Starting phenix.real_space_refine on Tue Sep 15 10:46:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6vol_21268/09_2026/6vol_21268.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vol_21268/09_2026/6vol_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6vol_21268/09_2026/6vol_21268.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vol_21268/09_2026/6vol_21268.map" model { file = "/net/cci-nas-00/data/ceres_data/6vol_21268/09_2026/6vol_21268.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vol_21268/09_2026/6vol_21268.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6vol_21268/09_2026/6vol_21268.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6vol_21268/09_2026/6vol_21268.cif" } 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): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: 7.45, per 1000 atoms: 0.19 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: 3.09 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.09 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: 8.04 Time building geometry restraints manager: 4.22 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: 23330 33.79 - 67.59: 581 67.59 - 101.38: 47 101.38 - 135.17: 3 135.17 - 168.96: 3 Dihedral angle restraints: 23964 sinusoidal: 9312 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 23961 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: 5.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.650 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 33.020 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.110 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:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 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 : 15.207 168.964 14578 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 are 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/Z covalent geometry : bond 0.00515 / 0.28 (39537) covalent geometry : angle 0.88985 / 0.56 (53623) hydrogen bonds : bond 0.12171 / 8.18 ( 2462) hydrogen bonds : angle 6.05160 / 4.26 ( 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 : 1.255 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: 0.7949 (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: 0.2623 time to fit residues: 372.9598 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 : 1.464 ------------------------------------------------------------------------------- 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... A 173 GLN 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: 50 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.136718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.117022 restraints weight = 88354.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.115777 restraints weight = 124756.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.115649 restraints weight = 111768.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.114561 restraints weight = 94790.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.114925 restraints weight = 86001.551| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 39537 Z= 0.161 Angle : 0.683 10.885 53623 Z= 0.344 Chirality : 0.044 0.248 6417 Planarity : 0.005 0.061 6914 Dihedral : 6.988 145.945 5560 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.62 % Favored : 95.27 % Rotamer: Outliers : 0.17 % Allowed : 5.74 % Favored : 94.09 % 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 are not related in a simple way. whole: -1.78 (0.11), residues: 5113 helix: -0.27 (0.09), residues: 2898 sheet: -2.30 (0.19), residues: 541 loop : -2.25 (0.14), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG U 50 TYR 0.033 0.002 TYR J 109 PHE 0.026 0.001 PHE S 59 TRP 0.017 0.001 TRP e 57 HIS 0.004 0.001 HIS E 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 (39537) covalent geometry : angle 0.68263 / 0.34 (53623) hydrogen bonds : bond 0.05238 / 3.49 ( 2462) hydrogen bonds : angle 5.04037 / 3.53 ( 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 797 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 790 time to evaluate : 1.544 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: 0.8002 (mt-10) cc_final: 0.7475 (mm-30) REVERT: B 149 THR cc_start: 0.8479 (t) cc_final: 0.7951 (m) REVERT: B 182 ASP cc_start: 0.6062 (m-30) cc_final: 0.5780 (m-30) REVERT: C 321 GLU cc_start: 0.8406 (tm-30) cc_final: 0.7779 (tm-30) REVERT: C 498 MET cc_start: 0.7124 (tpp) cc_final: 0.6060 (ttp) REVERT: D 79 MET cc_start: 0.8176 (mmp) cc_final: 0.7783 (mmp) REVERT: D 311 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7005 (mm-30) REVERT: E 89 MET cc_start: 0.8482 (mtt) cc_final: 0.8241 (mtt) REVERT: E 223 ASN cc_start: 0.7216 (t0) cc_final: 0.7003 (t0) REVERT: E 313 ILE cc_start: 0.8003 (mt) cc_final: 0.7788 (mt) REVERT: F 18 LYS cc_start: 0.7525 (mttt) cc_final: 0.7212 (mtmm) REVERT: F 254 LEU cc_start: 0.9184 (tp) cc_final: 0.8965 (tp) REVERT: F 292 MET cc_start: 0.7993 (mtt) cc_final: 0.7779 (mtt) REVERT: F 301 THR cc_start: 0.8926 (p) cc_final: 0.8563 (t) REVERT: F 374 MET cc_start: 0.8329 (mmp) cc_final: 0.8086 (mmp) REVERT: F 472 GLN cc_start: 0.7030 (mp10) cc_final: 0.6713 (tm-30) REVERT: e 50 ARG cc_start: 0.5856 (pmt170) cc_final: 0.5420 (ptt180) REVERT: e 110 ARG cc_start: 0.6782 (mtt180) cc_final: 0.5905 (mtp180) REVERT: I 105 ARG cc_start: 0.6496 (mtm-85) cc_final: 0.5348 (ttp80) REVERT: I 121 PHE cc_start: 0.6273 (p90) cc_final: 0.5397 (m-10) REVERT: J 182 GLU cc_start: 0.4902 (mt-10) cc_final: 0.3650 (tp30) REVERT: a 186 LEU cc_start: 0.4974 (tp) cc_final: 0.4251 (tp) REVERT: M 57 LEU cc_start: 0.5018 (mt) cc_final: 0.4495 (mt) REVERT: O 68 LEU cc_start: 0.4264 (tp) cc_final: 0.3909 (tt) REVERT: P 37 GLU cc_start: 0.7530 (pt0) cc_final: 0.7271 (pt0) REVERT: R 28 GLN cc_start: 0.6930 (mp10) cc_final: 0.6248 (mp10) REVERT: R 61 GLU cc_start: 0.2193 (mp0) cc_final: 0.1770 (mt-10) REVERT: T 22 ILE cc_start: 0.4704 (mt) cc_final: 0.4446 (mt) REVERT: T 48 LYS cc_start: 0.4872 (mtmm) cc_final: 0.4665 (mmtm) REVERT: X 28 GLN cc_start: 0.5343 (tt0) cc_final: 0.4929 (tt0) outliers start: 7 outliers final: 1 residues processed: 795 average time/residue: 0.2560 time to fit residues: 331.8876 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 : 1.453 ------------------------------------------------------------------------------- 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: 5.9990 chunk 9 optimal weight: 3.9990 chunk 172 optimal weight: 1.9990 chunk 150 optimal weight: 0.0470 chunk 140 optimal weight: 0.0060 chunk 247 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 274 optimal weight: 1.9990 chunk 318 optimal weight: 0.8980 chunk 143 optimal weight: 0.7980 chunk 184 optimal weight: 4.9990 overall best weight: 0.5494 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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** B 443 ASN C 66 ASN 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: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.137601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.117849 restraints weight = 88608.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.116451 restraints weight = 140360.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.116581 restraints weight = 126152.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.116093 restraints weight = 89612.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.116440 restraints weight = 75207.585| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 39537 Z= 0.144 Angle : 0.643 10.334 53623 Z= 0.322 Chirality : 0.043 0.226 6417 Planarity : 0.005 0.056 6914 Dihedral : 6.607 152.529 5560 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.11 % Favored : 95.78 % Rotamer: Outliers : 0.07 % Allowed : 4.59 % Favored : 95.34 % 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 are not related in a simple way. whole: -1.08 (0.11), residues: 5113 helix: 0.28 (0.09), residues: 2911 sheet: -1.99 (0.20), residues: 550 loop : -1.94 (0.14), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG e 50 TYR 0.038 0.002 TYR O 66 PHE 0.033 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/Z covalent geometry : bond 0.00310 / 0.14 (39537) covalent geometry : angle 0.64275 / 0.32 (53623) hydrogen bonds : bond 0.04866 / 3.25 ( 2462) hydrogen bonds : angle 4.74677 / 3.33 ( 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 779 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 776 time to evaluate : 1.556 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: A 18 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7614 (tt0) REVERT: A 22 ARG cc_start: 0.6549 (ptt-90) cc_final: 0.5717 (tpt90) REVERT: B 149 THR cc_start: 0.8428 (t) cc_final: 0.8068 (m) REVERT: B 182 ASP cc_start: 0.5660 (m-30) cc_final: 0.5355 (m-30) REVERT: B 278 LEU cc_start: 0.8612 (pp) cc_final: 0.8346 (tp) REVERT: C 321 GLU cc_start: 0.8349 (tm-30) cc_final: 0.7976 (tm-30) REVERT: C 498 MET cc_start: 0.6902 (tpp) cc_final: 0.5921 (ttp) REVERT: D 79 MET cc_start: 0.8190 (mmp) cc_final: 0.7795 (mmp) REVERT: E 223 ASN cc_start: 0.7243 (t0) cc_final: 0.6814 (t0) REVERT: E 313 ILE cc_start: 0.8085 (mt) cc_final: 0.7864 (mt) REVERT: F 292 MET cc_start: 0.8055 (mtt) cc_final: 0.7805 (mtt) REVERT: F 301 THR cc_start: 0.8896 (p) cc_final: 0.8548 (t) REVERT: F 374 MET cc_start: 0.8392 (mmp) cc_final: 0.8044 (mmp) REVERT: F 488 MET cc_start: 0.5109 (ttm) cc_final: 0.4855 (ttm) REVERT: F 489 ASN cc_start: 0.5571 (t0) cc_final: 0.5335 (t0) REVERT: e 50 ARG cc_start: 0.5781 (pmt170) cc_final: 0.5461 (ptt180) REVERT: e 63 MET cc_start: 0.4869 (mmm) cc_final: 0.4381 (mmm) REVERT: e 110 ARG cc_start: 0.6558 (mtt180) cc_final: 0.5893 (mtp180) REVERT: I 104 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7378 (mt-10) REVERT: I 105 ARG cc_start: 0.6504 (mtm-85) cc_final: 0.5350 (ttp80) REVERT: J 145 ASN cc_start: 0.4879 (m-40) cc_final: 0.4457 (t0) REVERT: J 182 GLU cc_start: 0.4965 (mt-10) cc_final: 0.3701 (tp30) REVERT: a 186 LEU cc_start: 0.4564 (tp) cc_final: 0.3893 (tp) REVERT: M 57 LEU cc_start: 0.4901 (mt) cc_final: 0.4691 (mt) REVERT: O 68 LEU cc_start: 0.4083 (tp) cc_final: 0.3838 (tt) REVERT: P 37 GLU cc_start: 0.7635 (pt0) cc_final: 0.7403 (pt0) REVERT: P 60 MET cc_start: 0.1523 (mmm) cc_final: 0.0312 (mtm) REVERT: P 68 LEU cc_start: 0.3313 (mp) cc_final: 0.3105 (mp) REVERT: S 60 MET cc_start: 0.3261 (tpp) cc_final: 0.2998 (tpt) REVERT: W 30 THR cc_start: 0.7275 (t) cc_final: 0.6983 (m) REVERT: W 49 ILE cc_start: 0.6597 (mt) cc_final: 0.6283 (tt) REVERT: Y 19 LEU cc_start: 0.5900 (mm) cc_final: 0.5688 (tp) outliers start: 3 outliers final: 0 residues processed: 777 average time/residue: 0.2450 time to fit residues: 314.3682 Evaluate side-chains 572 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 572 time to evaluate : 1.435 ------------------------------------------------------------------------------- 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: 0.3980 chunk 165 optimal weight: 0.7980 chunk 191 optimal weight: 0.8980 chunk 323 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 482 optimal weight: 9.9990 chunk 8 optimal weight: 0.8980 chunk 143 optimal weight: 4.9990 chunk 493 optimal weight: 4.9990 chunk 142 optimal weight: 0.9980 chunk 397 optimal weight: 9.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 187 GLN B 273 GLN ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 ASN C 423 GLN ** C 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 238 GLN E 223 ASN ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 479 ASN d 240 GLN 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 ** both conformations clash, **PLEASE CHECK MANUALLY** S 28 GLN ** S 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 34 GLN ** W 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 42 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.137152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.117028 restraints weight = 88142.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.115361 restraints weight = 144165.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.115509 restraints weight = 124863.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.115288 restraints weight = 78671.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.115614 restraints weight = 69669.758| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 39537 Z= 0.156 Angle : 0.647 10.322 53623 Z= 0.324 Chirality : 0.044 0.358 6417 Planarity : 0.004 0.050 6914 Dihedral : 6.488 153.693 5560 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.38 % Favored : 95.50 % Rotamer: Outliers : 0.07 % Allowed : 3.85 % Favored : 96.07 % 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 are not related in a simple way. whole: -0.78 (0.11), residues: 5113 helix: 0.52 (0.09), residues: 2912 sheet: -1.86 (0.20), residues: 545 loop : -1.80 (0.14), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 429 TYR 0.023 0.002 TYR a 148 PHE 0.027 0.002 PHE F 35 TRP 0.007 0.001 TRP e 57 HIS 0.002 0.001 HIS F 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 (39537) covalent geometry : angle 0.64706 / 0.32 (53623) hydrogen bonds : bond 0.04746 / 3.17 ( 2462) hydrogen bonds : angle 4.65230 / 3.26 ( 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 742 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 739 time to evaluate : 1.516 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: A 18 GLU cc_start: 0.7559 (mt-10) cc_final: 0.6849 (tt0) REVERT: A 230 ASP cc_start: 0.7178 (p0) cc_final: 0.6800 (p0) REVERT: B 149 THR cc_start: 0.8387 (t) cc_final: 0.8002 (m) REVERT: B 182 ASP cc_start: 0.5734 (m-30) cc_final: 0.5354 (m-30) REVERT: B 278 LEU cc_start: 0.8651 (pp) cc_final: 0.8339 (tp) REVERT: B 321 GLU cc_start: 0.7116 (tt0) cc_final: 0.6370 (tt0) REVERT: C 321 GLU cc_start: 0.8438 (tm-30) cc_final: 0.7924 (tm-30) REVERT: C 498 MET cc_start: 0.6910 (tpp) cc_final: 0.5966 (ttp) REVERT: D 79 MET cc_start: 0.8179 (mmp) cc_final: 0.7776 (mmp) REVERT: E 223 ASN cc_start: 0.6914 (t0) cc_final: 0.6709 (t0) REVERT: F 254 LEU cc_start: 0.9177 (tp) cc_final: 0.8906 (tp) REVERT: F 292 MET cc_start: 0.8078 (mtt) cc_final: 0.7872 (mtt) REVERT: F 301 THR cc_start: 0.8932 (p) cc_final: 0.8689 (t) REVERT: F 374 MET cc_start: 0.8395 (mmp) cc_final: 0.8033 (mmp) REVERT: e 63 MET cc_start: 0.4939 (mmm) cc_final: 0.4530 (mmm) REVERT: e 110 ARG cc_start: 0.6636 (mtt180) cc_final: 0.5985 (mtp180) REVERT: I 105 ARG cc_start: 0.6502 (mtm-85) cc_final: 0.5411 (ttp80) REVERT: J 145 ASN cc_start: 0.4818 (m-40) cc_final: 0.4433 (t0) REVERT: J 182 GLU cc_start: 0.4828 (mt-10) cc_final: 0.3757 (tp30) REVERT: a 186 LEU cc_start: 0.5017 (tp) cc_final: 0.4233 (tp) REVERT: O 52 THR cc_start: 0.5356 (m) cc_final: 0.4948 (m) REVERT: O 60 MET cc_start: 0.3133 (mmm) cc_final: 0.2880 (mmm) REVERT: P 37 GLU cc_start: 0.7612 (pt0) cc_final: 0.7230 (pt0) REVERT: P 60 MET cc_start: 0.1271 (mmm) cc_final: -0.0003 (mtt) REVERT: P 68 LEU cc_start: 0.3544 (mp) cc_final: 0.3317 (mp) REVERT: R 28 GLN cc_start: 0.6654 (mp10) cc_final: 0.6433 (mp10) REVERT: S 60 MET cc_start: 0.3151 (tpp) cc_final: 0.2626 (tpp) REVERT: S 63 LEU cc_start: 0.3681 (mm) cc_final: 0.3288 (tp) REVERT: W 30 THR cc_start: 0.7212 (t) cc_final: 0.6974 (m) outliers start: 3 outliers final: 1 residues processed: 740 average time/residue: 0.2461 time to fit residues: 300.2021 Evaluate side-chains 564 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 563 time to evaluate : 1.526 ------------------------------------------------------------------------------- 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: 0.9990 chunk 31 optimal weight: 1.9990 chunk 497 optimal weight: 2.9990 chunk 206 optimal weight: 5.9990 chunk 382 optimal weight: 0.9990 chunk 291 optimal weight: 4.9990 chunk 284 optimal weight: 0.6980 chunk 89 optimal weight: 0.1980 chunk 69 optimal weight: 0.8980 chunk 243 optimal weight: 2.9990 chunk 204 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 GLN ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 415 GLN ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 ASN ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 120 ASN ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 228 HIS e 56 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** ** T 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 28 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.137195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.116454 restraints weight = 88182.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.114438 restraints weight = 158911.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.115703 restraints weight = 128584.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.115244 restraints weight = 84153.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.115568 restraints weight = 75574.531| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 39537 Z= 0.150 Angle : 0.645 10.387 53623 Z= 0.321 Chirality : 0.043 0.263 6417 Planarity : 0.004 0.057 6914 Dihedral : 6.393 156.352 5560 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.09 % Favored : 95.83 % Rotamer: Outliers : 0.07 % Allowed : 2.65 % Favored : 97.28 % 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 are not related in a simple way. whole: -0.56 (0.11), residues: 5113 helix: 0.67 (0.09), residues: 2911 sheet: -1.74 (0.21), residues: 553 loop : -1.67 (0.15), residues: 1649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 172 TYR 0.041 0.002 TYR O 66 PHE 0.023 0.001 PHE g 217 TRP 0.004 0.001 TRP a 117 HIS 0.003 0.001 HIS D 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (39537) covalent geometry : angle 0.64505 / 0.32 (53623) hydrogen bonds : bond 0.04682 / 3.13 ( 2462) hydrogen bonds : angle 4.58574 / 3.21 ( 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 718 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 715 time to evaluate : 2.009 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: 0.7144 (p0) cc_final: 0.6476 (p0) REVERT: B 149 THR cc_start: 0.8322 (t) cc_final: 0.8002 (m) REVERT: B 182 ASP cc_start: 0.5705 (m-30) cc_final: 0.5325 (m-30) REVERT: B 278 LEU cc_start: 0.8621 (pp) cc_final: 0.8278 (tp) REVERT: B 321 GLU cc_start: 0.6989 (tt0) cc_final: 0.6411 (tt0) REVERT: C 216 ARG cc_start: 0.6969 (mmm160) cc_final: 0.6734 (mmm160) REVERT: C 248 GLU cc_start: 0.7296 (tt0) cc_final: 0.6734 (tt0) REVERT: C 321 GLU cc_start: 0.8316 (tm-30) cc_final: 0.7853 (tm-30) REVERT: C 498 MET cc_start: 0.6937 (tpp) cc_final: 0.5963 (ttp) REVERT: D 79 MET cc_start: 0.8203 (mmp) cc_final: 0.7789 (mmt) REVERT: D 273 ASP cc_start: 0.8183 (t70) cc_final: 0.7972 (t70) REVERT: D 306 MET cc_start: 0.8296 (tpt) cc_final: 0.8069 (mmm) REVERT: D 311 GLU cc_start: 0.7472 (mt-10) cc_final: 0.6900 (mm-30) REVERT: D 325 GLN cc_start: 0.7343 (pt0) cc_final: 0.7103 (pt0) REVERT: E 313 ILE cc_start: 0.8200 (mt) cc_final: 0.7966 (mt) REVERT: E 490 LEU cc_start: 0.8128 (pp) cc_final: 0.7326 (tt) REVERT: F 33 VAL cc_start: 0.8694 (p) cc_final: 0.8487 (m) REVERT: F 254 LEU cc_start: 0.9137 (tp) cc_final: 0.8933 (tp) REVERT: F 301 THR cc_start: 0.8950 (p) cc_final: 0.8653 (t) REVERT: F 374 MET cc_start: 0.8378 (mmp) cc_final: 0.8078 (mmp) REVERT: g 284 PHE cc_start: 0.5305 (p90) cc_final: 0.4993 (p90) REVERT: e 63 MET cc_start: 0.4926 (mmm) cc_final: 0.4469 (mmm) REVERT: e 110 ARG cc_start: 0.6597 (mtt180) cc_final: 0.6060 (mtp180) REVERT: I 105 ARG cc_start: 0.6398 (mtm-85) cc_final: 0.5283 (tmm160) REVERT: I 160 LEU cc_start: 0.5589 (mt) cc_final: 0.5088 (pp) REVERT: J 182 GLU cc_start: 0.4930 (mt-10) cc_final: 0.3913 (tp30) REVERT: O 60 MET cc_start: 0.3409 (mmm) cc_final: 0.3079 (mmm) REVERT: P 37 GLU cc_start: 0.7520 (pt0) cc_final: 0.7184 (pt0) REVERT: P 60 MET cc_start: 0.1379 (mmm) cc_final: -0.0205 (mtt) REVERT: P 68 LEU cc_start: 0.3730 (mp) cc_final: 0.3438 (mp) REVERT: S 60 MET cc_start: 0.3323 (tpp) cc_final: 0.2712 (tpp) REVERT: S 63 LEU cc_start: 0.3609 (mm) cc_final: 0.3219 (tp) REVERT: W 30 THR cc_start: 0.7216 (t) cc_final: 0.6950 (m) REVERT: X 60 MET cc_start: 0.6287 (mtt) cc_final: 0.5613 (tpp) outliers start: 3 outliers final: 1 residues processed: 717 average time/residue: 0.2419 time to fit residues: 288.2586 Evaluate side-chains 550 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 549 time to evaluate : 1.649 ------------------------------------------------------------------------------- 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: 0.6980 chunk 489 optimal weight: 3.9990 chunk 272 optimal weight: 2.9990 chunk 275 optimal weight: 1.9990 chunk 174 optimal weight: 0.7980 chunk 149 optimal weight: 0.4980 chunk 288 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 177 optimal weight: 0.5980 chunk 1 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 273 GLN B 295 HIS ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 473 GLN D 238 GLN E 112 ASN ** E 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 228 HIS ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** M 42 GLN ** 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** X 28 GLN ** X 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 28 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.137630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.117443 restraints weight = 88356.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.115968 restraints weight = 143691.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.115733 restraints weight = 133020.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.114910 restraints weight = 103537.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.115261 restraints weight = 93077.107| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 39537 Z= 0.143 Angle : 0.638 10.173 53623 Z= 0.317 Chirality : 0.043 0.294 6417 Planarity : 0.004 0.050 6914 Dihedral : 6.316 158.907 5560 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.13 % Favored : 95.80 % Rotamer: Outliers : 0.02 % Allowed : 2.75 % Favored : 97.23 % 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 are not related in a simple way. whole: -0.39 (0.12), residues: 5113 helix: 0.81 (0.09), residues: 2902 sheet: -1.66 (0.21), residues: 552 loop : -1.57 (0.15), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 172 TYR 0.021 0.002 TYR a 148 PHE 0.043 0.002 PHE A 390 TRP 0.007 0.001 TRP e 15 HIS 0.003 0.000 HIS A 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (39537) covalent geometry : angle 0.63759 / 0.32 (53623) hydrogen bonds : bond 0.04576 / 3.06 ( 2462) hydrogen bonds : angle 4.51475 / 3.16 ( 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 707 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 706 time to evaluate : 1.470 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: A 230 ASP cc_start: 0.7192 (p0) cc_final: 0.6527 (p0) REVERT: B 149 THR cc_start: 0.8429 (t) cc_final: 0.8053 (m) REVERT: B 182 ASP cc_start: 0.5825 (m-30) cc_final: 0.5411 (m-30) REVERT: B 278 LEU cc_start: 0.8633 (pp) cc_final: 0.8387 (tp) REVERT: B 321 GLU cc_start: 0.6968 (tt0) cc_final: 0.6439 (tt0) REVERT: B 436 MET cc_start: 0.7267 (tmm) cc_final: 0.6963 (tmm) REVERT: C 29 THR cc_start: 0.8762 (t) cc_final: 0.8552 (m) REVERT: C 85 GLU cc_start: 0.7870 (tt0) cc_final: 0.7578 (tt0) REVERT: C 248 GLU cc_start: 0.7358 (tt0) cc_final: 0.7143 (tt0) REVERT: C 321 GLU cc_start: 0.8341 (tm-30) cc_final: 0.7993 (tm-30) REVERT: C 498 MET cc_start: 0.6983 (tpp) cc_final: 0.6098 (ttp) REVERT: D 79 MET cc_start: 0.8076 (mmp) cc_final: 0.7833 (mmt) REVERT: D 311 GLU cc_start: 0.7491 (mt-10) cc_final: 0.6886 (mm-30) REVERT: D 325 GLN cc_start: 0.7389 (pt0) cc_final: 0.7177 (pt0) REVERT: D 362 TYR cc_start: 0.7806 (m-10) cc_final: 0.7594 (m-80) REVERT: E 313 ILE cc_start: 0.8085 (mt) cc_final: 0.7881 (mt) REVERT: E 490 LEU cc_start: 0.8254 (pp) cc_final: 0.7496 (tt) REVERT: F 33 VAL cc_start: 0.8808 (p) cc_final: 0.8539 (m) REVERT: F 64 GLU cc_start: 0.7024 (mt-10) cc_final: 0.6731 (mt-10) REVERT: F 301 THR cc_start: 0.8959 (p) cc_final: 0.8639 (t) REVERT: F 374 MET cc_start: 0.8356 (mmp) cc_final: 0.8081 (mmp) REVERT: F 385 TYR cc_start: 0.7844 (t80) cc_final: 0.7410 (t80) REVERT: g 284 PHE cc_start: 0.5220 (p90) cc_final: 0.4996 (p90) REVERT: e 63 MET cc_start: 0.4871 (mmm) cc_final: 0.4463 (mmm) REVERT: e 110 ARG cc_start: 0.6609 (mtt180) cc_final: 0.5998 (mtp180) REVERT: I 105 ARG cc_start: 0.6407 (mtm-85) cc_final: 0.5310 (tmm160) REVERT: J 182 GLU cc_start: 0.4895 (mt-10) cc_final: 0.3771 (tp30) REVERT: a 186 LEU cc_start: 0.5381 (tp) cc_final: 0.4685 (tp) REVERT: N 4 LEU cc_start: 0.4836 (tp) cc_final: 0.4557 (mp) REVERT: O 60 MET cc_start: 0.3387 (mmm) cc_final: 0.2963 (mmm) REVERT: O 66 TYR cc_start: 0.4260 (m-10) cc_final: 0.4032 (m-80) REVERT: P 37 GLU cc_start: 0.7561 (pt0) cc_final: 0.7075 (pt0) REVERT: P 60 MET cc_start: 0.1387 (mmm) cc_final: 0.0013 (mtt) REVERT: Q 44 GLU cc_start: 0.5839 (mm-30) cc_final: 0.5620 (mm-30) REVERT: S 60 MET cc_start: 0.3352 (tpp) cc_final: 0.2815 (tpp) REVERT: S 63 LEU cc_start: 0.3716 (mm) cc_final: 0.3338 (tp) REVERT: X 60 MET cc_start: 0.6165 (mtt) cc_final: 0.5639 (tpp) outliers start: 1 outliers final: 0 residues processed: 707 average time/residue: 0.2408 time to fit residues: 282.4003 Evaluate side-chains 538 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 538 time to evaluate : 1.495 ------------------------------------------------------------------------------- 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: 4.9990 chunk 324 optimal weight: 0.1980 chunk 287 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 257 optimal weight: 0.9990 chunk 286 optimal weight: 1.9990 chunk 39 optimal weight: 0.0870 chunk 450 optimal weight: 6.9990 chunk 355 optimal weight: 0.6980 chunk 152 optimal weight: 4.9990 chunk 485 optimal weight: 0.8980 overall best weight: 0.5760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 334 ASN B 415 GLN ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 ASN E 120 ASN E 210 ASN ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 45 ASN ** F 133 HIS ** 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 228 HIS e 56 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 T 28 GLN 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.138139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.117267 restraints weight = 87729.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.115238 restraints weight = 163264.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.116299 restraints weight = 129078.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.116094 restraints weight = 91624.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.116343 restraints weight = 83084.570| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 39537 Z= 0.141 Angle : 0.643 12.029 53623 Z= 0.318 Chirality : 0.043 0.275 6417 Planarity : 0.004 0.050 6914 Dihedral : 6.236 162.376 5560 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.97 % Favored : 95.95 % Rotamer: Outliers : 0.07 % Allowed : 1.91 % Favored : 98.01 % 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 are not related in a simple way. whole: -0.25 (0.12), residues: 5113 helix: 0.92 (0.10), residues: 2904 sheet: -1.68 (0.21), residues: 560 loop : -1.48 (0.15), residues: 1649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 248 TYR 0.027 0.002 TYR C 439 PHE 0.022 0.001 PHE g 199 TRP 0.006 0.001 TRP e 15 HIS 0.002 0.000 HIS F 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (39537) covalent geometry : angle 0.64291 / 0.32 (53623) hydrogen bonds : bond 0.04470 / 2.99 ( 2462) hydrogen bonds : angle 4.49352 / 3.15 ( 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 711 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 708 time to evaluate : 1.562 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 186 ASN cc_start: 0.7563 (t0) cc_final: 0.7194 (t0) REVERT: A 230 ASP cc_start: 0.7155 (p0) cc_final: 0.6451 (p0) REVERT: A 340 ASP cc_start: 0.8860 (m-30) cc_final: 0.8499 (t0) REVERT: B 138 MET cc_start: 0.6608 (tpp) cc_final: 0.6367 (tpp) REVERT: B 149 THR cc_start: 0.8409 (t) cc_final: 0.7973 (m) REVERT: B 182 ASP cc_start: 0.5645 (m-30) cc_final: 0.5327 (m-30) REVERT: B 278 LEU cc_start: 0.8603 (pp) cc_final: 0.8344 (tp) REVERT: B 321 GLU cc_start: 0.6885 (tt0) cc_final: 0.6394 (tt0) REVERT: B 436 MET cc_start: 0.7212 (tmm) cc_final: 0.6953 (tmm) REVERT: C 321 GLU cc_start: 0.8304 (tm-30) cc_final: 0.7902 (tm-30) REVERT: C 498 MET cc_start: 0.6920 (tpp) cc_final: 0.6045 (ttp) REVERT: D 79 MET cc_start: 0.8133 (mmp) cc_final: 0.7802 (mmp) REVERT: D 311 GLU cc_start: 0.7453 (mt-10) cc_final: 0.6881 (mm-30) REVERT: D 362 TYR cc_start: 0.7705 (m-10) cc_final: 0.7468 (m-80) REVERT: E 334 LEU cc_start: 0.8090 (mt) cc_final: 0.7194 (tt) REVERT: E 490 LEU cc_start: 0.8165 (pp) cc_final: 0.7433 (tt) REVERT: F 79 MET cc_start: 0.8404 (mmm) cc_final: 0.8035 (mmm) REVERT: F 301 THR cc_start: 0.8933 (p) cc_final: 0.8628 (t) REVERT: F 374 MET cc_start: 0.8331 (mmp) cc_final: 0.8083 (mmp) REVERT: F 385 TYR cc_start: 0.7751 (t80) cc_final: 0.7282 (t80) REVERT: d 129 LEU cc_start: 0.8345 (mt) cc_final: 0.8135 (mt) REVERT: e 63 MET cc_start: 0.4986 (mmm) cc_final: 0.4578 (mmm) REVERT: e 110 ARG cc_start: 0.6491 (mtt180) cc_final: 0.6010 (mtp180) REVERT: I 105 ARG cc_start: 0.6340 (mtm-85) cc_final: 0.5256 (tmm160) REVERT: J 182 GLU cc_start: 0.4911 (mt-10) cc_final: 0.3853 (tp30) REVERT: a 186 LEU cc_start: 0.4847 (tp) cc_final: 0.4489 (tp) REVERT: M 37 GLU cc_start: 0.4613 (tp30) cc_final: 0.4401 (tp30) REVERT: N 4 LEU cc_start: 0.4746 (tp) cc_final: 0.4425 (mp) REVERT: O 41 ARG cc_start: 0.3900 (ttp-170) cc_final: 0.3517 (ttp80) REVERT: O 60 MET cc_start: 0.3071 (mmm) cc_final: 0.2648 (mmm) REVERT: P 37 GLU cc_start: 0.7474 (pt0) cc_final: 0.7158 (pt0) REVERT: P 60 MET cc_start: 0.1300 (mmm) cc_final: -0.0032 (mtm) REVERT: S 60 MET cc_start: 0.3469 (tpp) cc_final: 0.2936 (tpp) REVERT: S 63 LEU cc_start: 0.3694 (mm) cc_final: 0.3307 (tp) REVERT: X 60 MET cc_start: 0.6334 (mtt) cc_final: 0.5749 (tpp) REVERT: Z 60 MET cc_start: -0.0398 (tpp) cc_final: -0.0626 (tmm) outliers start: 3 outliers final: 1 residues processed: 710 average time/residue: 0.2390 time to fit residues: 283.9809 Evaluate side-chains 538 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 537 time to evaluate : 1.547 ------------------------------------------------------------------------------- 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: 0.5980 chunk 340 optimal weight: 0.9990 chunk 208 optimal weight: 3.9990 chunk 364 optimal weight: 1.9990 chunk 353 optimal weight: 0.7980 chunk 394 optimal weight: 0.4980 chunk 387 optimal weight: 0.3980 chunk 321 optimal weight: 4.9990 chunk 32 optimal weight: 0.4980 chunk 108 optimal weight: 0.8980 chunk 350 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 434 GLN B 351 ASN ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 238 GLN D 325 GLN D 376 GLN E 25 GLN ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 120 ASN ** F 133 HIS ** 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 228 HIS I 133 GLN ** 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** W 28 GLN 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.138195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.118173 restraints weight = 87666.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.116925 restraints weight = 132494.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.116688 restraints weight = 121517.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.115507 restraints weight = 103740.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.115971 restraints weight = 86517.634| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 39537 Z= 0.138 Angle : 0.640 9.728 53623 Z= 0.317 Chirality : 0.043 0.279 6417 Planarity : 0.004 0.049 6914 Dihedral : 6.190 164.865 5560 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.11 % Favored : 95.81 % Rotamer: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % 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 are not related in a simple way. whole: -0.18 (0.12), residues: 5113 helix: 0.94 (0.09), residues: 2903 sheet: -1.55 (0.21), residues: 572 loop : -1.42 (0.15), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 172 TYR 0.021 0.001 TYR C 20 PHE 0.038 0.001 PHE A 390 TRP 0.008 0.001 TRP a 117 HIS 0.002 0.000 HIS F 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (39537) covalent geometry : angle 0.64046 / 0.32 (53623) hydrogen bonds : bond 0.04389 / 2.93 ( 2462) hydrogen bonds : angle 4.50036 / 3.15 ( 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 678 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 678 time to evaluate : 1.573 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: A 186 ASN cc_start: 0.7620 (t0) cc_final: 0.7271 (t0) REVERT: A 230 ASP cc_start: 0.7153 (p0) cc_final: 0.6599 (p0) REVERT: A 340 ASP cc_start: 0.8878 (m-30) cc_final: 0.8486 (t0) REVERT: B 149 THR cc_start: 0.8405 (t) cc_final: 0.7972 (m) REVERT: B 182 ASP cc_start: 0.5715 (m-30) cc_final: 0.5316 (m-30) REVERT: B 278 LEU cc_start: 0.8612 (pp) cc_final: 0.8369 (tp) REVERT: B 321 GLU cc_start: 0.6924 (tt0) cc_final: 0.6398 (tt0) REVERT: C 321 GLU cc_start: 0.8311 (tm-30) cc_final: 0.7929 (tm-30) REVERT: C 498 MET cc_start: 0.6935 (tpp) cc_final: 0.6079 (ttp) REVERT: D 79 MET cc_start: 0.8134 (mmp) cc_final: 0.7808 (mmt) REVERT: D 89 MET cc_start: 0.7748 (mtt) cc_final: 0.7229 (mtp) REVERT: D 311 GLU cc_start: 0.7429 (mt-10) cc_final: 0.6757 (mm-30) REVERT: D 362 TYR cc_start: 0.7665 (m-10) cc_final: 0.7369 (m-10) REVERT: E 40 MET cc_start: 0.6758 (mmm) cc_final: 0.6328 (mmt) REVERT: E 334 LEU cc_start: 0.8134 (mt) cc_final: 0.7148 (tt) REVERT: E 335 THR cc_start: 0.7410 (p) cc_final: 0.7045 (p) REVERT: E 490 LEU cc_start: 0.8143 (pp) cc_final: 0.7385 (tt) REVERT: F 79 MET cc_start: 0.8585 (mmm) cc_final: 0.8315 (mmt) REVERT: F 301 THR cc_start: 0.8874 (p) cc_final: 0.8608 (t) REVERT: F 374 MET cc_start: 0.8342 (mmp) cc_final: 0.7975 (mmp) REVERT: F 385 TYR cc_start: 0.7650 (t80) cc_final: 0.7246 (t80) REVERT: d 206 ASN cc_start: 0.7197 (t0) cc_final: 0.6825 (t0) REVERT: e 63 MET cc_start: 0.4931 (mmm) cc_final: 0.4596 (mmm) REVERT: e 110 ARG cc_start: 0.6479 (mtt180) cc_final: 0.6030 (mtp180) REVERT: I 105 ARG cc_start: 0.6428 (mtm-85) cc_final: 0.5223 (tmm160) REVERT: J 145 ASN cc_start: 0.4622 (m-40) cc_final: 0.4382 (t0) REVERT: J 182 GLU cc_start: 0.4725 (mt-10) cc_final: 0.3683 (tp30) REVERT: a 186 LEU cc_start: 0.5451 (tp) cc_final: 0.4865 (tp) REVERT: N 4 LEU cc_start: 0.4752 (tp) cc_final: 0.4418 (mp) REVERT: N 30 THR cc_start: 0.6038 (p) cc_final: 0.5606 (p) REVERT: O 41 ARG cc_start: 0.3884 (ttp-170) cc_final: 0.3521 (ttp80) REVERT: O 60 MET cc_start: 0.3135 (mmm) cc_final: 0.2669 (mmm) REVERT: O 68 LEU cc_start: 0.3944 (tp) cc_final: 0.3731 (tt) REVERT: P 37 GLU cc_start: 0.7525 (pt0) cc_final: 0.7143 (pt0) REVERT: P 60 MET cc_start: 0.1593 (mmm) cc_final: 0.0525 (mtm) REVERT: Q 60 MET cc_start: 0.1252 (ttm) cc_final: 0.1035 (ttm) REVERT: S 60 MET cc_start: 0.3511 (tpp) cc_final: 0.2983 (tpp) REVERT: S 63 LEU cc_start: 0.3642 (mm) cc_final: 0.3256 (tp) REVERT: X 60 MET cc_start: 0.6229 (mtt) cc_final: 0.5706 (tpp) outliers start: 0 outliers final: 0 residues processed: 678 average time/residue: 0.2368 time to fit residues: 268.8982 Evaluate side-chains 534 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 534 time to evaluate : 1.630 ------------------------------------------------------------------------------- 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: 0.0070 chunk 10 optimal weight: 0.8980 chunk 413 optimal weight: 5.9990 chunk 255 optimal weight: 0.9990 chunk 365 optimal weight: 9.9990 chunk 129 optimal weight: 0.4980 chunk 384 optimal weight: 0.9980 chunk 223 optimal weight: 0.0270 chunk 28 optimal weight: 0.8980 chunk 283 optimal weight: 4.9990 chunk 438 optimal weight: 1.9990 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 334 ASN B 415 GLN ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 310 GLN E 112 ASN E 120 ASN ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 133 HIS ** 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 228 HIS ** 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** N 34 GLN 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.138480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.119756 restraints weight = 87172.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.117965 restraints weight = 155813.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.118234 restraints weight = 140608.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.117665 restraints weight = 98880.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.117918 restraints weight = 83187.290| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 39537 Z= 0.134 Angle : 0.649 12.963 53623 Z= 0.320 Chirality : 0.043 0.268 6417 Planarity : 0.004 0.048 6914 Dihedral : 6.135 169.216 5560 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.99 % Favored : 95.93 % Rotamer: Outliers : 0.05 % Allowed : 0.66 % Favored : 99.29 % 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 are not related in a simple way. whole: -0.06 (0.12), residues: 5113 helix: 1.02 (0.10), residues: 2908 sheet: -1.47 (0.21), residues: 563 loop : -1.36 (0.15), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG E 423 TYR 0.020 0.001 TYR a 148 PHE 0.034 0.001 PHE A 390 TRP 0.009 0.001 TRP e 57 HIS 0.004 0.001 HIS F 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (39537) covalent geometry : angle 0.64914 / 0.32 (53623) hydrogen bonds : bond 0.04331 / 2.90 ( 2462) hydrogen bonds : angle 4.46089 / 3.12 ( 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 692 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 690 time to evaluate : 1.616 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 186 ASN cc_start: 0.7556 (t0) cc_final: 0.7226 (t0) REVERT: A 230 ASP cc_start: 0.7265 (p0) cc_final: 0.6816 (p0) REVERT: A 334 ASN cc_start: 0.8000 (m-40) cc_final: 0.7486 (m110) REVERT: A 340 ASP cc_start: 0.8950 (m-30) cc_final: 0.8474 (t0) REVERT: B 149 THR cc_start: 0.8388 (t) cc_final: 0.7969 (m) REVERT: B 182 ASP cc_start: 0.5548 (m-30) cc_final: 0.5267 (m-30) REVERT: B 278 LEU cc_start: 0.8625 (pp) cc_final: 0.8364 (tp) REVERT: B 321 GLU cc_start: 0.6920 (tt0) cc_final: 0.6402 (tt0) REVERT: C 321 GLU cc_start: 0.8316 (tm-30) cc_final: 0.7890 (tm-30) REVERT: C 498 MET cc_start: 0.6952 (tpp) cc_final: 0.6023 (ttp) REVERT: D 79 MET cc_start: 0.8165 (mmp) cc_final: 0.7792 (mmp) REVERT: D 311 GLU cc_start: 0.7400 (mt-10) cc_final: 0.6698 (mm-30) REVERT: D 362 TYR cc_start: 0.7617 (m-10) cc_final: 0.7278 (m-10) REVERT: E 64 GLU cc_start: 0.7693 (tt0) cc_final: 0.7435 (tt0) REVERT: E 313 ILE cc_start: 0.7906 (mt) cc_final: 0.7692 (mt) REVERT: E 334 LEU cc_start: 0.8101 (mt) cc_final: 0.7111 (tt) REVERT: E 335 THR cc_start: 0.7397 (p) cc_final: 0.7043 (p) REVERT: E 490 LEU cc_start: 0.8133 (pp) cc_final: 0.7388 (tt) REVERT: F 79 MET cc_start: 0.8578 (mmm) cc_final: 0.8319 (mmm) REVERT: F 301 THR cc_start: 0.8963 (p) cc_final: 0.8630 (t) REVERT: F 374 MET cc_start: 0.8294 (mmp) cc_final: 0.7907 (mmp) REVERT: F 385 TYR cc_start: 0.7604 (t80) cc_final: 0.7219 (t80) REVERT: g 220 LEU cc_start: 0.6083 (mt) cc_final: 0.5657 (mt) REVERT: e 63 MET cc_start: 0.4974 (mmm) cc_final: 0.4558 (mmm) REVERT: e 110 ARG cc_start: 0.6429 (mtt180) cc_final: 0.6046 (mtp180) REVERT: I 105 ARG cc_start: 0.6282 (mtm-85) cc_final: 0.5114 (tmm160) REVERT: I 179 MET cc_start: 0.3021 (tmm) cc_final: 0.2701 (tpt) REVERT: J 182 GLU cc_start: 0.4458 (mt-10) cc_final: 0.3486 (tp30) REVERT: a 186 LEU cc_start: 0.4936 (tp) cc_final: 0.4423 (tp) REVERT: N 4 LEU cc_start: 0.4924 (tp) cc_final: 0.4535 (mp) REVERT: N 30 THR cc_start: 0.5229 (p) cc_final: 0.4954 (p) REVERT: O 41 ARG cc_start: 0.3947 (ttp-170) cc_final: 0.3599 (ttp80) REVERT: O 60 MET cc_start: 0.3273 (mmm) cc_final: 0.2708 (mmm) REVERT: P 37 GLU cc_start: 0.7483 (pt0) cc_final: 0.7095 (pt0) REVERT: P 60 MET cc_start: 0.1501 (mmm) cc_final: 0.0247 (mtm) REVERT: Q 44 GLU cc_start: 0.5908 (mm-30) cc_final: 0.5675 (mm-30) REVERT: S 60 MET cc_start: 0.3404 (tpp) cc_final: 0.2948 (tpp) REVERT: S 63 LEU cc_start: 0.3449 (mm) cc_final: 0.3064 (tp) REVERT: V 49 ILE cc_start: 0.5389 (mm) cc_final: 0.5185 (mm) REVERT: V 60 MET cc_start: 0.7316 (ttm) cc_final: 0.6825 (tpp) REVERT: X 60 MET cc_start: 0.6182 (mtt) cc_final: 0.5669 (tpp) REVERT: Z 60 MET cc_start: -0.0347 (tpp) cc_final: -0.0911 (tmm) outliers start: 2 outliers final: 2 residues processed: 692 average time/residue: 0.2387 time to fit residues: 275.9780 Evaluate side-chains 543 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 541 time to evaluate : 1.414 ------------------------------------------------------------------------------- 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: 0.7980 chunk 52 optimal weight: 2.9990 chunk 474 optimal weight: 5.9990 chunk 215 optimal weight: 0.5980 chunk 323 optimal weight: 3.9990 chunk 167 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 499 optimal weight: 1.9990 chunk 407 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 267 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 238 GLN ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 120 ASN ** F 133 HIS ** 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 228 HIS ** I 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 109 ASN ** M 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 28 GLN ** X 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 28 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.137770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.119103 restraints weight = 87141.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.117243 restraints weight = 150083.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.117354 restraints weight = 131255.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.116771 restraints weight = 94002.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.117149 restraints weight = 79432.799| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 39537 Z= 0.155 Angle : 0.671 11.483 53623 Z= 0.332 Chirality : 0.044 0.299 6417 Planarity : 0.004 0.048 6914 Dihedral : 6.199 172.831 5560 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.22 % Favored : 95.70 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % 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 are not related in a simple way. whole: -0.08 (0.12), residues: 5113 helix: 1.00 (0.09), residues: 2903 sheet: -1.42 (0.21), residues: 580 loop : -1.35 (0.15), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 172 TYR 0.033 0.002 TYR O 66 PHE 0.028 0.002 PHE B 482 TRP 0.087 0.004 TRP a 44 HIS 0.006 0.001 HIS F 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 (39537) covalent geometry : angle 0.67110 / 0.33 (53623) hydrogen bonds : bond 0.04436 / 2.96 ( 2462) hydrogen bonds : angle 4.50702 / 3.15 ( 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 668 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 668 time to evaluate : 1.589 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: A 186 ASN cc_start: 0.7691 (t0) cc_final: 0.7345 (t0) REVERT: A 230 ASP cc_start: 0.7263 (p0) cc_final: 0.6816 (p0) REVERT: A 340 ASP cc_start: 0.8911 (m-30) cc_final: 0.8485 (t0) REVERT: B 149 THR cc_start: 0.8343 (t) cc_final: 0.7941 (m) REVERT: B 182 ASP cc_start: 0.5721 (m-30) cc_final: 0.5419 (m-30) REVERT: B 278 LEU cc_start: 0.8604 (pp) cc_final: 0.8340 (tp) REVERT: B 321 GLU cc_start: 0.6934 (tt0) cc_final: 0.6364 (tt0) REVERT: C 321 GLU cc_start: 0.8332 (tm-30) cc_final: 0.7933 (tm-30) REVERT: C 498 MET cc_start: 0.6996 (tpp) cc_final: 0.6146 (ttp) REVERT: D 79 MET cc_start: 0.8156 (mmp) cc_final: 0.7782 (mmp) REVERT: D 239 MET cc_start: 0.7500 (mtm) cc_final: 0.7106 (mtp) REVERT: D 311 GLU cc_start: 0.7472 (mt-10) cc_final: 0.6743 (mm-30) REVERT: E 64 GLU cc_start: 0.7690 (tt0) cc_final: 0.7422 (tt0) REVERT: E 334 LEU cc_start: 0.8119 (mt) cc_final: 0.7166 (tt) REVERT: E 335 THR cc_start: 0.7436 (p) cc_final: 0.7096 (p) REVERT: E 490 LEU cc_start: 0.8146 (pp) cc_final: 0.7394 (tt) REVERT: F 254 LEU cc_start: 0.9175 (tp) cc_final: 0.8947 (tp) REVERT: F 301 THR cc_start: 0.8967 (p) cc_final: 0.8652 (t) REVERT: F 374 MET cc_start: 0.8282 (mmp) cc_final: 0.7912 (mmp) REVERT: F 385 TYR cc_start: 0.7607 (t80) cc_final: 0.7140 (t80) REVERT: F 488 MET cc_start: 0.5020 (ttm) cc_final: 0.4796 (ttm) REVERT: g 220 LEU cc_start: 0.5900 (mt) cc_final: 0.5561 (mt) REVERT: e 63 MET cc_start: 0.4884 (mmm) cc_final: 0.4443 (mmm) REVERT: e 110 ARG cc_start: 0.6470 (mtt180) cc_final: 0.6095 (mtp180) REVERT: I 105 ARG cc_start: 0.6347 (mtm-85) cc_final: 0.5116 (tmm160) REVERT: I 179 MET cc_start: 0.2924 (tmm) cc_final: 0.2555 (tpt) REVERT: J 182 GLU cc_start: 0.4412 (mt-10) cc_final: 0.3476 (tp30) REVERT: a 186 LEU cc_start: 0.5253 (tp) cc_final: 0.4578 (tp) REVERT: N 4 LEU cc_start: 0.4914 (tp) cc_final: 0.4550 (mp) REVERT: O 60 MET cc_start: 0.3148 (mmm) cc_final: 0.2609 (mmm) REVERT: P 37 GLU cc_start: 0.7454 (pt0) cc_final: 0.7078 (pt0) REVERT: P 60 MET cc_start: 0.1413 (mmm) cc_final: 0.0285 (mtm) REVERT: S 60 MET cc_start: 0.3488 (tpp) cc_final: 0.2991 (tpp) REVERT: V 49 ILE cc_start: 0.5364 (mm) cc_final: 0.5137 (mm) REVERT: X 60 MET cc_start: 0.6240 (mtt) cc_final: 0.5615 (tpp) REVERT: Z 60 MET cc_start: -0.0508 (tpp) cc_final: -0.0851 (tmm) outliers start: 0 outliers final: 0 residues processed: 668 average time/residue: 0.2259 time to fit residues: 253.9079 Evaluate side-chains 530 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 530 time to evaluate : 1.480 ------------------------------------------------------------------------------- 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: 0.5980 chunk 138 optimal weight: 0.4980 chunk 262 optimal weight: 2.9990 chunk 328 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 276 optimal weight: 0.5980 chunk 290 optimal weight: 2.9990 chunk 155 optimal weight: 4.9990 chunk 95 optimal weight: 0.8980 chunk 51 optimal weight: 7.9990 chunk 485 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 434 GLN B 415 GLN ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 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 228 HIS ** I 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 109 ASN ** M 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.136508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.117892 restraints weight = 87940.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.116009 restraints weight = 155580.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.116128 restraints weight = 139953.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.115065 restraints weight = 104804.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.115330 restraints weight = 105784.759| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 39537 Z= 0.174 Angle : 0.687 10.973 53623 Z= 0.341 Chirality : 0.045 0.309 6417 Planarity : 0.005 0.050 6914 Dihedral : 6.305 179.186 5560 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.52 % Favored : 95.40 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % 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 are not related in a simple way. whole: -0.14 (0.12), residues: 5113 helix: 0.93 (0.09), residues: 2900 sheet: -1.46 (0.21), residues: 581 loop : -1.33 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 172 TYR 0.026 0.002 TYR A 464 PHE 0.042 0.002 PHE A 390 TRP 0.088 0.004 TRP a 44 HIS 0.004 0.001 HIS F 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 (39537) covalent geometry : angle 0.68657 / 0.34 (53623) hydrogen bonds : bond 0.04575 / 3.06 ( 2462) hydrogen bonds : angle 4.56874 / 3.20 ( 7257) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7029.90 seconds wall clock time: 122 minutes 25.29 seconds (7345.29 seconds total)