: 0.6563 (mtm-85) cc_final: 0.5415 (ttp80) REVERT: J 145 ASN cc_start: 0.4873 (m-40) cc_final: 0.4433 (t0) REVERT: J 182 GLU cc_start: 0.4988 (mt-10) cc_final: 0.3706 (tp30) REVERT: a 117 TRP cc_start: 0.4438 (m100) cc_final: 0.4188 (m100) REVERT: a 186 LEU cc_start: 0.4651 (tp) cc_final: 0.3962 (tp) REVERT: O 68 LEU cc_start: 0.4101 (tp) cc_final: 0.3820 (tt) REVERT: P 68 LEU cc_start: 0.3341 (mp) cc_final: 0.3110 (mp) REVERT: S 60 MET cc_start: 0.3277 (tpp) cc_final: 0.2554 (tpp) REVERT: W 30 THR cc_start: 0.7290 (t) cc_final: 0.7023 (m) REVERT: Y 19 LEU cc_start: 0.5910 (mm) cc_final: 0.5639 (tp) outliers start: 4 outliers final: 1 residues processed: 775 average time/residue: 0.2059 time to fit residues: 262.0622 Evaluate side-chains 573 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 572 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 78 optimal weight: 0.8980 chunk 165 optimal weight: 1.9990 chunk 191 optimal weight: 3.9990 chunk 323 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 482 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 143 optimal weight: 3.9990 chunk 493 optimal weight: 4.9990 chunk 142 optimal weight: 0.5980 chunk 397 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 187 GLN B 273 GLN ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 ASN ** C 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 ASN ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 238 GLN E 67 GLN E 223 ASN ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 76 GLN g 228 HIS I 146 GLN I 150 GLN ** I 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 109 ASN M 28 GLN S 28 GLN ** S 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 34 GLN X 42 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.137205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.116683 restraints weight = 88207.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.114999 restraints weight = 153107.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.115869 restraints weight = 129017.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.115237 restraints weight = 87491.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.115413 restraints weight = 87987.107| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 39537 Z= 0.158 Angle : 0.654 10.130 53623 Z= 0.327 Chirality : 0.044 0.339 6417 Planarity : 0.004 0.052 6914 Dihedral : 7.466 152.821 5700 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.48 % Favored : 95.40 % Rotamer: Outliers : 0.05 % Allowed : 3.78 % Favored : 96.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.81 (0.11), residues: 5113 helix: 0.49 (0.09), residues: 2911 sheet: -1.85 (0.21), residues: 536 loop : -1.82 (0.14), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 172 TYR 0.023 0.002 TYR a 148 PHE 0.031 0.002 PHE B 482 TRP 0.008 0.001 TRP a 117 HIS 0.003 0.001 HIS F 193 Details of bonding type rmsd covalent geometry : bond 0.00351 (39537) covalent geometry : angle 0.65377 (53623) hydrogen bonds : bond 0.04778 ( 2462) hydrogen bonds : angle 4.69098 ( 7257) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10226 Ramachandran restraints generated. 5113 Oldfield, 0 Emsley, 5113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10226 Ramachandran restraints generated. 5113 Oldfield, 0 Emsley, 5113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 738 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 736 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 MET cc_start: 0.8155 (mtp) cc_final: 0.7926 (mtp) REVERT: B 149 THR cc_start: 0.8389 (t) cc_final: 0.7998 (m) REVERT: B 182 ASP cc_start: 0.5787 (m-30) cc_final: 0.5390 (m-30) REVERT: B 278 LEU cc_start: 0.8631 (pp) cc_final: 0.8314 (tp) REVERT: B 321 GLU cc_start: 0.7109 (tt0) cc_final: 0.6320 (tt0) REVERT: C 321 GLU cc_start: 0.8435 (tm-30) cc_final: 0.7922 (tm-30) REVERT: C 498 MET cc_start: 0.6933 (tpp) cc_final: 0.6012 (ttp) REVERT: D 79 MET cc_start: 0.8204 (mmp) cc_final: 0.7778 (mmp) REVERT: E 223 ASN cc_start: 0.6930 (t0) cc_final: 0.6720 (t0) REVERT: F 254 LEU cc_start: 0.9173 (tp) cc_final: 0.8908 (tp) REVERT: F 292 MET cc_start: 0.8106 (mtt) cc_final: 0.7896 (mtt) REVERT: F 301 THR cc_start: 0.8927 (p) cc_final: 0.8680 (t) REVERT: F 311 GLU cc_start: 0.7468 (mm-30) cc_final: 0.7211 (mm-30) REVERT: F 374 MET cc_start: 0.8409 (mmp) cc_final: 0.8049 (mmp) REVERT: e 36 ASN cc_start: 0.5837 (t0) cc_final: 0.5423 (t0) REVERT: e 63 MET cc_start: 0.5007 (mmm) cc_final: 0.4588 (mmm) REVERT: e 110 ARG cc_start: 0.6622 (mtt180) cc_final: 0.5975 (mtp180) REVERT: I 105 ARG cc_start: 0.6532 (mtm-85) cc_final: 0.5501 (ttp80) REVERT: J 145 ASN cc_start: 0.4860 (m-40) cc_final: 0.4461 (t0) REVERT: J 182 GLU cc_start: 0.4875 (mt-10) cc_final: 0.3801 (tp30) REVERT: a 186 LEU cc_start: 0.5066 (tp) cc_final: 0.4273 (tp) REVERT: O 52 THR cc_start: 0.5336 (m) cc_final: 0.4935 (m) REVERT: O 60 MET cc_start: 0.3213 (mmm) cc_final: 0.2922 (mmm) REVERT: P 60 MET cc_start: 0.1256 (mmm) cc_final: 0.0089 (mtt) REVERT: S 60 MET cc_start: 0.3099 (tpp) cc_final: 0.2593 (tpp) REVERT: S 63 LEU cc_start: 0.3729 (mm) cc_final: 0.3309 (tp) REVERT: W 30 THR cc_start: 0.7210 (t) cc_final: 0.6967 (m) outliers start: 2 outliers final: 0 residues processed: 737 average time/residue: 0.2017 time to fit residues: 245.5332 Evaluate side-chains 557 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 557 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 430 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 497 optimal weight: 0.9990 chunk 206 optimal weight: 6.9990 chunk 382 optimal weight: 3.9990 chunk 291 optimal weight: 4.9990 chunk 284 optimal weight: 0.6980 chunk 89 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 chunk 243 optimal weight: 0.9990 chunk 204 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 415 GLN ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 423 GLN C 473 GLN D 57 GLN E 67 GLN E 120 ASN ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 479 ASN ** d 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 228 HIS ** e 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 56 GLN I 133 GLN ** I 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 42 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.136668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.115801 restraints weight = 88243.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.113321 restraints weight = 170482.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.114215 restraints weight = 136597.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.114486 restraints weight = 87374.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.114652 restraints weight = 76450.575| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 39537 Z= 0.157 Angle : 0.647 10.212 53623 Z= 0.322 Chirality : 0.043 0.261 6417 Planarity : 0.004 0.052 6914 Dihedral : 7.387 155.148 5700 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.30 % Favored : 95.62 % Rotamer: Outliers : 0.07 % Allowed : 2.99 % Favored : 96.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.62 (0.11), residues: 5113 helix: 0.63 (0.09), residues: 2910 sheet: -1.74 (0.21), residues: 542 loop : -1.71 (0.14), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 172 TYR 0.027 0.002 TYR I 100 PHE 0.025 0.001 PHE g 217 TRP 0.003 0.001 TRP a 117 HIS 0.004 0.001 HIS D 193 Details of bonding type rmsd covalent geometry : bond 0.00350 (39537) covalent geometry : angle 0.64697 (53623) hydrogen bonds : bond 0.04740 ( 2462) hydrogen bonds : angle 4.62324 ( 7257) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10226 Ramachandran restraints generated. 5113 Oldfield, 0 Emsley, 5113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10226 Ramachandran restraints generated. 5113 Oldfield, 0 Emsley, 5113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 713 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 710 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 ASP cc_start: 0.7263 (p0) cc_final: 0.6923 (p0) REVERT: A 262 ASP cc_start: 0.7599 (t0) cc_final: 0.7305 (t0) REVERT: A 274 MET cc_start: 0.8012 (ptm) cc_final: 0.7700 (tpt) REVERT: B 149 THR cc_start: 0.8315 (t) cc_final: 0.7943 (m) REVERT: B 182 ASP cc_start: 0.5738 (m-30) cc_final: 0.5374 (m-30) REVERT: B 278 LEU cc_start: 0.8607 (pp) cc_final: 0.8260 (tp) REVERT: B 321 GLU cc_start: 0.7007 (tt0) cc_final: 0.6437 (tt0) REVERT: C 248 GLU cc_start: 0.7107 (tt0) cc_final: 0.6670 (tt0) REVERT: C 321 GLU cc_start: 0.8320 (tm-30) cc_final: 0.8034 (tm-30) REVERT: C 498 MET cc_start: 0.6972 (tpp) cc_final: 0.6021 (ttp) REVERT: D 79 MET cc_start: 0.8217 (mmp) cc_final: 0.7865 (mmt) REVERT: E 313 ILE cc_start: 0.8125 (mt) cc_final: 0.7911 (mt) REVERT: E 490 LEU cc_start: 0.8003 (pp) cc_final: 0.7275 (tt) REVERT: F 247 MET cc_start: 0.6791 (ttp) cc_final: 0.6526 (ttp) REVERT: F 301 THR cc_start: 0.8957 (p) cc_final: 0.8680 (t) REVERT: F 374 MET cc_start: 0.8401 (mmp) cc_final: 0.8137 (mmp) REVERT: F 488 MET cc_start: 0.4871 (ttm) cc_final: 0.4613 (ttm) REVERT: e 63 MET cc_start: 0.4950 (mmm) cc_final: 0.4482 (mmm) REVERT: e 110 ARG cc_start: 0.6594 (mtt180) cc_final: 0.6042 (mtp180) REVERT: I 105 ARG cc_start: 0.6491 (mtm-85) cc_final: 0.5380 (ttp80) REVERT: I 160 LEU cc_start: 0.5529 (mt) cc_final: 0.5005 (pp) REVERT: J 182 GLU cc_start: 0.4957 (mt-10) cc_final: 0.3882 (tp30) REVERT: O 60 MET cc_start: 0.3223 (mmm) cc_final: 0.2962 (mmm) REVERT: P 60 MET cc_start: 0.1292 (mmm) cc_final: -0.0002 (mtt) REVERT: S 60 MET cc_start: 0.3344 (tpp) cc_final: 0.2420 (tpp) REVERT: W 30 THR cc_start: 0.7232 (t) cc_final: 0.6951 (m) REVERT: X 60 MET cc_start: 0.6401 (mtt) cc_final: 0.5664 (tpp) outliers start: 3 outliers final: 1 residues processed: 712 average time/residue: 0.2098 time to fit residues: 246.8709 Evaluate side-chains 548 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 547 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 237 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 489 optimal weight: 0.7980 chunk 272 optimal weight: 0.9980 chunk 275 optimal weight: 0.3980 chunk 174 optimal weight: 0.5980 chunk 149 optimal weight: 1.9990 chunk 288 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 177 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 238 GLN ** E 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 223 ASN ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 45 ASN F 133 HIS ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 228 HIS ** e 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 72 ASN ** I 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 109 ASN M 28 GLN M 42 GLN ** R 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 28 GLN ** X 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.136984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.117253 restraints weight = 87739.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.115661 restraints weight = 144128.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.116081 restraints weight = 126292.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.115655 restraints weight = 85451.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.115873 restraints weight = 73987.259| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 39537 Z= 0.148 Angle : 0.649 10.212 53623 Z= 0.323 Chirality : 0.043 0.278 6417 Planarity : 0.004 0.059 6914 Dihedral : 7.314 157.374 5700 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.20 % Favored : 95.72 % Rotamer: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.12), residues: 5113 helix: 0.75 (0.09), residues: 2903 sheet: -1.69 (0.21), residues: 545 loop : -1.62 (0.15), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 172 TYR 0.046 0.002 TYR O 66 PHE 0.044 0.002 PHE A 390 TRP 0.007 0.001 TRP e 15 HIS 0.003 0.001 HIS A 295 Details of bonding type rmsd covalent geometry : bond 0.00329 (39537) covalent geometry : angle 0.64923 (53623) hydrogen bonds : bond 0.04645 ( 2462) hydrogen bonds : angle 4.57578 ( 7257) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10226 Ramachandran restraints generated. 5113 Oldfield, 0 Emsley, 5113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10226 Ramachandran restraints generated. 5113 Oldfield, 0 Emsley, 5113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 700 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 700 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 ILE cc_start: 0.8272 (mm) cc_final: 0.8053 (mm) REVERT: A 230 ASP cc_start: 0.7199 (p0) cc_final: 0.6512 (p0) REVERT: A 262 ASP cc_start: 0.7579 (t0) cc_final: 0.7375 (t0) REVERT: A 274 MET cc_start: 0.8011 (ptm) cc_final: 0.7677 (tpt) REVERT: B 149 THR cc_start: 0.8396 (t) cc_final: 0.7926 (m) REVERT: B 182 ASP cc_start: 0.5612 (m-30) cc_final: 0.5262 (m-30) REVERT: B 321 GLU cc_start: 0.6978 (tt0) cc_final: 0.6399 (tt0) REVERT: B 436 MET cc_start: 0.7159 (tmm) cc_final: 0.6870 (tmm) REVERT: C 29 THR cc_start: 0.8743 (t) cc_final: 0.8529 (m) REVERT: C 248 GLU cc_start: 0.7372 (tt0) cc_final: 0.7067 (tt0) REVERT: C 321 GLU cc_start: 0.8429 (tm-30) cc_final: 0.8099 (tm-30) REVERT: C 498 MET cc_start: 0.6975 (tpp) cc_final: 0.6106 (ttp) REVERT: D 79 MET cc_start: 0.8136 (mmp) cc_final: 0.7847 (mmt) REVERT: D 311 GLU cc_start: 0.7478 (mt-10) cc_final: 0.6901 (mm-30) REVERT: E 254 LEU cc_start: 0.8726 (tp) cc_final: 0.8511 (tp) REVERT: E 313 ILE cc_start: 0.8119 (mt) cc_final: 0.7863 (mt) REVERT: E 490 LEU cc_start: 0.8105 (pp) cc_final: 0.7278 (tt) REVERT: F 254 LEU cc_start: 0.9137 (tp) cc_final: 0.8931 (tp) REVERT: F 301 THR cc_start: 0.8975 (p) cc_final: 0.8687 (t) REVERT: F 374 MET cc_start: 0.8337 (mmp) cc_final: 0.8050 (mmp) REVERT: F 488 MET cc_start: 0.4917 (ttm) cc_final: 0.4671 (ttm) REVERT: g 233 LEU cc_start: 0.7092 (mp) cc_final: 0.6703 (mp) REVERT: g 284 PHE cc_start: 0.5145 (p90) cc_final: 0.4892 (p90) REVERT: e 63 MET cc_start: 0.4888 (mmm) cc_final: 0.4407 (mmm) REVERT: e 110 ARG cc_start: 0.6529 (mtt180) cc_final: 0.6050 (mtp180) REVERT: I 105 ARG cc_start: 0.6274 (mtm-85) cc_final: 0.5222 (tmm160) REVERT: J 182 GLU cc_start: 0.4828 (mt-10) cc_final: 0.3872 (tp30) REVERT: a 186 LEU cc_start: 0.5290 (tp) cc_final: 0.4635 (tp) REVERT: N 4 LEU cc_start: 0.4922 (tp) cc_final: 0.4593 (mp) REVERT: O 60 MET cc_start: 0.3289 (mmm) cc_final: 0.2909 (mmm) REVERT: P 60 MET cc_start: 0.1227 (mmm) cc_final: -0.0045 (mtt) REVERT: Q 44 GLU cc_start: 0.5834 (mm-30) cc_final: 0.5509 (mm-30) REVERT: S 60 MET cc_start: 0.3332 (tpp) cc_final: 0.2736 (tpp) REVERT: S 63 LEU cc_start: 0.3673 (mm) cc_final: 0.3275 (tp) REVERT: X 60 MET cc_start: 0.6150 (mtt) cc_final: 0.5694 (tpp) outliers start: 0 outliers final: 0 residues processed: 700 average time/residue: 0.2072 time to fit residues: 238.5312 Evaluate side-chains 543 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 543 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 107 optimal weight: 6.9990 chunk 324 optimal weight: 3.9990 chunk 287 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 257 optimal weight: 1.9990 chunk 286 optimal weight: 0.0370 chunk 39 optimal weight: 1.9990 chunk 450 optimal weight: 0.8980 chunk 355 optimal weight: 0.9990 chunk 152 optimal weight: 4.9990 chunk 485 optimal weight: 4.9990 overall best weight: 0.9862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN B 273 GLN B 415 GLN ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 25 GLN E 112 ASN ** E 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 396 GLN g 228 HIS ** e 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 56 GLN I 133 GLN ** I 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 34 GLN X 28 GLN ** X 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 42 GLN Z 28 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.136545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.116883 restraints weight = 88335.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.115748 restraints weight = 125108.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.114747 restraints weight = 119668.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.114356 restraints weight = 98747.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.114627 restraints weight = 89340.881| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 39537 Z= 0.166 Angle : 0.668 12.347 53623 Z= 0.331 Chirality : 0.044 0.288 6417 Planarity : 0.004 0.054 6914 Dihedral : 7.259 158.494 5700 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.56 % Favored : 95.36 % Rotamer: Outliers : 0.05 % Allowed : 1.91 % Favored : 98.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.12), residues: 5113 helix: 0.77 (0.09), residues: 2899 sheet: -1.64 (0.21), residues: 565 loop : -1.55 (0.15), residues: 1649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 172 TYR 0.023 0.002 TYR A 330 PHE 0.021 0.002 PHE g 199 TRP 0.005 0.001 TRP e 15 HIS 0.003 0.001 HIS B 295 Details of bonding type rmsd covalent geometry : bond 0.00373 (39537) covalent geometry : angle 0.66830 (53623) hydrogen bonds : bond 0.04686 ( 2462) hydrogen bonds : angle 4.60511 ( 7257) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10226 Ramachandran restraints generated. 5113 Oldfield, 0 Emsley, 5113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10226 Ramachandran restraints generated. 5113 Oldfield, 0 Emsley, 5113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 680 time to evaluate : 1.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 ASP cc_start: 0.7190 (p0) cc_final: 0.6798 (p0) REVERT: A 274 MET cc_start: 0.7991 (ptm) cc_final: 0.7734 (tpt) REVERT: A 340 ASP cc_start: 0.8898 (m-30) cc_final: 0.8528 (t0) REVERT: B 149 THR cc_start: 0.8353 (t) cc_final: 0.7928 (m) REVERT: B 182 ASP cc_start: 0.5705 (m-30) cc_final: 0.5380 (m-30) REVERT: B 321 GLU cc_start: 0.6973 (tt0) cc_final: 0.6431 (tt0) REVERT: B 436 MET cc_start: 0.7210 (tmm) cc_final: 0.6962 (tmm) REVERT: B 454 VAL cc_start: 0.8836 (m) cc_final: 0.8620 (t) REVERT: C 321 GLU cc_start: 0.8344 (tm-30) cc_final: 0.8009 (tm-30) REVERT: C 498 MET cc_start: 0.6986 (tpp) cc_final: 0.6145 (ttp) REVERT: D 79 MET cc_start: 0.8127 (mmp) cc_final: 0.7852 (mmt) REVERT: E 313 ILE cc_start: 0.8206 (mt) cc_final: 0.7977 (mt) REVERT: E 334 LEU cc_start: 0.8079 (mt) cc_final: 0.7177 (tt) REVERT: E 335 THR cc_start: 0.7031 (p) cc_final: 0.6702 (p) REVERT: E 490 LEU cc_start: 0.8124 (pp) cc_final: 0.7332 (tt) REVERT: F 247 MET cc_start: 0.7028 (ttp) cc_final: 0.6820 (ttp) REVERT: F 301 THR cc_start: 0.8931 (p) cc_final: 0.8658 (t) REVERT: F 374 MET cc_start: 0.8322 (mmp) cc_final: 0.8062 (mmp) REVERT: g 233 LEU cc_start: 0.7521 (mp) cc_final: 0.7232 (mp) REVERT: g 257 LEU cc_start: 0.6908 (tp) cc_final: 0.6685 (tp) REVERT: g 284 PHE cc_start: 0.5218 (p90) cc_final: 0.4899 (p90) REVERT: e 63 MET cc_start: 0.4902 (mmm) cc_final: 0.4451 (mmm) REVERT: e 110 ARG cc_start: 0.6574 (mtt180) cc_final: 0.6051 (mtp180) REVERT: I 105 ARG cc_start: 0.6215 (mtm-85) cc_final: 0.5175 (tmm160) REVERT: I 179 MET cc_start: 0.2947 (tmm) cc_final: 0.2664 (tpt) REVERT: J 182 GLU cc_start: 0.5038 (mt-10) cc_final: 0.3913 (tp30) REVERT: a 186 LEU cc_start: 0.4933 (tp) cc_final: 0.4733 (tp) REVERT: M 37 GLU cc_start: 0.4817 (tp30) cc_final: 0.4599 (tp30) REVERT: N 4 LEU cc_start: 0.4890 (tp) cc_final: 0.4520 (mp) REVERT: O 60 MET cc_start: 0.3131 (mmm) cc_final: 0.2744 (mmm) REVERT: P 60 MET cc_start: 0.1242 (mmm) cc_final: 0.0009 (mtt) REVERT: Q 44 GLU cc_start: 0.5740 (mm-30) cc_final: 0.5467 (mm-30) REVERT: S 60 MET cc_start: 0.3355 (tpp) cc_final: 0.3011 (tpp) REVERT: V 68 LEU cc_start: 0.6335 (mm) cc_final: 0.6115 (mm) REVERT: X 60 MET cc_start: 0.6375 (mtt) cc_final: 0.5827 (tpp) outliers start: 2 outliers final: 0 residues processed: 681 average time/residue: 0.2135 time to fit residues: 241.7125 Evaluate side-chains 531 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 531 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 147 optimal weight: 0.9990 chunk 340 optimal weight: 0.9980 chunk 208 optimal weight: 0.9990 chunk 364 optimal weight: 0.9980 chunk 353 optimal weight: 0.7980 chunk 394 optimal weight: 0.9990 chunk 387 optimal weight: 0.6980 chunk 321 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 chunk 108 optimal weight: 0.9980 chunk 350 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 434 GLN ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 HIS ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 238 GLN E 112 ASN ** E 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 396 GLN ** d 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 228 HIS ** e 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 28 GLN ** X 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.137054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.116963 restraints weight = 88385.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.115637 restraints weight = 139128.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.115792 restraints weight = 121164.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.114927 restraints weight = 90769.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.115177 restraints weight = 93047.136| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 39537 Z= 0.153 Angle : 0.662 12.012 53623 Z= 0.328 Chirality : 0.044 0.275 6417 Planarity : 0.004 0.059 6914 Dihedral : 7.145 160.328 5700 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.28 % Favored : 95.64 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.12), residues: 5113 helix: 0.81 (0.09), residues: 2908 sheet: -1.55 (0.21), residues: 555 loop : -1.50 (0.15), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG e 50 TYR 0.021 0.002 TYR A 464 PHE 0.037 0.002 PHE A 390 TRP 0.006 0.001 TRP e 15 HIS 0.002 0.001 HIS F 193 Details of bonding type rmsd covalent geometry : bond 0.00344 (39537) covalent geometry : angle 0.66241 (53623) hydrogen bonds : bond 0.04608 ( 2462) hydrogen bonds : angle 4.57590 ( 7257) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10226 Ramachandran restraints generated. 5113 Oldfield, 0 Emsley, 5113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10226 Ramachandran restraints generated. 5113 Oldfield, 0 Emsley, 5113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 683 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 ASN cc_start: 0.7747 (t0) cc_final: 0.7443 (t0) REVERT: A 230 ASP cc_start: 0.7219 (p0) cc_final: 0.6716 (p0) REVERT: A 262 ASP cc_start: 0.7427 (t0) cc_final: 0.7146 (t0) REVERT: A 274 MET cc_start: 0.7959 (ptm) cc_final: 0.7703 (tpt) REVERT: A 340 ASP cc_start: 0.8871 (m-30) cc_final: 0.8465 (t0) REVERT: B 138 MET cc_start: 0.6715 (tpp) cc_final: 0.6492 (tpp) REVERT: B 149 THR cc_start: 0.8370 (t) cc_final: 0.7915 (m) REVERT: B 182 ASP cc_start: 0.5889 (m-30) cc_final: 0.5519 (m-30) REVERT: B 321 GLU cc_start: 0.6962 (tt0) cc_final: 0.6437 (tt0) REVERT: B 436 MET cc_start: 0.7319 (tmm) cc_final: 0.7088 (tmm) REVERT: C 321 GLU cc_start: 0.8374 (tm-30) cc_final: 0.7989 (tm-30) REVERT: C 498 MET cc_start: 0.7027 (tpp) cc_final: 0.6202 (ttp) REVERT: D 79 MET cc_start: 0.8197 (mmp) cc_final: 0.7874 (mmt) REVERT: D 306 MET cc_start: 0.8396 (tpt) cc_final: 0.8167 (mmm) REVERT: D 311 GLU cc_start: 0.7537 (mt-10) cc_final: 0.6840 (mm-30) REVERT: E 306 MET cc_start: 0.8376 (tpp) cc_final: 0.8144 (tpp) REVERT: E 334 LEU cc_start: 0.8119 (mt) cc_final: 0.7193 (tt) REVERT: E 335 THR cc_start: 0.7115 (p) cc_final: 0.6786 (p) REVERT: E 490 LEU cc_start: 0.8155 (pp) cc_final: 0.7393 (tt) REVERT: F 254 LEU cc_start: 0.9188 (tp) cc_final: 0.8980 (tp) REVERT: F 301 THR cc_start: 0.8945 (p) cc_final: 0.8683 (t) REVERT: F 374 MET cc_start: 0.8333 (mmp) cc_final: 0.7939 (mmp) REVERT: F 385 TYR cc_start: 0.7867 (t80) cc_final: 0.7443 (t80) REVERT: g 113 ARG cc_start: 0.5314 (mpt180) cc_final: 0.5042 (mmt90) REVERT: g 284 PHE cc_start: 0.5230 (p90) cc_final: 0.4947 (p90) REVERT: e 63 MET cc_start: 0.4885 (mmm) cc_final: 0.4392 (mmm) REVERT: e 110 ARG cc_start: 0.6505 (mtt180) cc_final: 0.5991 (mtp180) REVERT: I 105 ARG cc_start: 0.6208 (mtm-85) cc_final: 0.5169 (tmm160) REVERT: I 179 MET cc_start: 0.2987 (tmm) cc_final: 0.2694 (tpt) REVERT: J 182 GLU cc_start: 0.5038 (mt-10) cc_final: 0.3926 (tp30) REVERT: a 186 LEU cc_start: 0.5398 (tp) cc_final: 0.4709 (tp) REVERT: M 37 GLU cc_start: 0.4938 (tp30) cc_final: 0.4738 (tp30) REVERT: N 4 LEU cc_start: 0.4792 (tp) cc_final: 0.4421 (mp) REVERT: N 30 THR cc_start: 0.6077 (p) cc_final: 0.4828 (p) REVERT: O 60 MET cc_start: 0.3364 (mmm) cc_final: 0.3006 (mmm) REVERT: P 60 MET cc_start: 0.1672 (mmm) cc_final: 0.0449 (mtt) REVERT: R 57 LEU cc_start: 0.6553 (mt) cc_final: 0.6242 (mt) REVERT: S 60 MET cc_start: 0.3470 (tpp) cc_final: 0.2908 (tpp) REVERT: S 63 LEU cc_start: 0.3424 (mm) cc_final: 0.3049 (tp) REVERT: X 60 MET cc_start: 0.6416 (mtt) cc_final: 0.5837 (tpp) outliers start: 0 outliers final: 0 residues processed: 683 average time/residue: 0.1916 time to fit residues: 219.2957 Evaluate side-chains 531 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 531 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 162 optimal weight: 0.0000 chunk 10 optimal weight: 1.9990 chunk 413 optimal weight: 5.9990 chunk 255 optimal weight: 2.9990 chunk 365 optimal weight: 9.9990 chunk 129 optimal weight: 0.9990 chunk 384 optimal weight: 1.9990 chunk 223 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 283 optimal weight: 5.9990 chunk 438 optimal weight: 2.9990 overall best weight: 1.1190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 351 ASN B 415 GLN ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 ASN E 210 ASN ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 228 HIS ** e 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 56 GLN ** I 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 109 ASN a 135 ASN ** M 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 28 GLN V 34 GLN W 28 GLN X 28 GLN ** X 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 42 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.136215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.116909 restraints weight = 88027.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.114779 restraints weight = 172428.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.115769 restraints weight = 142692.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.115508 restraints weight = 91341.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.115659 restraints weight = 85998.593| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 39537 Z= 0.174 Angle : 0.685 13.966 53623 Z= 0.340 Chirality : 0.045 0.302 6417 Planarity : 0.005 0.057 6914 Dihedral : 7.155 161.077 5700 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.67 % Favored : 95.25 % Rotamer: Outliers : 0.02 % Allowed : 1.08 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.12), residues: 5113 helix: 0.78 (0.09), residues: 2907 sheet: -1.61 (0.21), residues: 545 loop : -1.48 (0.15), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 172 TYR 0.024 0.002 TYR A 330 PHE 0.036 0.002 PHE A 390 TRP 0.005 0.001 TRP e 57 HIS 0.003 0.001 HIS F 193 Details of bonding type rmsd covalent geometry : bond 0.00394 (39537) covalent geometry : angle 0.68538 (53623) hydrogen bonds : bond 0.04734 ( 2462) hydrogen bonds : angle 4.61984 ( 7257) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10226 Ramachandran restraints generated. 5113 Oldfield, 0 Emsley, 5113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10226 Ramachandran restraints generated. 5113 Oldfield, 0 Emsley, 5113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 662 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 ILE cc_start: 0.8296 (mm) cc_final: 0.8072 (mm) REVERT: A 230 ASP cc_start: 0.7373 (p0) cc_final: 0.7001 (p0) REVERT: A 340 ASP cc_start: 0.8938 (m-30) cc_final: 0.8471 (t0) REVERT: B 138 MET cc_start: 0.6756 (tpp) cc_final: 0.6547 (tpp) REVERT: B 149 THR cc_start: 0.8314 (t) cc_final: 0.7897 (m) REVERT: B 182 ASP cc_start: 0.5846 (m-30) cc_final: 0.5586 (m-30) REVERT: B 321 GLU cc_start: 0.6973 (tt0) cc_final: 0.6395 (tt0) REVERT: B 436 MET cc_start: 0.7304 (tmm) cc_final: 0.7099 (tmm) REVERT: C 248 GLU cc_start: 0.7370 (tt0) cc_final: 0.7125 (tt0) REVERT: C 252 TYR cc_start: 0.7020 (m-10) cc_final: 0.6697 (m-10) REVERT: C 321 GLU cc_start: 0.8381 (tm-30) cc_final: 0.7884 (tm-30) REVERT: C 498 MET cc_start: 0.7093 (tpp) cc_final: 0.6216 (ttp) REVERT: D 79 MET cc_start: 0.8219 (mmp) cc_final: 0.7865 (mmt) REVERT: D 301 THR cc_start: 0.8929 (p) cc_final: 0.8220 (p) REVERT: D 311 GLU cc_start: 0.7512 (mt-10) cc_final: 0.6809 (mm-30) REVERT: E 313 ILE cc_start: 0.8155 (mt) cc_final: 0.7906 (mt) REVERT: E 334 LEU cc_start: 0.8190 (mt) cc_final: 0.7284 (tt) REVERT: E 335 THR cc_start: 0.7236 (p) cc_final: 0.6877 (p) REVERT: E 490 LEU cc_start: 0.8169 (pp) cc_final: 0.7383 (tt) REVERT: F 301 THR cc_start: 0.8954 (p) cc_final: 0.8684 (t) REVERT: F 374 MET cc_start: 0.8334 (mmp) cc_final: 0.7962 (mmp) REVERT: g 233 LEU cc_start: 0.7131 (mp) cc_final: 0.6731 (mp) REVERT: g 284 PHE cc_start: 0.5343 (p90) cc_final: 0.5068 (p90) REVERT: e 63 MET cc_start: 0.5032 (mmm) cc_final: 0.4475 (mmm) REVERT: e 110 ARG cc_start: 0.6459 (mtt180) cc_final: 0.5960 (mtp180) REVERT: I 105 ARG cc_start: 0.6356 (mtm-85) cc_final: 0.5175 (tmm160) REVERT: I 179 MET cc_start: 0.3020 (tmm) cc_final: 0.2623 (tpt) REVERT: J 182 GLU cc_start: 0.4969 (mt-10) cc_final: 0.3871 (tp30) REVERT: a 186 LEU cc_start: 0.5019 (tp) cc_final: 0.4554 (tp) REVERT: N 30 THR cc_start: 0.5970 (p) cc_final: 0.4884 (p) REVERT: O 60 MET cc_start: 0.3356 (mmm) cc_final: 0.2819 (mmm) REVERT: P 60 MET cc_start: 0.1501 (mmm) cc_final: 0.0475 (mtm) REVERT: S 60 MET cc_start: 0.3287 (tpp) cc_final: 0.2904 (tpp) REVERT: S 63 LEU cc_start: 0.3174 (mm) cc_final: 0.2885 (tp) REVERT: W 30 THR cc_start: 0.7101 (t) cc_final: 0.6816 (m) REVERT: X 60 MET cc_start: 0.6536 (mtt) cc_final: 0.5975 (tpp) outliers start: 1 outliers final: 1 residues processed: 663 average time/residue: 0.1955 time to fit residues: 215.8287 Evaluate side-chains 517 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 516 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 172 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 474 optimal weight: 0.8980 chunk 215 optimal weight: 0.7980 chunk 323 optimal weight: 1.9990 chunk 167 optimal weight: 4.9990 chunk 160 optimal weight: 2.9990 chunk 499 optimal weight: 0.9980 chunk 407 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 267 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 434 GLN ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 ASN D 238 GLN E 112 ASN E 210 ASN ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 228 HIS ** e 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 28 GLN ** X 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.136633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.116638 restraints weight = 88082.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.115303 restraints weight = 141855.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.115551 restraints weight = 128040.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.115149 restraints weight = 86432.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.115443 restraints weight = 74959.481| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7039 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 39537 Z= 0.162 Angle : 0.684 11.553 53623 Z= 0.339 Chirality : 0.044 0.299 6417 Planarity : 0.004 0.057 6914 Dihedral : 7.108 162.890 5700 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.36 % Favored : 95.56 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.33 (0.12), residues: 5113 helix: 0.79 (0.09), residues: 2909 sheet: -1.58 (0.21), residues: 548 loop : -1.44 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 172 TYR 0.028 0.002 TYR E 475 PHE 0.020 0.001 PHE S 59 TRP 0.007 0.001 TRP e 57 HIS 0.003 0.001 HIS F 193 Details of bonding type rmsd covalent geometry : bond 0.00363 (39537) covalent geometry : angle 0.68450 (53623) hydrogen bonds : bond 0.04681 ( 2462) hydrogen bonds : angle 4.62862 ( 7257) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10226 Ramachandran restraints generated. 5113 Oldfield, 0 Emsley, 5113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10226 Ramachandran restraints generated. 5113 Oldfield, 0 Emsley, 5113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 665 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 ILE cc_start: 0.8322 (mm) cc_final: 0.8121 (mm) REVERT: A 230 ASP cc_start: 0.7328 (p0) cc_final: 0.6930 (p0) REVERT: A 340 ASP cc_start: 0.8919 (m-30) cc_final: 0.8482 (t0) REVERT: B 138 MET cc_start: 0.6718 (tpp) cc_final: 0.6238 (tpp) REVERT: B 149 THR cc_start: 0.8313 (t) cc_final: 0.7873 (m) REVERT: B 182 ASP cc_start: 0.5794 (m-30) cc_final: 0.5521 (m-30) REVERT: B 321 GLU cc_start: 0.6936 (tt0) cc_final: 0.6423 (tt0) REVERT: B 436 MET cc_start: 0.7272 (tmm) cc_final: 0.7043 (tmm) REVERT: C 248 GLU cc_start: 0.7377 (tt0) cc_final: 0.7044 (tt0) REVERT: C 252 TYR cc_start: 0.7009 (m-10) cc_final: 0.6659 (m-10) REVERT: C 321 GLU cc_start: 0.8412 (tm-30) cc_final: 0.7982 (tm-30) REVERT: C 498 MET cc_start: 0.6976 (tpp) cc_final: 0.6133 (ttp) REVERT: D 306 MET cc_start: 0.8223 (tpt) cc_final: 0.7953 (mmm) REVERT: D 311 GLU cc_start: 0.7526 (mt-10) cc_final: 0.6821 (mm-30) REVERT: E 334 LEU cc_start: 0.8177 (mt) cc_final: 0.7268 (tt) REVERT: E 335 THR cc_start: 0.7183 (p) cc_final: 0.6807 (p) REVERT: E 490 LEU cc_start: 0.8205 (pp) cc_final: 0.7410 (tt) REVERT: F 254 LEU cc_start: 0.9179 (tp) cc_final: 0.8957 (tp) REVERT: F 301 THR cc_start: 0.8936 (p) cc_final: 0.8659 (t) REVERT: F 374 MET cc_start: 0.8255 (mmp) cc_final: 0.7921 (mmp) REVERT: d 206 ASN cc_start: 0.7459 (t0) cc_final: 0.7119 (t0) REVERT: g 233 LEU cc_start: 0.7179 (mp) cc_final: 0.6764 (mp) REVERT: g 284 PHE cc_start: 0.5272 (p90) cc_final: 0.5005 (p90) REVERT: e 63 MET cc_start: 0.5041 (mmm) cc_final: 0.4796 (mmm) REVERT: e 110 ARG cc_start: 0.6447 (mtt180) cc_final: 0.6113 (mtp180) REVERT: I 56 ARG cc_start: 0.1987 (ttp80) cc_final: 0.1698 (ttp-110) REVERT: I 105 ARG cc_start: 0.6387 (mtm-85) cc_final: 0.5121 (tmm160) REVERT: I 179 MET cc_start: 0.2845 (tmm) cc_final: 0.2501 (tpt) REVERT: J 182 GLU cc_start: 0.4828 (mt-10) cc_final: 0.3781 (tp30) REVERT: a 186 LEU cc_start: 0.5230 (tp) cc_final: 0.4425 (tp) REVERT: N 30 THR cc_start: 0.5795 (p) cc_final: 0.4749 (p) REVERT: N 74 LEU cc_start: 0.7648 (mt) cc_final: 0.6906 (tp) REVERT: O 60 MET cc_start: 0.3274 (mmm) cc_final: 0.2746 (mmm) REVERT: O 68 LEU cc_start: 0.4002 (tp) cc_final: 0.3781 (tt) REVERT: P 60 MET cc_start: 0.1508 (mmm) cc_final: 0.0504 (mtm) REVERT: S 60 MET cc_start: 0.3292 (tpp) cc_final: 0.2917 (tpp) REVERT: S 63 LEU cc_start: 0.3210 (mm) cc_final: 0.2989 (tp) REVERT: W 30 THR cc_start: 0.7067 (t) cc_final: 0.6793 (m) REVERT: X 60 MET cc_start: 0.6465 (mtt) cc_final: 0.5916 (tpp) outliers start: 0 outliers final: 0 residues processed: 665 average time/residue: 0.1997 time to fit residues: 221.8219 Evaluate side-chains 521 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 521 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 69 optimal weight: 0.8980 chunk 138 optimal weight: 0.0980 chunk 262 optimal weight: 3.9990 chunk 328 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 276 optimal weight: 0.9990 chunk 290 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 485 optimal weight: 6.9990 overall best weight: 0.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 415 GLN ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 ASN E 210 ASN ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 389 GLN ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 228 HIS ** e 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 56 GLN ** I 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 28 GLN ** X 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 42 GLN ** Z 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.136827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.118021 restraints weight = 88035.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.116067 restraints weight = 167453.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.116815 restraints weight = 139689.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.116258 restraints weight = 93393.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.116533 restraints weight = 82449.538| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 39537 Z= 0.154 Angle : 0.676 11.218 53623 Z= 0.335 Chirality : 0.044 0.297 6417 Planarity : 0.005 0.083 6914 Dihedral : 7.041 165.971 5700 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.60 % Favored : 95.33 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.12), residues: 5113 helix: 0.85 (0.09), residues: 2907 sheet: -1.57 (0.21), residues: 540 loop : -1.39 (0.15), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 172 TYR 0.026 0.002 TYR A 464 PHE 0.039 0.002 PHE A 390 TRP 0.008 0.001 TRP e 57 HIS 0.003 0.001 HIS F 193 Details of bonding type rmsd covalent geometry : bond 0.00343 (39537) covalent geometry : angle 0.67595 (53623) hydrogen bonds : bond 0.04567 ( 2462) hydrogen bonds : angle 4.58814 ( 7257) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5822.53 seconds wall clock time: 101 minutes 35.07 seconds (6095.07 seconds total)