Starting phenix.real_space_refine on Tue Sep 15 11:40:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6voj_21266/09_2026/6voj_21266.cif Found real_map, /net/cci-nas-00/data/ceres_data/6voj_21266/09_2026/6voj_21266.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6voj_21266/09_2026/6voj_21266.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6voj_21266/09_2026/6voj_21266.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6voj_21266/09_2026/6voj_21266.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6voj_21266/09_2026/6voj_21266.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6voj_21266/09_2026/6voj_21266.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6voj_21266/09_2026/6voj_21266.cif" } resolution = 4.34 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 24849 2.51 5 N 6674 2.21 5 O 7487 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 90 residue(s): 0.04s 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: 39155 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 3827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3827 Classifications: {'peptide': 498} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 479} 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: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3849 Classifications: {'peptide': 501} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 482} Chain: "D" 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: "E" 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: "F" 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: "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: "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: "g" Number of atoms: 2502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2502 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 12, 'TRANS': 309} Chain: "I" Number of atoms: 1244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1244 Classifications: {'peptide': 154} Link IDs: {'TRANS': 153} Chain: "J" Number of atoms: 1049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1049 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "a" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1734 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 14, 'TRANS': 207} 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: 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} 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: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.74, per 1000 atoms: 0.20 Number of scatterers: 39155 At special positions: 0 Unit cell: (169.533, 174.798, 210.6, 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 7487 8.00 N 6674 7.00 C 24849 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: 3.59 Conformation dependent library (CDL) restraints added in 1.8 seconds 10266 Ramachandran restraints generated. 5133 Oldfield, 0 Emsley, 5133 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9420 Finding SS restraints... Secondary structure from input PDB file: 193 helices and 32 sheets defined 60.0% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 10 through 25 Processing helix chain 'A' and resid 101 through 105 removed outlier: 3.756A pdb=" N TYR A 104 " --> pdb=" O SER A 101 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LEU A 105 " --> pdb=" O GLU A 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 101 through 105' Processing helix chain 'A' and resid 151 through 158 Processing helix chain 'A' and resid 175 through 187 removed outlier: 3.960A pdb=" N ILE A 184 " --> pdb=" O ALA A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 216 Processing helix chain 'A' and resid 217 through 221 removed outlier: 3.616A pdb=" N TYR A 221 " --> pdb=" O ALA A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 253 removed outlier: 3.667A pdb=" N GLN A 236 " --> pdb=" O PRO A 232 " (cutoff:3.500A) Proline residue: A 240 - end of helix Processing helix chain 'A' and resid 263 through 278 removed outlier: 3.662A pdb=" N GLN A 267 " --> pdb=" O ASP A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 287 removed outlier: 3.739A pdb=" N ALA A 286 " --> pdb=" O GLY A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 300 removed outlier: 3.809A pdb=" N LEU A 298 " --> pdb=" O LEU A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 339 Processing helix chain 'A' and resid 346 through 351 Processing helix chain 'A' and resid 367 through 372 removed outlier: 4.025A pdb=" N ALA A 370 " --> pdb=" O VAL A 367 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA A 371 " --> pdb=" O GLY A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 393 removed outlier: 4.122A pdb=" N LYS A 378 " --> pdb=" O LYS A 374 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N VAL A 379 " --> pdb=" O ALA A 375 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU A 393 " --> pdb=" O GLN A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 401 removed outlier: 3.521A pdb=" N ALA A 400 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N SER A 401 " --> pdb=" O GLN A 398 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 397 through 401' Processing helix chain 'A' and resid 404 through 422 removed outlier: 3.668A pdb=" N LYS A 422 " --> pdb=" O ARG A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 443 removed outlier: 3.736A pdb=" N ASN A 443 " --> pdb=" O TYR A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 469 Processing helix chain 'A' and resid 470 through 480 Processing helix chain 'A' and resid 483 through 503 removed outlier: 3.783A pdb=" N LEU A 503 " --> pdb=" O GLU A 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 19 removed outlier: 4.131A pdb=" N GLY B 19 " --> pdb=" O GLU B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 157 Processing helix chain 'B' and resid 175 through 186 Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 232 through 253 Proline residue: B 240 - end of helix Processing helix chain 'B' and resid 264 through 278 removed outlier: 3.775A pdb=" N MET B 274 " --> pdb=" O ALA B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 287 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 300 Processing helix chain 'B' and resid 306 through 310 removed outlier: 3.710A pdb=" N GLY B 310 " --> pdb=" O SER B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 339 Processing helix chain 'B' and resid 346 through 351 Processing helix chain 'B' and resid 367 through 372 removed outlier: 3.816A pdb=" N ALA B 370 " --> pdb=" O VAL B 367 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN B 372 " --> pdb=" O SER B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 380 Processing helix chain 'B' and resid 382 through 397 removed outlier: 3.863A pdb=" N PHE B 396 " --> pdb=" O GLU B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 420 Processing helix chain 'B' and resid 430 through 443 Processing helix chain 'B' and resid 452 through 469 removed outlier: 4.154A pdb=" N LYS B 456 " --> pdb=" O ASP B 452 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU B 460 " --> pdb=" O LYS B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 479 removed outlier: 3.923A pdb=" N GLN B 473 " --> pdb=" O LYS B 469 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR B 479 " --> pdb=" O ILE B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 504 Processing helix chain 'C' and resid 5 through 16 removed outlier: 3.719A pdb=" N ILE C 9 " --> pdb=" O ARG C 5 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N SER C 10 " --> pdb=" O ALA C 6 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N LYS C 11 " --> pdb=" O ASP C 7 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N ARG C 14 " --> pdb=" O SER C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 105 removed outlier: 3.838A pdb=" N TYR C 104 " --> pdb=" O SER C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 138 No H-bonds generated for 'chain 'C' and resid 136 through 138' Processing helix chain 'C' and resid 151 through 158 Processing helix chain 'C' and resid 175 through 186 Processing helix chain 'C' and resid 202 through 216 Processing helix chain 'C' and resid 218 through 220 No H-bonds generated for 'chain 'C' and resid 218 through 220' Processing helix chain 'C' and resid 232 through 253 removed outlier: 3.519A pdb=" N GLN C 236 " --> pdb=" O PRO C 232 " (cutoff:3.500A) Proline residue: C 240 - end of helix removed outlier: 4.262A pdb=" N PHE C 250 " --> pdb=" O LEU C 246 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG C 253 " --> pdb=" O TYR C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 278 removed outlier: 3.540A pdb=" N GLN C 267 " --> pdb=" O ASP C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 287 removed outlier: 3.633A pdb=" N TYR C 287 " --> pdb=" O ARG C 284 " (cutoff:3.500A) 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: 4.155A pdb=" N LEU C 298 " --> pdb=" O LEU C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 326 Processing helix chain 'C' and resid 329 through 339 removed outlier: 3.575A pdb=" N SER C 337 " --> pdb=" O THR C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 351 Processing helix chain 'C' and resid 373 through 395 removed outlier: 5.711A pdb=" N LYS C 382 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LEU C 383 " --> pdb=" O VAL C 379 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ALA C 395 " --> pdb=" O ALA C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 413 Processing helix chain 'C' and resid 414 through 421 Processing helix chain 'C' and resid 430 through 444 removed outlier: 3.527A pdb=" N GLY C 441 " --> pdb=" O THR C 437 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY C 444 " --> pdb=" O THR C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 468 removed outlier: 3.583A pdb=" N TYR C 457 " --> pdb=" O GLN C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 480 removed outlier: 4.215A pdb=" N GLU C 474 " --> pdb=" O PRO C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 503 Processing helix chain 'D' and resid 138 through 142 removed outlier: 3.753A pdb=" N LEU D 142 " --> pdb=" O PHE D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 158 Processing helix chain 'D' and resid 177 through 190 Processing helix chain 'D' and resid 205 through 219 Processing helix chain 'D' and resid 242 through 263 removed outlier: 3.614A pdb=" N ARG D 246 " --> pdb=" O PRO D 242 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N GLY D 250 " --> pdb=" O ARG D 246 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N LEU D 251 " --> pdb=" O MET D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 289 removed outlier: 3.531A pdb=" N PHE D 278 " --> pdb=" O ASN D 274 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU D 288 " --> pdb=" O GLU D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 311 Processing helix chain 'D' and resid 330 through 333 Processing helix chain 'D' and resid 336 through 343 Processing helix chain 'D' and resid 344 through 346 No H-bonds generated for 'chain 'D' and resid 344 through 346' Processing helix chain 'D' and resid 353 through 360 Processing helix chain 'D' and resid 376 through 381 Processing helix chain 'D' and resid 381 through 406 removed outlier: 3.608A pdb=" N TYR D 385 " --> pdb=" O GLY D 381 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ASP D 403 " --> pdb=" O LYS D 399 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ILE D 404 " --> pdb=" O GLU D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 431 removed outlier: 4.413A pdb=" N ARG D 429 " --> pdb=" O ARG D 425 " (cutoff:3.500A) 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 removed outlier: 4.035A pdb=" N PHE D 474 " --> pdb=" O GLU D 471 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR D 475 " --> pdb=" O GLN D 472 " (cutoff:3.500A) Processing helix chain 'D' and resid 479 through 496 Processing helix chain 'E' and resid 138 through 142 Processing helix chain 'E' and resid 153 through 158 Processing helix chain 'E' and resid 177 through 190 Processing helix chain 'E' and resid 205 through 220 removed outlier: 3.618A pdb=" N GLY E 209 " --> pdb=" O ARG E 205 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR E 213 " --> pdb=" O GLY E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 231 removed outlier: 3.502A pdb=" N SER E 230 " --> pdb=" O ILE E 227 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LYS E 231 " --> pdb=" O ALA E 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 227 through 231' Processing helix chain 'E' and resid 242 through 265 removed outlier: 5.105A pdb=" N GLY E 250 " --> pdb=" O ARG E 246 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N LEU E 251 " --> pdb=" O MET E 247 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N PHE E 260 " --> pdb=" O MET E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 287 removed outlier: 3.584A pdb=" N GLY E 282 " --> pdb=" O PHE E 278 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA E 287 " --> pdb=" O SER E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 311 removed outlier: 3.786A pdb=" N LEU E 309 " --> pdb=" O GLU E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 314 No H-bonds generated for 'chain 'E' and resid 312 through 314' Processing helix chain 'E' and resid 330 through 333 Processing helix chain 'E' and resid 336 through 344 removed outlier: 4.447A pdb=" N ALA E 344 " --> pdb=" O ALA E 340 " (cutoff:3.500A) Processing helix chain 'E' and resid 353 through 359 removed outlier: 3.823A pdb=" N ALA E 357 " --> pdb=" O SER E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 376 through 408 removed outlier: 7.730A pdb=" N GLU E 382 " --> pdb=" O ARG E 378 " (cutoff:3.500A) removed outlier: 8.915A pdb=" N GLU E 383 " --> pdb=" O ILE E 379 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N HIS E 384 " --> pdb=" O VAL E 380 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR E 385 " --> pdb=" O GLY E 381 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ASP E 403 " --> pdb=" O LYS E 399 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N ILE E 404 " --> pdb=" O GLU E 400 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 431 removed outlier: 3.918A pdb=" N THR E 420 " --> pdb=" O GLU E 416 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ARG E 429 " --> pdb=" O ARG E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 437 through 441 Processing helix chain 'E' and resid 450 through 464 removed outlier: 4.138A pdb=" N ARG E 456 " --> pdb=" O ALA E 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 470 through 474 removed outlier: 3.747A pdb=" N ALA E 473 " --> pdb=" O PRO E 470 " (cutoff:3.500A) Processing helix chain 'E' and resid 479 through 491 Processing helix chain 'F' and resid 154 through 159 Processing helix chain 'F' and resid 177 through 193 removed outlier: 3.701A pdb=" N LEU F 181 " --> pdb=" O GLY F 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 219 Processing helix chain 'F' and resid 244 through 264 removed outlier: 4.846A pdb=" N GLY F 250 " --> pdb=" O ARG F 246 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LEU F 251 " --> pdb=" O MET F 247 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N PHE F 260 " --> pdb=" O MET F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 290 removed outlier: 3.753A pdb=" N PHE F 278 " --> pdb=" O ASN F 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 311 removed outlier: 3.731A pdb=" N GLU F 305 " --> pdb=" O THR F 301 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 329 through 333 removed outlier: 3.635A pdb=" N ASP F 332 " --> pdb=" O VAL F 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 336 through 344 removed outlier: 3.536A pdb=" N ALA F 344 " --> pdb=" O ALA F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 353 through 360 removed outlier: 3.805A pdb=" N GLY F 360 " --> pdb=" O LEU F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 376 through 381 Processing helix chain 'F' and resid 381 through 401 removed outlier: 3.522A pdb=" N GLU F 400 " --> pdb=" O GLN F 396 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 432 removed outlier: 4.358A pdb=" N SER F 432 " --> pdb=" O GLU F 428 " (cutoff:3.500A) Processing helix chain 'F' and resid 438 through 443 Processing helix chain 'F' and resid 450 through 463 Processing helix chain 'F' and resid 470 through 474 Processing helix chain 'F' and resid 479 through 495 Processing helix chain 'd' and resid 75 through 90 Processing helix chain 'd' and resid 91 through 106 removed outlier: 3.703A pdb=" N SER d 97 " --> pdb=" O GLU d 93 " (cutoff:3.500A) Processing helix chain 'd' and resid 108 through 117 removed outlier: 3.861A pdb=" N TYR d 112 " --> pdb=" O GLU d 108 " (cutoff:3.500A) Processing helix chain 'd' and resid 121 through 137 removed outlier: 3.762A pdb=" N LYS d 125 " --> pdb=" O SER d 121 " (cutoff:3.500A) Processing helix chain 'd' and resid 139 through 152 removed outlier: 4.540A pdb=" N PHE d 145 " --> pdb=" O HIS d 141 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE d 146 " --> pdb=" O THR d 142 " (cutoff:3.500A) 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 173 removed outlier: 3.903A pdb=" N GLU d 166 " --> pdb=" O LEU d 162 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ASP d 167 " --> pdb=" O ASN d 163 " (cutoff:3.500A) Processing helix chain 'd' and resid 187 through 203 removed outlier: 3.626A pdb=" N LEU d 191 " --> pdb=" O GLU d 187 " (cutoff:3.500A) Processing helix chain 'd' and resid 237 through 247 Processing helix chain 'e' and resid 88 through 103 Processing helix chain 'e' and resid 104 through 106 No H-bonds generated for 'chain 'e' and resid 104 through 106' Processing helix chain 'e' and resid 108 through 131 removed outlier: 4.030A pdb=" N ILE e 113 " --> pdb=" O LYS e 109 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU e 114 " --> pdb=" O ARG e 110 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA e 118 " --> pdb=" O GLU e 114 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ALA e 128 " --> pdb=" O THR e 124 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR e 131 " --> pdb=" O GLU e 127 " (cutoff:3.500A) Processing helix chain 'g' and resid 43 through 81 removed outlier: 3.596A pdb=" N GLU g 77 " --> pdb=" O ARG g 73 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL g 80 " --> pdb=" O GLN g 76 " (cutoff:3.500A) Processing helix chain 'g' and resid 82 through 96 removed outlier: 3.730A pdb=" N VAL g 92 " --> pdb=" O THR g 88 " (cutoff:3.500A) Processing helix chain 'g' and resid 97 through 100 Processing helix chain 'g' and resid 131 through 148 removed outlier: 4.791A pdb=" N ASN g 135 " --> pdb=" O GLY g 131 " (cutoff:3.500A) Processing helix chain 'g' and resid 161 through 170 Processing helix chain 'g' and resid 188 through 204 removed outlier: 3.925A pdb=" N SER g 204 " --> pdb=" O SER g 200 " (cutoff:3.500A) Processing helix chain 'g' and resid 246 through 251 removed outlier: 3.650A pdb=" N ALA g 249 " --> pdb=" O CYS g 246 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU g 251 " --> pdb=" O ASP g 248 " (cutoff:3.500A) Processing helix chain 'g' and resid 287 through 363 Proline residue: g 297 - end of helix removed outlier: 3.642A pdb=" N CYS g 363 " --> pdb=" O GLY g 359 " (cutoff:3.500A) Processing helix chain 'I' and resid 31 through 158 removed outlier: 4.070A pdb=" N VAL I 36 " --> pdb=" O ILE I 32 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N VAL I 37 " --> pdb=" O ASN I 33 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N PHE I 145 " --> pdb=" O ARG I 141 " (cutoff:3.500A) Processing helix chain 'I' and resid 164 through 180 Processing helix chain 'J' and resid 88 through 202 removed outlier: 4.925A pdb=" N THR J 110 " --> pdb=" O LYS J 106 " (cutoff:3.500A) Proline residue: J 111 - end of helix Processing helix chain 'J' and resid 203 through 219 removed outlier: 3.562A pdb=" N ILE J 214 " --> pdb=" O LEU J 210 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N VAL J 215 " --> pdb=" O SER J 211 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LYS J 216 " --> pdb=" O ASP J 212 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS J 217 " --> pdb=" O ASP J 213 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU J 219 " --> pdb=" O VAL J 215 " (cutoff:3.500A) Processing helix chain 'a' and resid 37 through 59 Processing helix chain 'a' and resid 69 through 87 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 115 removed outlier: 4.212A pdb=" N ILE a 105 " --> pdb=" O MET a 101 " (cutoff:3.500A) Processing helix chain 'a' and resid 133 through 155 removed outlier: 4.365A pdb=" N THR a 137 " --> pdb=" O ASP a 133 " (cutoff:3.500A) Processing helix chain 'a' and resid 168 through 170 No H-bonds generated for 'chain 'a' and resid 168 through 170' Processing helix chain 'a' and resid 171 through 207 Proline residue: a 183 - end of helix removed outlier: 4.034A pdb=" N LEU a 190 " --> pdb=" O LEU a 186 " (cutoff:3.500A) Processing helix chain 'a' and resid 213 through 244 removed outlier: 3.587A pdb=" N GLY a 225 " --> pdb=" O LEU a 221 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 20 Processing helix chain 'M' and resid 21 through 42 Processing helix chain 'M' and resid 45 through 76 removed outlier: 4.487A pdb=" N GLY M 51 " --> pdb=" O GLY M 47 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N THR M 52 " --> pdb=" O LYS M 48 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR M 64 " --> pdb=" O MET M 60 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLY M 67 " --> pdb=" O LEU M 63 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 21 removed outlier: 3.858A pdb=" N VAL N 17 " --> pdb=" O ALA N 13 " (cutoff:3.500A) Processing helix chain 'N' and resid 22 through 42 removed outlier: 3.873A pdb=" N GLY N 29 " --> pdb=" O GLY N 25 " (cutoff:3.500A) Processing helix chain 'N' and resid 45 through 76 removed outlier: 5.183A pdb=" N GLY N 51 " --> pdb=" O GLY N 47 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N THR N 52 " --> pdb=" O LYS N 48 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU N 63 " --> pdb=" O PHE N 59 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N THR N 64 " --> pdb=" O MET N 60 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLY N 67 " --> pdb=" O LEU N 63 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 20 removed outlier: 3.690A pdb=" N VAL O 17 " --> pdb=" O ALA O 13 " (cutoff:3.500A) Processing helix chain 'O' and resid 21 through 42 removed outlier: 3.599A pdb=" N GLY O 29 " --> pdb=" O GLY O 25 " (cutoff:3.500A) Processing helix chain 'O' and resid 45 through 76 removed outlier: 4.189A pdb=" N GLY O 51 " --> pdb=" O GLY O 47 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N THR O 52 " --> pdb=" O LYS O 48 " (cutoff:3.500A) removed outlier: 3.666A 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: 3.916A pdb=" N GLY O 67 " --> pdb=" O LEU O 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 4 through 21 removed outlier: 4.076A pdb=" N VAL P 17 " --> pdb=" O ALA P 13 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER P 21 " --> pdb=" O VAL P 17 " (cutoff:3.500A) Processing helix chain 'P' and resid 22 through 42 removed outlier: 3.658A pdb=" N VAL P 26 " --> pdb=" O ILE P 22 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY P 38 " --> pdb=" O GLN P 34 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE P 39 " --> pdb=" O ALA P 35 " (cutoff:3.500A) Processing helix chain 'P' and resid 45 through 76 removed outlier: 4.646A pdb=" N GLY P 51 " --> pdb=" O GLY P 47 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR P 52 " --> pdb=" O LYS P 48 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU P 63 " --> pdb=" O PHE P 59 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N THR P 64 " --> pdb=" O MET P 60 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLY P 67 " --> pdb=" O LEU P 63 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 20 removed outlier: 4.207A pdb=" N VAL Q 17 " --> pdb=" O ALA Q 13 " (cutoff:3.500A) Processing helix chain 'Q' and resid 21 through 42 removed outlier: 3.552A pdb=" N GLY Q 29 " --> pdb=" O GLY Q 25 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLY Q 38 " --> pdb=" O GLN Q 34 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ALA Q 40 " --> pdb=" O VAL Q 36 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG Q 41 " --> pdb=" O GLU Q 37 " (cutoff:3.500A) Processing helix chain 'Q' and resid 45 through 76 removed outlier: 4.082A pdb=" N THR Q 52 " --> pdb=" O LYS Q 48 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU Q 63 " --> pdb=" O PHE Q 59 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR Q 64 " --> pdb=" O MET Q 60 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLY Q 67 " --> pdb=" O LEU Q 63 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 19 removed outlier: 3.537A pdb=" N VAL R 17 " --> pdb=" O ALA R 13 " (cutoff:3.500A) Processing helix chain 'R' and resid 21 through 42 removed outlier: 3.768A pdb=" N VAL R 26 " --> pdb=" O ILE R 22 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY R 29 " --> pdb=" O GLY R 25 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY R 38 " --> pdb=" O GLN R 34 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA R 40 " --> pdb=" O VAL R 36 " (cutoff:3.500A) Processing helix chain 'R' and resid 45 through 76 removed outlier: 3.677A pdb=" N ARG R 50 " --> pdb=" O GLU R 46 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N THR R 52 " --> pdb=" O LYS R 48 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU R 63 " --> pdb=" O PHE R 59 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N THR R 64 " --> pdb=" O MET R 60 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLY R 67 " --> pdb=" O LEU R 63 " (cutoff:3.500A) Processing helix chain 'S' and resid 4 through 20 removed outlier: 3.543A pdb=" N VAL S 17 " --> pdb=" O ALA S 13 " (cutoff:3.500A) Processing helix chain 'S' and resid 22 through 42 removed outlier: 4.055A pdb=" N GLY S 38 " --> pdb=" O GLN S 34 " (cutoff:3.500A) Processing helix chain 'S' and resid 45 through 76 removed outlier: 3.937A pdb=" N GLY S 51 " --> pdb=" O GLY S 47 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR S 52 " --> pdb=" O LYS S 48 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU S 63 " --> pdb=" O PHE S 59 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N THR S 64 " --> pdb=" O MET S 60 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLY S 67 " --> pdb=" O LEU S 63 " (cutoff:3.500A) Processing helix chain 'T' and resid 4 through 20 Processing helix chain 'T' and resid 21 through 42 removed outlier: 3.629A pdb=" N VAL T 26 " --> pdb=" O ILE T 22 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLY T 29 " --> pdb=" O GLY T 25 " (cutoff:3.500A) Processing helix chain 'T' and resid 46 through 76 removed outlier: 4.118A pdb=" N GLY T 51 " --> pdb=" O GLY T 47 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N THR T 52 " --> pdb=" O LYS T 48 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU T 63 " --> pdb=" O PHE T 59 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR T 64 " --> pdb=" O MET T 60 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY T 67 " --> pdb=" O LEU T 63 " (cutoff:3.500A) Processing helix chain 'U' and resid 4 through 21 removed outlier: 3.662A pdb=" N VAL U 17 " --> pdb=" O ALA U 13 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N SER U 21 " --> pdb=" O VAL U 17 " (cutoff:3.500A) Processing helix chain 'U' and resid 21 through 42 removed outlier: 3.736A pdb=" N VAL U 26 " --> pdb=" O ILE U 22 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY U 29 " --> pdb=" O GLY U 25 " (cutoff:3.500A) Processing helix chain 'U' and resid 45 through 76 removed outlier: 4.258A pdb=" N GLY U 51 " --> pdb=" O GLY U 47 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N THR U 52 " --> pdb=" O LYS U 48 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU U 63 " --> pdb=" O PHE U 59 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N THR U 64 " --> pdb=" O MET U 60 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY U 67 " --> pdb=" O LEU U 63 " (cutoff:3.500A) Processing helix chain 'V' and resid 4 through 21 removed outlier: 4.009A pdb=" N VAL V 17 " --> pdb=" O ALA V 13 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER V 21 " --> pdb=" O VAL V 17 " (cutoff:3.500A) Processing helix chain 'V' and resid 21 through 42 removed outlier: 4.006A pdb=" N VAL V 26 " --> pdb=" O ILE V 22 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY V 38 " --> pdb=" O GLN V 34 " (cutoff:3.500A) Processing helix chain 'V' and resid 45 through 76 removed outlier: 4.250A pdb=" N GLY V 51 " --> pdb=" O GLY V 47 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N THR V 52 " --> pdb=" O LYS V 48 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU V 63 " --> pdb=" O PHE V 59 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR V 64 " --> pdb=" O MET V 60 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY V 67 " --> pdb=" O LEU V 63 " (cutoff:3.500A) Processing helix chain 'W' and resid 4 through 20 removed outlier: 3.905A pdb=" N VAL W 17 " --> pdb=" O ALA W 13 " (cutoff:3.500A) Processing helix chain 'W' and resid 21 through 37 removed outlier: 3.737A pdb=" N GLY W 29 " --> pdb=" O GLY W 25 " (cutoff:3.500A) Processing helix chain 'W' and resid 37 through 42 removed outlier: 3.589A pdb=" N ARG W 41 " --> pdb=" O GLU W 37 " (cutoff:3.500A) Processing helix chain 'W' and resid 45 through 76 removed outlier: 5.641A pdb=" N GLY W 51 " --> pdb=" O GLY W 47 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N THR W 52 " --> pdb=" O LYS W 48 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU W 63 " --> pdb=" O PHE W 59 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N THR W 64 " --> pdb=" O MET W 60 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLY W 67 " --> pdb=" O LEU W 63 " (cutoff:3.500A) Processing helix chain 'X' and resid 4 through 20 removed outlier: 3.622A pdb=" N VAL X 17 " --> pdb=" O ALA X 13 " (cutoff:3.500A) Processing helix chain 'X' and resid 21 through 40 removed outlier: 3.619A pdb=" N VAL X 26 " --> pdb=" O ILE X 22 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY X 38 " --> pdb=" O GLN X 34 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE X 39 " --> pdb=" O ALA X 35 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA X 40 " --> pdb=" O VAL X 36 " (cutoff:3.500A) Processing helix chain 'X' and resid 42 through 44 No H-bonds generated for 'chain 'X' and resid 42 through 44' Processing helix chain 'X' and resid 45 through 76 removed outlier: 4.507A pdb=" N GLY X 51 " --> pdb=" O GLY X 47 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR X 52 " --> pdb=" O LYS X 48 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEU X 63 " --> pdb=" O PHE X 59 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THR X 64 " --> pdb=" O MET X 60 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLY X 67 " --> pdb=" O LEU X 63 " (cutoff:3.500A) Processing helix chain 'Y' and resid 4 through 21 removed outlier: 4.122A pdb=" N VAL Y 17 " --> pdb=" O ALA Y 13 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER Y 21 " --> pdb=" O VAL Y 17 " (cutoff:3.500A) Processing helix chain 'Y' and resid 22 through 38 removed outlier: 4.227A pdb=" N GLY Y 29 " --> pdb=" O GLY Y 25 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY Y 38 " --> pdb=" O GLN Y 34 " (cutoff:3.500A) Processing helix chain 'Y' and resid 39 through 41 No H-bonds generated for 'chain 'Y' and resid 39 through 41' Processing helix chain 'Y' and resid 45 through 76 removed outlier: 4.081A pdb=" N GLY Y 51 " --> pdb=" O GLY Y 47 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N THR Y 52 " --> pdb=" O LYS Y 48 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU Y 63 " --> pdb=" O PHE Y 59 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR Y 64 " --> pdb=" O MET Y 60 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLY Y 67 " --> pdb=" O LEU Y 63 " (cutoff:3.500A) Processing helix chain 'Z' and resid 4 through 21 removed outlier: 3.651A pdb=" N VAL Z 17 " --> pdb=" O ALA Z 13 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N SER Z 21 " --> pdb=" O VAL Z 17 " (cutoff:3.500A) Processing helix chain 'Z' and resid 21 through 38 removed outlier: 3.889A pdb=" N VAL Z 26 " --> pdb=" O ILE Z 22 " (cutoff:3.500A) Processing helix chain 'Z' and resid 39 through 42 removed outlier: 3.653A pdb=" N GLN Z 42 " --> pdb=" O ILE Z 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 39 through 42' Processing helix chain 'Z' and resid 43 through 44 No H-bonds generated for 'chain 'Z' and resid 43 through 44' Processing helix chain 'Z' and resid 45 through 76 removed outlier: 3.674A pdb=" N THR Z 52 " --> pdb=" O LYS Z 48 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU Z 63 " --> pdb=" O PHE Z 59 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR Z 64 " --> pdb=" O MET Z 60 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLY Z 67 " --> pdb=" O LEU Z 63 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 34 removed outlier: 6.835A pdb=" N ARG A 41 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ASN A 71 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N LEU A 67 " --> pdb=" O ASN A 71 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N GLY A 73 " --> pdb=" O LEU A 65 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 20 through 27 current: chain 'A' and resid 89 through 91 Processing sheet with id=AA2, first strand: chain 'A' and resid 30 through 34 removed outlier: 6.835A pdb=" N ARG A 41 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ASN A 71 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N LEU A 67 " --> pdb=" O ASN A 71 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N GLY A 73 " --> pdb=" O LEU A 65 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 61 through 67 current: chain 'F' and resid 46 through 50 removed outlier: 5.720A pdb=" N VAL F 65 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL F 77 " --> pdb=" O VAL F 65 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN F 67 " --> pdb=" O ARG F 75 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL F 30 " --> pdb=" O ILE F 26 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ILE F 26 " --> pdb=" O VAL F 30 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ASP F 32 " --> pdb=" O ALA F 24 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 20 through 27 current: chain 'A' and resid 89 through 91 Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 100 removed outlier: 3.922A pdb=" N GLU A 126 " --> pdb=" O VAL A 100 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 319 through 321 removed outlier: 3.629A pdb=" N VAL A 320 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY A 170 " --> pdb=" O VAL A 320 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 223 through 228 removed outlier: 6.110A pdb=" N CYS A 194 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N VAL A 225 " --> pdb=" O CYS A 194 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N TYR A 196 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N GLU A 227 " --> pdb=" O TYR A 196 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ALA A 198 " --> pdb=" O GLU A 227 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR A 315 " --> pdb=" O THR A 257 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 53 through 55 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 21 through 27 current: chain 'B' and resid 39 through 44 removed outlier: 6.234A pdb=" N ILE B 39 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N VAL B 35 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ARG B 41 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY B 30 " --> pdb=" O VAL B 89 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 53 through 55 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 61 through 67 current: chain 'D' and resid 46 through 52 removed outlier: 3.551A pdb=" N VAL D 49 " --> pdb=" O VAL D 61 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL D 61 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N ARG D 75 " --> pdb=" O GLN D 66 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N LEU D 68 " --> pdb=" O ARG D 73 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ARG D 73 " --> pdb=" O LEU D 68 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL D 30 " --> pdb=" O ILE D 26 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ILE D 26 " --> pdb=" O VAL D 30 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ASP D 32 " --> pdb=" O ALA D 24 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 21 through 27 current: chain 'B' and resid 39 through 44 removed outlier: 6.234A pdb=" N ILE B 39 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N VAL B 35 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ARG B 41 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY B 30 " --> pdb=" O VAL B 89 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 97 through 99 Processing sheet with id=AA9, first strand: chain 'B' and resid 108 through 109 Processing sheet with id=AB1, first strand: chain 'B' and resid 319 through 321 removed outlier: 3.554A pdb=" N VAL B 320 " --> pdb=" O ILE B 168 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 193 through 198 Processing sheet with id=AB3, first strand: chain 'C' and resid 27 through 28 removed outlier: 3.617A pdb=" N VAL d 233 " --> pdb=" O ILE d 223 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ILE d 223 " --> pdb=" O VAL d 233 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N GLU d 176 " --> pdb=" O ARG d 208 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N LYS d 210 " --> pdb=" O GLU d 176 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ALA d 178 " --> pdb=" O LYS d 210 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N VAL d 212 " --> pdb=" O ALA d 178 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL d 180 " --> pdb=" O VAL d 212 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 39 through 42 removed outlier: 6.355A pdb=" N VAL C 75 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N ALA C 64 " --> pdb=" O VAL C 75 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 54 through 56 Processing sheet with id=AB6, first strand: chain 'C' and resid 97 through 99 Processing sheet with id=AB7, first strand: chain 'C' and resid 108 through 109 removed outlier: 8.470A pdb=" N ILE C 223 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N CYS C 194 " --> pdb=" O ILE C 223 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N VAL C 225 " --> pdb=" O CYS C 194 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N TYR C 196 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N GLU C 227 " --> pdb=" O TYR C 196 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N ALA C 198 " --> pdb=" O GLU C 227 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU C 258 " --> pdb=" O ILE C 193 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 140 through 141 removed outlier: 4.243A pdb=" N LYS C 304 " --> pdb=" O ARG C 141 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 319 through 321 removed outlier: 6.758A pdb=" N LEU C 167 " --> pdb=" O ILE C 343 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N LEU C 345 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ILE C 169 " --> pdb=" O LEU C 345 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 100 through 101 Processing sheet with id=AC2, first strand: chain 'D' and resid 110 through 111 removed outlier: 6.072A pdb=" N PHE D 111 " --> pdb=" O TYR D 236 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N SER D 197 " --> pdb=" O ALA D 233 " (cutoff:3.500A) removed outlier: 8.558A pdb=" N VAL D 235 " --> pdb=" O SER D 197 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N PHE D 199 " --> pdb=" O VAL D 235 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N GLY D 237 " --> pdb=" O PHE D 199 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLY D 201 " --> pdb=" O GLY D 237 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU D 269 " --> pdb=" O VAL D 196 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N VAL D 268 " --> pdb=" O THR D 322 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N ILE D 324 " --> pdb=" O VAL D 268 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N LEU D 270 " --> pdb=" O ILE D 324 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ALA D 326 " --> pdb=" O LEU D 270 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ILE D 272 " --> pdb=" O ALA D 326 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N TYR D 328 " --> pdb=" O ILE D 272 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ILE D 168 " --> pdb=" O GLN D 325 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL D 327 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N LEU D 170 " --> pdb=" O VAL D 327 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N THR D 350 " --> pdb=" O LYS D 167 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N GLY D 169 " --> pdb=" O THR D 350 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 20 through 27 removed outlier: 6.689A pdb=" N ASP E 32 " --> pdb=" O ALA E 24 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ILE E 26 " --> pdb=" O VAL E 30 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL E 30 " --> pdb=" O ILE E 26 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N ARG E 73 " --> pdb=" O LEU E 68 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N LEU E 68 " --> pdb=" O ARG E 73 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ARG E 75 " --> pdb=" O GLN E 66 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ASN E 45 " --> pdb=" O VAL E 65 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ALA E 46 " --> pdb=" O THR E 94 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 99 through 101 Processing sheet with id=AC5, first strand: chain 'E' and resid 110 through 111 removed outlier: 7.011A pdb=" N PHE E 111 " --> pdb=" O TYR E 236 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N VAL E 235 " --> pdb=" O SER E 197 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N PHE E 199 " --> pdb=" O VAL E 235 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N GLY E 237 " --> pdb=" O PHE E 199 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLY E 201 " --> pdb=" O GLY E 237 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE E 168 " --> pdb=" O GLN E 325 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N VAL E 327 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LEU E 170 " --> pdb=" O VAL E 327 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N LEU E 352 " --> pdb=" O GLY E 169 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N PHE E 171 " --> pdb=" O LEU E 352 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 148 through 149 removed outlier: 3.679A pdb=" N TYR E 162 " --> pdb=" O PHE E 149 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 99 through 101 Processing sheet with id=AC8, first strand: chain 'F' and resid 110 through 111 removed outlier: 6.125A pdb=" N PHE F 111 " --> pdb=" O TYR F 236 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N VAL F 196 " --> pdb=" O LEU F 269 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N PHE F 271 " --> pdb=" O VAL F 196 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL F 198 " --> pdb=" O PHE F 271 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ILE F 272 " --> pdb=" O ILE F 324 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LYS F 167 " --> pdb=" O ALA F 348 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N THR F 350 " --> pdb=" O LYS F 167 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N GLY F 169 " --> pdb=" O THR F 350 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 148 through 149 removed outlier: 4.484A pdb=" N TYR F 162 " --> pdb=" O PHE F 149 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'e' and resid 3 through 4 Processing sheet with id=AD2, first strand: chain 'e' and resid 13 through 15 Processing sheet with id=AD3, first strand: chain 'e' and resid 30 through 31 removed outlier: 3.516A pdb=" N LEU e 24 " --> pdb=" O ILE e 31 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'g' and resid 176 through 179 removed outlier: 8.380A pdb=" N ILE g 157 " --> pdb=" O ASP g 177 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N TYR g 179 " --> pdb=" O ILE g 157 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N SER g 159 " --> pdb=" O TYR g 179 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N ALA g 119 " --> pdb=" O GLU g 211 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N LEU g 213 " --> pdb=" O ALA g 119 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N MET g 121 " --> pdb=" O LEU g 213 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'a' and resid 28 through 30 2324 hydrogen bonds defined for protein. 6864 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: 8.08 Time building geometry restraints manager: 4.60 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: 13037 1.34 - 1.46: 6886 1.46 - 1.58: 19512 1.58 - 1.70: 26 1.70 - 1.82: 246 Bond restraints: 39707 Sorted by residual: bond pdb=" C4 ATP C 601 " pdb=" C5 ATP C 601 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.32e+01 bond pdb=" C4 ATP B 601 " pdb=" C5 ATP B 601 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.14e+01 bond pdb=" C4 ATP A 600 " pdb=" C5 ATP A 600 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.13e+01 bond pdb=" C4 ATP E 601 " pdb=" C5 ATP E 601 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.77e+01 bond pdb=" C5 ATP A 600 " pdb=" C6 ATP A 600 " ideal model delta sigma weight residual 1.409 1.479 -0.070 1.00e-02 1.00e+04 4.88e+01 ... (remaining 39702 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.87: 53467 3.87 - 7.74: 331 7.74 - 11.61: 48 11.61 - 15.49: 2 15.49 - 19.36: 7 Bond angle restraints: 53855 Sorted by residual: angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 120.51 19.36 1.00e+00 1.00e+00 3.75e+02 angle pdb=" PB ATP C 601 " pdb=" O3B ATP C 601 " pdb=" PG ATP C 601 " ideal model delta sigma weight residual 139.87 120.63 19.24 1.00e+00 1.00e+00 3.70e+02 angle pdb=" PA ATP C 601 " pdb=" O3A ATP C 601 " pdb=" PB ATP C 601 " ideal model delta sigma weight residual 136.83 118.02 18.81 1.00e+00 1.00e+00 3.54e+02 angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 121.16 18.71 1.00e+00 1.00e+00 3.50e+02 angle pdb=" PA ATP A 600 " pdb=" O3A ATP A 600 " pdb=" PB ATP A 600 " ideal model delta sigma weight residual 136.83 118.26 18.57 1.00e+00 1.00e+00 3.45e+02 ... (remaining 53850 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.09: 23061 30.09 - 60.19: 880 60.19 - 90.28: 108 90.28 - 120.37: 1 120.37 - 150.46: 2 Dihedral angle restraints: 24052 sinusoidal: 9345 harmonic: 14707 Sorted by residual: dihedral pdb=" CA ALA E 295 " pdb=" C ALA E 295 " pdb=" N VAL E 296 " pdb=" CA VAL E 296 " ideal model delta harmonic sigma weight residual -180.00 -128.09 -51.91 0 5.00e+00 4.00e-02 1.08e+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 -129.87 -50.13 0 5.00e+00 4.00e-02 1.01e+02 dihedral pdb=" CA PRO g 276 " pdb=" C PRO g 276 " pdb=" N ALA g 277 " pdb=" CA ALA g 277 " ideal model delta harmonic sigma weight residual 180.00 141.85 38.15 0 5.00e+00 4.00e-02 5.82e+01 ... (remaining 24049 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 5315 0.066 - 0.132: 1035 0.132 - 0.197: 82 0.197 - 0.263: 7 0.263 - 0.329: 1 Chirality restraints: 6440 Sorted by residual: chirality pdb=" C9 TTX C 602 " pdb=" C10 TTX C 602 " pdb=" C8 TTX C 602 " pdb=" N3 TTX C 602 " both_signs ideal model delta sigma weight residual False -2.28 -2.61 0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" CB ILE g 227 " pdb=" CA ILE g 227 " pdb=" CG1 ILE g 227 " pdb=" CG2 ILE g 227 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" C1' ATP E 601 " pdb=" C2' ATP E 601 " pdb=" N9 ATP E 601 " pdb=" O4' ATP E 601 " both_signs ideal model delta sigma weight residual False 2.41 2.65 -0.24 2.00e-01 2.50e+01 1.49e+00 ... (remaining 6437 not shown) Planarity restraints: 6944 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C11 TTX C 602 " -0.411 2.00e-02 2.50e+03 3.54e-01 1.88e+03 pdb=" C12 TTX C 602 " -0.051 2.00e-02 2.50e+03 pdb=" C13 TTX C 602 " 0.467 2.00e-02 2.50e+03 pdb=" C9 TTX C 602 " 0.434 2.00e-02 2.50e+03 pdb=" N3 TTX C 602 " -0.020 2.00e-02 2.50e+03 pdb=" O3 TTX C 602 " -0.419 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C15 TTX C 602 " -0.183 2.00e-02 2.50e+03 1.70e-01 4.32e+02 pdb=" C5 TTX C 602 " 0.220 2.00e-02 2.50e+03 pdb=" C6 TTX C 602 " -0.039 2.00e-02 2.50e+03 pdb=" C7 TTX C 602 " 0.227 2.00e-02 2.50e+03 pdb=" N1 TTX C 602 " -0.033 2.00e-02 2.50e+03 pdb=" O1 TTX C 602 " -0.193 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5 TTX C 602 " -0.170 2.00e-02 2.50e+03 1.40e-01 2.44e+02 pdb=" C8 TTX C 602 " 0.062 2.00e-02 2.50e+03 pdb=" C9 TTX C 602 " -0.129 2.00e-02 2.50e+03 pdb=" N2 TTX C 602 " 0.219 2.00e-02 2.50e+03 pdb=" O2 TTX C 602 " 0.018 2.00e-02 2.50e+03 ... (remaining 6941 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 5663 2.75 - 3.29: 40494 3.29 - 3.83: 68354 3.83 - 4.36: 78972 4.36 - 4.90: 133667 Nonbonded interactions: 327150 Sorted by model distance: nonbonded pdb=" O THR C 228 " pdb=" OG SER C 231 " model vdw 2.217 3.040 nonbonded pdb=" O ALA D 438 " pdb=" OG1 THR D 442 " model vdw 2.223 3.040 nonbonded pdb=" O GLY D 360 " pdb=" OH TYR D 475 " model vdw 2.233 3.040 nonbonded pdb=" O VAL d 198 " pdb=" OG1 THR d 202 " model vdw 2.234 3.040 nonbonded pdb=" O PRO F 337 " pdb=" OG1 THR F 341 " model vdw 2.265 3.040 ... (remaining 327145 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 7 through 503) selection = (chain 'B' and resid 7 through 503) selection = (chain 'C' and resid 7 through 503) } 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: 4.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.680 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 33.970 Find NCS groups from input model: 0.920 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:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6638 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 39707 Z= 0.270 Angle : 0.932 19.357 53855 Z= 0.554 Chirality : 0.050 0.329 6440 Planarity : 0.008 0.354 6944 Dihedral : 15.900 150.465 14632 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.88 % Favored : 94.04 % Rotamer: Outliers : 0.39 % Allowed : 10.66 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.12 % Twisted Proline : 0.49 % Twisted General : 0.08 % 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: -3.58 (0.10), residues: 5133 helix: -1.87 (0.08), residues: 2811 sheet: -2.71 (0.20), residues: 510 loop : -2.85 (0.12), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 312 TYR 0.028 0.002 TYR a 148 PHE 0.021 0.002 PHE S 59 TRP 0.023 0.002 TRP e 57 HIS 0.006 0.001 HIS d 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.27 (39707) covalent geometry : angle 0.93180 / 0.55 (53855) hydrogen bonds : bond 0.13341 / 8.88 ( 2308) hydrogen bonds : angle 6.72555 / 4.62 ( 6864) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10266 Ramachandran restraints generated. 5133 Oldfield, 0 Emsley, 5133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10266 Ramachandran restraints generated. 5133 Oldfield, 0 Emsley, 5133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 957 residues out of total 4091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 941 time to evaluate : 1.559 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: symmetry clash REVERT: A 68 GLU cc_start: 0.7278 (mm-30) cc_final: 0.6778 (mm-30) REVERT: A 82 MET cc_start: 0.7734 (mmt) cc_final: 0.7450 (mmm) REVERT: A 172 ARG cc_start: 0.7946 (tmm160) cc_final: 0.6826 (ptt90) REVERT: A 219 MET cc_start: 0.8458 (tpt) cc_final: 0.8257 (tpp) REVERT: A 251 MET cc_start: 0.7486 (ttp) cc_final: 0.7237 (ttm) REVERT: A 473 GLN cc_start: 0.8332 (tt0) cc_final: 0.7641 (tp40) REVERT: A 501 PHE cc_start: 0.5586 (t80) cc_final: 0.5354 (t80) REVERT: B 387 LEU cc_start: 0.8548 (mt) cc_final: 0.8190 (tt) REVERT: B 429 LEU cc_start: 0.7990 (mt) cc_final: 0.7679 (mt) REVERT: B 433 GLU cc_start: 0.7590 (mt-10) cc_final: 0.6885 (tt0) REVERT: B 466 LYS cc_start: 0.6625 (mttm) cc_final: 0.6172 (tppt) REVERT: C 58 GLU cc_start: 0.5731 (mp0) cc_final: 0.5467 (mp0) REVERT: C 81 LEU cc_start: 0.7278 (mt) cc_final: 0.7062 (mp) REVERT: C 90 LYS cc_start: 0.7491 (mttt) cc_final: 0.7072 (mttm) REVERT: C 154 ILE cc_start: 0.9064 (mm) cc_final: 0.8826 (mm) REVERT: C 272 ARG cc_start: 0.7417 (ttp-110) cc_final: 0.7068 (ttm170) REVERT: C 290 ASP cc_start: 0.7558 (m-30) cc_final: 0.6049 (m-30) REVERT: C 358 ILE cc_start: 0.8894 (mm) cc_final: 0.8692 (tt) REVERT: C 364 VAL cc_start: 0.7900 (t) cc_final: 0.7697 (t) REVERT: C 452 ASP cc_start: 0.7353 (m-30) cc_final: 0.7004 (m-30) REVERT: C 470 PRO cc_start: 0.7095 (Cg_endo) cc_final: 0.6762 (Cg_exo) REVERT: D 102 VAL cc_start: 0.7023 (m) cc_final: 0.6657 (m) REVERT: D 110 ILE cc_start: 0.8080 (mm) cc_final: 0.7823 (mt) REVERT: D 247 MET cc_start: 0.7874 (ttp) cc_final: 0.7321 (ttp) REVERT: D 335 THR cc_start: 0.7947 (m) cc_final: 0.7744 (m) REVERT: D 343 PHE cc_start: 0.7283 (m-80) cc_final: 0.6957 (m-80) REVERT: D 404 ILE cc_start: 0.6137 (mp) cc_final: 0.5754 (mp) REVERT: D 479 ASN cc_start: 0.6406 (t0) cc_final: 0.5749 (m110) REVERT: E 85 LEU cc_start: 0.9050 (mm) cc_final: 0.8628 (mm) REVERT: E 306 MET cc_start: 0.8116 (tpp) cc_final: 0.7802 (tpp) REVERT: E 428 GLU cc_start: 0.6678 (pp20) cc_final: 0.6363 (pp20) REVERT: F 57 GLN cc_start: 0.6388 (pm20) cc_final: 0.5454 (tm-30) REVERT: F 269 LEU cc_start: 0.8312 (tp) cc_final: 0.7982 (tp) REVERT: F 288 LEU cc_start: 0.7633 (mt) cc_final: 0.7338 (mt) REVERT: F 462 LEU cc_start: 0.6416 (mt) cc_final: 0.6090 (pp) REVERT: F 492 MET cc_start: 0.6631 (mmm) cc_final: 0.6377 (mmm) REVERT: d 234 ASP cc_start: 0.5961 (p0) cc_final: 0.5556 (p0) REVERT: d 243 GLU cc_start: 0.6440 (tp30) cc_final: 0.6222 (mm-30) REVERT: e 105 LYS cc_start: 0.7120 (mtmt) cc_final: 0.6786 (mtmm) REVERT: g 74 ARG cc_start: 0.6380 (mmt180) cc_final: 0.5990 (ttp80) REVERT: g 130 CYS cc_start: 0.7382 (m) cc_final: 0.7109 (t) REVERT: g 135 ASN cc_start: 0.6569 (m-40) cc_final: 0.5439 (t0) REVERT: g 138 LEU cc_start: 0.7828 (mt) cc_final: 0.7408 (mm) REVERT: g 227 ILE cc_start: 0.7263 (tp) cc_final: 0.7020 (mt) REVERT: g 236 LYS cc_start: 0.5686 (mmtm) cc_final: 0.5284 (ttmm) REVERT: g 343 ARG cc_start: 0.6682 (mtm110) cc_final: 0.5998 (mtm180) REVERT: g 353 ILE cc_start: 0.8820 (mt) cc_final: 0.8569 (tp) REVERT: I 134 GLN cc_start: 0.6486 (mm-40) cc_final: 0.5826 (tp40) REVERT: I 153 LEU cc_start: 0.7160 (tt) cc_final: 0.6835 (mt) REVERT: J 116 MET cc_start: 0.3641 (mmt) cc_final: 0.2789 (mmt) REVERT: J 181 ILE cc_start: 0.6516 (mm) cc_final: 0.6044 (mm) REVERT: J 185 LEU cc_start: 0.7392 (tp) cc_final: 0.7126 (tt) REVERT: J 198 ASP cc_start: 0.3759 (m-30) cc_final: 0.3442 (m-30) REVERT: a 178 GLU cc_start: 0.4337 (tt0) cc_final: 0.4089 (tm-30) REVERT: a 184 LEU cc_start: 0.8191 (tt) cc_final: 0.7477 (tp) REVERT: a 190 LEU cc_start: 0.5413 (mt) cc_final: 0.5202 (mt) REVERT: a 195 LEU cc_start: 0.5749 (tp) cc_final: 0.5546 (tt) REVERT: a 223 THR cc_start: 0.6687 (p) cc_final: 0.6318 (m) REVERT: M 28 GLN cc_start: 0.4277 (mt0) cc_final: 0.3870 (mt0) REVERT: M 60 MET cc_start: 0.3061 (mtm) cc_final: 0.2423 (mmt) REVERT: N 46 GLU cc_start: 0.4890 (tt0) cc_final: 0.4439 (pp20) REVERT: N 57 LEU cc_start: 0.7722 (mt) cc_final: 0.7395 (mt) REVERT: P 61 GLU cc_start: 0.5474 (tp30) cc_final: 0.5236 (mm-30) REVERT: Q 50 ARG cc_start: 0.3903 (mmm-85) cc_final: 0.3595 (ttt180) REVERT: R 75 LEU cc_start: 0.5993 (mt) cc_final: 0.5714 (tp) REVERT: S 60 MET cc_start: 0.4456 (mtm) cc_final: 0.3997 (tpp) REVERT: T 60 MET cc_start: 0.3942 (mtm) cc_final: 0.3265 (ttm) REVERT: W 37 GLU cc_start: 0.5878 (tt0) cc_final: 0.5149 (tp30) REVERT: W 48 LYS cc_start: 0.4076 (mttt) cc_final: 0.3829 (mptt) REVERT: Y 60 MET cc_start: 0.3974 (mmt) cc_final: 0.3508 (mmm) REVERT: Y 68 LEU cc_start: 0.3686 (tp) cc_final: 0.3370 (mm) outliers start: 16 outliers final: 6 residues processed: 952 average time/residue: 0.2581 time to fit residues: 399.3273 Evaluate side-chains 635 residues out of total 4091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 629 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 432 optimal weight: 6.9990 chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 3.9990 chunk 455 optimal weight: 10.0000 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.7980 chunk 494 optimal weight: 3.9990 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 5.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 ASN ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 HIS A 372 GLN B 186 ASN B 187 GLN ** B 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 HIS C 187 GLN C 256 HIS C 372 GLN C 389 GLN C 410 GLN D 25 GLN ** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 376 GLN D 389 GLN E 25 GLN E 472 GLN F 274 ASN F 310 GLN d 193 GLN e 37 HIS e 54 ASN g 76 GLN ** g 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 58 GLN I 120 GLN I 134 GLN ** I 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 126 GLN a 36 HIS ** a 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 42 GLN T 28 GLN W 28 GLN Y 28 GLN ** Y 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.115388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.098554 restraints weight = 133269.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.097255 restraints weight = 128255.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.097954 restraints weight = 106988.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.098343 restraints weight = 82171.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.098451 restraints weight = 66823.947| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6716 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 39707 Z= 0.211 Angle : 0.756 19.656 53855 Z= 0.380 Chirality : 0.046 0.283 6440 Planarity : 0.006 0.069 6944 Dihedral : 6.889 149.708 5581 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.90 % Favored : 94.02 % Rotamer: Outliers : 0.12 % Allowed : 6.50 % Favored : 93.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.12 % Twisted Proline : 0.49 % 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: -2.41 (0.11), residues: 5133 helix: -0.74 (0.09), residues: 2815 sheet: -2.50 (0.20), residues: 520 loop : -2.56 (0.13), residues: 1798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG d 208 TYR 0.023 0.002 TYR C 457 PHE 0.035 0.002 PHE g 284 TRP 0.016 0.002 TRP e 57 HIS 0.008 0.001 HIS a 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.21 (39707) covalent geometry : angle 0.75577 / 0.38 (53855) hydrogen bonds : bond 0.04860 / 3.31 ( 2308) hydrogen bonds : angle 5.36284 / 3.71 ( 6864) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10266 Ramachandran restraints generated. 5133 Oldfield, 0 Emsley, 5133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10266 Ramachandran restraints generated. 5133 Oldfield, 0 Emsley, 5133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 775 residues out of total 4091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 770 time to evaluate : 1.546 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 68 GLU cc_start: 0.7175 (mm-30) cc_final: 0.6801 (mm-30) REVERT: A 82 MET cc_start: 0.7890 (mmt) cc_final: 0.7517 (mmm) REVERT: A 138 MET cc_start: 0.5724 (mmp) cc_final: 0.5518 (mmp) REVERT: A 172 ARG cc_start: 0.7490 (tmm160) cc_final: 0.6410 (ptm-80) REVERT: A 219 MET cc_start: 0.8508 (tpt) cc_final: 0.8251 (tpp) REVERT: A 473 GLN cc_start: 0.8368 (tt0) cc_final: 0.7798 (tp40) REVERT: B 387 LEU cc_start: 0.8465 (mt) cc_final: 0.8127 (tt) REVERT: B 433 GLU cc_start: 0.7496 (mt-10) cc_final: 0.6619 (mt-10) REVERT: B 466 LYS cc_start: 0.6566 (mttm) cc_final: 0.6167 (tppt) REVERT: C 75 VAL cc_start: 0.9265 (t) cc_final: 0.9007 (t) REVERT: C 154 ILE cc_start: 0.9116 (mm) cc_final: 0.8909 (mm) REVERT: C 227 GLU cc_start: 0.6697 (mm-30) cc_final: 0.6422 (mm-30) REVERT: C 290 ASP cc_start: 0.7631 (m-30) cc_final: 0.7194 (m-30) REVERT: C 294 LEU cc_start: 0.8410 (tp) cc_final: 0.7220 (tp) REVERT: C 297 ARG cc_start: 0.7380 (ptt180) cc_final: 0.6593 (ptt-90) REVERT: C 358 ILE cc_start: 0.8948 (mm) cc_final: 0.8679 (tt) REVERT: C 390 PHE cc_start: 0.6974 (t80) cc_final: 0.6718 (t80) REVERT: C 470 PRO cc_start: 0.7011 (Cg_endo) cc_final: 0.6723 (Cg_exo) REVERT: D 110 ILE cc_start: 0.8183 (mm) cc_final: 0.7820 (mt) REVERT: D 479 ASN cc_start: 0.6272 (t0) cc_final: 0.5693 (m110) REVERT: E 85 LEU cc_start: 0.9007 (mm) cc_final: 0.8678 (mm) REVERT: E 435 PHE cc_start: 0.7411 (m-80) cc_final: 0.6992 (m-80) REVERT: F 269 LEU cc_start: 0.8353 (tp) cc_final: 0.8034 (tp) REVERT: F 462 LEU cc_start: 0.6535 (mt) cc_final: 0.6057 (pp) REVERT: d 167 ASP cc_start: 0.8368 (m-30) cc_final: 0.8042 (m-30) REVERT: d 234 ASP cc_start: 0.5738 (p0) cc_final: 0.5291 (p0) REVERT: e 105 LYS cc_start: 0.7247 (mtmt) cc_final: 0.6809 (mtmm) REVERT: g 45 ARG cc_start: 0.6658 (tpp80) cc_final: 0.6456 (tpt170) REVERT: g 74 ARG cc_start: 0.6362 (mmt180) cc_final: 0.5843 (ttp80) REVERT: g 130 CYS cc_start: 0.7361 (m) cc_final: 0.7129 (t) REVERT: g 135 ASN cc_start: 0.6519 (m-40) cc_final: 0.5428 (t0) REVERT: g 236 LYS cc_start: 0.5691 (mmtm) cc_final: 0.5276 (ttmm) REVERT: g 270 MET cc_start: 0.3862 (tpt) cc_final: 0.3302 (mmm) REVERT: g 288 PRO cc_start: 0.4274 (Cg_exo) cc_final: 0.3981 (Cg_endo) REVERT: g 320 MET cc_start: 0.7350 (tmm) cc_final: 0.7068 (tmm) REVERT: g 323 MET cc_start: 0.7380 (mmp) cc_final: 0.7046 (mmp) REVERT: I 58 GLN cc_start: 0.5804 (tp40) cc_final: 0.4412 (pt0) REVERT: I 153 LEU cc_start: 0.7058 (tt) cc_final: 0.6731 (mt) REVERT: I 175 MET cc_start: 0.5671 (mtp) cc_final: 0.5432 (mtm) REVERT: J 116 MET cc_start: 0.3797 (mmt) cc_final: 0.3439 (mmm) REVERT: a 175 ASN cc_start: 0.5505 (t0) cc_final: 0.4755 (p0) REVERT: a 193 ASN cc_start: 0.7266 (t0) cc_final: 0.6998 (t0) REVERT: N 46 GLU cc_start: 0.5168 (tt0) cc_final: 0.4561 (pp20) REVERT: N 57 LEU cc_start: 0.7586 (mt) cc_final: 0.7256 (mt) REVERT: P 34 GLN cc_start: 0.6037 (mt0) cc_final: 0.5773 (mt0) REVERT: P 50 ARG cc_start: 0.3009 (mtt-85) cc_final: 0.1281 (mtp-110) REVERT: P 60 MET cc_start: 0.3756 (mtt) cc_final: 0.3537 (mtt) REVERT: P 61 GLU cc_start: 0.5786 (tp30) cc_final: 0.5244 (mm-30) REVERT: R 75 LEU cc_start: 0.5860 (mt) cc_final: 0.5495 (tp) REVERT: S 60 MET cc_start: 0.4633 (mtm) cc_final: 0.4077 (tpp) REVERT: T 60 MET cc_start: 0.3903 (mtm) cc_final: 0.3635 (tpp) REVERT: V 24 PRO cc_start: 0.7048 (Cg_exo) cc_final: 0.6801 (Cg_endo) REVERT: W 37 GLU cc_start: 0.6023 (tt0) cc_final: 0.5194 (tp30) REVERT: W 60 MET cc_start: 0.4620 (mtp) cc_final: 0.3927 (mpp) REVERT: Y 68 LEU cc_start: 0.3817 (tp) cc_final: 0.3349 (mm) outliers start: 5 outliers final: 1 residues processed: 773 average time/residue: 0.2448 time to fit residues: 311.9138 Evaluate side-chains 582 residues out of total 4091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 581 time to evaluate : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 156 optimal weight: 8.9990 chunk 207 optimal weight: 0.9990 chunk 298 optimal weight: 1.9990 chunk 326 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 435 optimal weight: 0.3980 chunk 116 optimal weight: 0.7980 chunk 87 optimal weight: 0.6980 chunk 206 optimal weight: 0.7980 chunk 417 optimal weight: 0.9980 chunk 233 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 186 ASN ** B 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 ASN C 187 GLN ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 389 GLN C 495 GLN D 25 GLN D 66 GLN ** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 389 GLN ** I 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 36 HIS ** a 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 28 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.116998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.099843 restraints weight = 131397.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.098625 restraints weight = 124471.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.099324 restraints weight = 101496.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.099862 restraints weight = 72444.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.099905 restraints weight = 60337.937| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6671 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 39707 Z= 0.145 Angle : 0.684 19.305 53855 Z= 0.338 Chirality : 0.044 0.167 6440 Planarity : 0.005 0.067 6944 Dihedral : 6.431 143.183 5581 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.81 % Favored : 95.13 % Rotamer: Outliers : 0.02 % Allowed : 4.82 % Favored : 95.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.12 % Twisted Proline : 0.49 % 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: -1.66 (0.11), residues: 5133 helix: -0.09 (0.09), residues: 2819 sheet: -2.21 (0.21), residues: 515 loop : -2.30 (0.13), residues: 1799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 41 TYR 0.034 0.002 TYR W 66 PHE 0.029 0.002 PHE W 59 TRP 0.016 0.001 TRP e 57 HIS 0.005 0.001 HIS a 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (39707) covalent geometry : angle 0.68384 / 0.34 (53855) hydrogen bonds : bond 0.04261 / 2.91 ( 2308) hydrogen bonds : angle 4.90820 / 3.40 ( 6864) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10266 Ramachandran restraints generated. 5133 Oldfield, 0 Emsley, 5133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10266 Ramachandran restraints generated. 5133 Oldfield, 0 Emsley, 5133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 777 residues out of total 4091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 776 time to evaluate : 1.552 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 68 GLU cc_start: 0.7149 (mm-30) cc_final: 0.6770 (mm-30) REVERT: A 172 ARG cc_start: 0.7569 (tmm160) cc_final: 0.6549 (ptm-80) REVERT: A 251 MET cc_start: 0.7781 (ttp) cc_final: 0.7576 (ttp) REVERT: A 314 MET cc_start: 0.6518 (ttp) cc_final: 0.5808 (ttp) REVERT: A 344 PHE cc_start: 0.6811 (m-80) cc_final: 0.6203 (m-80) REVERT: A 473 GLN cc_start: 0.8236 (tt0) cc_final: 0.7645 (tp40) REVERT: B 387 LEU cc_start: 0.8361 (mt) cc_final: 0.8128 (tt) REVERT: B 429 LEU cc_start: 0.7721 (mt) cc_final: 0.7364 (mt) REVERT: C 57 GLU cc_start: 0.6390 (mm-30) cc_final: 0.6147 (mm-30) REVERT: C 81 LEU cc_start: 0.7068 (mt) cc_final: 0.6532 (mt) REVERT: C 109 ILE cc_start: 0.7951 (tt) cc_final: 0.7732 (tt) REVERT: C 154 ILE cc_start: 0.9137 (mm) cc_final: 0.8868 (mm) REVERT: C 227 GLU cc_start: 0.6729 (mm-30) cc_final: 0.6403 (mm-30) REVERT: C 285 GLU cc_start: 0.7036 (mp0) cc_final: 0.6439 (mp0) REVERT: C 294 LEU cc_start: 0.8441 (tp) cc_final: 0.7268 (tp) REVERT: C 297 ARG cc_start: 0.7175 (ptt180) cc_final: 0.6446 (ptt-90) REVERT: C 358 ILE cc_start: 0.8951 (mm) cc_final: 0.8578 (tt) REVERT: C 390 PHE cc_start: 0.7071 (t80) cc_final: 0.6800 (t80) REVERT: C 470 PRO cc_start: 0.7139 (Cg_endo) cc_final: 0.6838 (Cg_exo) REVERT: D 110 ILE cc_start: 0.8221 (mm) cc_final: 0.7975 (mt) REVERT: D 429 ARG cc_start: 0.6666 (mpt-90) cc_final: 0.6308 (mtt-85) REVERT: D 479 ASN cc_start: 0.6028 (t0) cc_final: 0.5796 (m110) REVERT: E 85 LEU cc_start: 0.8991 (mm) cc_final: 0.8681 (mm) REVERT: E 146 LEU cc_start: 0.8273 (mt) cc_final: 0.8064 (mt) REVERT: E 204 GLU cc_start: 0.3219 (mm-30) cc_final: 0.3017 (mm-30) REVERT: E 306 MET cc_start: 0.8297 (tpp) cc_final: 0.7995 (tpp) REVERT: E 435 PHE cc_start: 0.7310 (m-80) cc_final: 0.6994 (m-80) REVERT: F 57 GLN cc_start: 0.6651 (pm20) cc_final: 0.5986 (tm-30) REVERT: F 269 LEU cc_start: 0.8294 (tp) cc_final: 0.7939 (tp) REVERT: F 382 GLU cc_start: 0.7432 (mp0) cc_final: 0.6951 (mp0) REVERT: F 411 ASP cc_start: 0.7507 (t70) cc_final: 0.7031 (t0) REVERT: F 462 LEU cc_start: 0.6491 (mt) cc_final: 0.6004 (pp) REVERT: d 167 ASP cc_start: 0.8450 (m-30) cc_final: 0.8044 (m-30) REVERT: e 105 LYS cc_start: 0.7283 (mtmt) cc_final: 0.6773 (mtmm) REVERT: g 74 ARG cc_start: 0.6386 (mmt180) cc_final: 0.5867 (ttp80) REVERT: g 130 CYS cc_start: 0.7460 (m) cc_final: 0.7147 (t) REVERT: g 135 ASN cc_start: 0.6513 (m-40) cc_final: 0.5426 (t0) REVERT: g 268 ARG cc_start: 0.4338 (tpp80) cc_final: 0.3957 (tpp80) REVERT: g 270 MET cc_start: 0.3787 (tpt) cc_final: 0.3120 (mmm) REVERT: g 288 PRO cc_start: 0.4489 (Cg_exo) cc_final: 0.4178 (Cg_endo) REVERT: g 320 MET cc_start: 0.7190 (tmm) cc_final: 0.6959 (tmm) REVERT: I 58 GLN cc_start: 0.5922 (tp40) cc_final: 0.4605 (pt0) REVERT: I 134 GLN cc_start: 0.6257 (mm110) cc_final: 0.5578 (tp40) REVERT: I 153 LEU cc_start: 0.7105 (tt) cc_final: 0.6773 (mt) REVERT: I 175 MET cc_start: 0.5713 (mtp) cc_final: 0.5488 (mtm) REVERT: J 116 MET cc_start: 0.3578 (mmt) cc_final: 0.3233 (mmm) REVERT: J 169 GLU cc_start: 0.5002 (tt0) cc_final: 0.4729 (mm-30) REVERT: J 181 ILE cc_start: 0.6415 (mm) cc_final: 0.5842 (mm) REVERT: N 57 LEU cc_start: 0.7536 (mt) cc_final: 0.7196 (mt) REVERT: P 50 ARG cc_start: 0.2640 (mtt-85) cc_final: 0.1121 (mtp-110) REVERT: P 60 MET cc_start: 0.3659 (mtt) cc_final: 0.2094 (ttm) REVERT: P 61 GLU cc_start: 0.5882 (tp30) cc_final: 0.5623 (mm-30) REVERT: Q 60 MET cc_start: 0.1484 (mtp) cc_final: 0.0559 (tpp) REVERT: S 60 MET cc_start: 0.4391 (mtm) cc_final: 0.3944 (tpp) REVERT: V 24 PRO cc_start: 0.6430 (Cg_exo) cc_final: 0.5730 (Cg_endo) REVERT: W 37 GLU cc_start: 0.6042 (tt0) cc_final: 0.5250 (tp30) REVERT: Y 60 MET cc_start: 0.3962 (mmt) cc_final: 0.3600 (mmm) REVERT: Y 68 LEU cc_start: 0.3951 (tp) cc_final: 0.3512 (mm) REVERT: Z 59 PHE cc_start: 0.4074 (m-10) cc_final: 0.3808 (m-10) REVERT: Z 60 MET cc_start: 0.5528 (ttm) cc_final: 0.5262 (ttm) outliers start: 1 outliers final: 0 residues processed: 776 average time/residue: 0.2415 time to fit residues: 311.0081 Evaluate side-chains 571 residues out of total 4091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 571 time to evaluate : 1.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 308 optimal weight: 8.9990 chunk 441 optimal weight: 0.7980 chunk 362 optimal weight: 3.9990 chunk 414 optimal weight: 4.9990 chunk 388 optimal weight: 0.0980 chunk 24 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 105 optimal weight: 6.9990 chunk 354 optimal weight: 0.9980 chunk 389 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 472 GLN F 25 GLN F 66 GLN F 479 ASN g 76 GLN g 286 GLN ** I 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 36 HIS ** a 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 34 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.115535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.098751 restraints weight = 132749.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.097445 restraints weight = 132468.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.098269 restraints weight = 110207.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.098563 restraints weight = 81661.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.098687 restraints weight = 66330.421| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6702 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 39707 Z= 0.182 Angle : 0.709 18.421 53855 Z= 0.354 Chirality : 0.045 0.314 6440 Planarity : 0.005 0.070 6944 Dihedral : 6.384 141.172 5581 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.98 % Favored : 93.98 % Rotamer: Outliers : 0.07 % Allowed : 5.13 % Favored : 94.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.12 % Twisted Proline : 0.49 % 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: -1.46 (0.11), residues: 5133 helix: 0.10 (0.09), residues: 2828 sheet: -2.19 (0.21), residues: 513 loop : -2.25 (0.14), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 425 TYR 0.032 0.002 TYR O 66 PHE 0.039 0.002 PHE E 343 TRP 0.015 0.002 TRP e 57 HIS 0.004 0.001 HIS a 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.18 (39707) covalent geometry : angle 0.70866 / 0.35 (53855) hydrogen bonds : bond 0.04371 / 2.98 ( 2308) hydrogen bonds : angle 4.86467 / 3.37 ( 6864) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10266 Ramachandran restraints generated. 5133 Oldfield, 0 Emsley, 5133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10266 Ramachandran restraints generated. 5133 Oldfield, 0 Emsley, 5133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 734 residues out of total 4091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 731 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.7172 (mm-30) cc_final: 0.6898 (mm-30) REVERT: A 82 MET cc_start: 0.8012 (mmp) cc_final: 0.7631 (mmm) REVERT: A 172 ARG cc_start: 0.7606 (tmm160) cc_final: 0.7262 (ptt90) REVERT: A 219 MET cc_start: 0.8150 (tpp) cc_final: 0.7849 (tpp) REVERT: A 344 PHE cc_start: 0.7031 (m-80) cc_final: 0.6565 (m-80) REVERT: A 473 GLN cc_start: 0.8160 (tt0) cc_final: 0.7640 (tp40) REVERT: B 266 LYS cc_start: 0.7264 (mmmm) cc_final: 0.6834 (mmmt) REVERT: B 387 LEU cc_start: 0.8465 (mt) cc_final: 0.8046 (tt) REVERT: B 434 GLN cc_start: 0.8253 (mt0) cc_final: 0.8052 (tt0) REVERT: B 436 MET cc_start: 0.7966 (ptp) cc_final: 0.7655 (ptp) REVERT: C 81 LEU cc_start: 0.7058 (mt) cc_final: 0.6454 (mt) REVERT: C 154 ILE cc_start: 0.9126 (mm) cc_final: 0.8878 (mm) REVERT: C 237 TYR cc_start: 0.8240 (t80) cc_final: 0.8006 (t80) REVERT: C 290 ASP cc_start: 0.7690 (m-30) cc_final: 0.6887 (m-30) REVERT: C 294 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8298 (tt) REVERT: C 358 ILE cc_start: 0.9047 (mm) cc_final: 0.8663 (tt) REVERT: C 390 PHE cc_start: 0.7027 (t80) cc_final: 0.6753 (t80) REVERT: C 470 PRO cc_start: 0.7099 (Cg_endo) cc_final: 0.6819 (Cg_exo) REVERT: D 110 ILE cc_start: 0.8279 (mm) cc_final: 0.7947 (mt) REVERT: D 239 MET cc_start: 0.7742 (mtp) cc_final: 0.7305 (mtp) REVERT: D 429 ARG cc_start: 0.6716 (mpt-90) cc_final: 0.6346 (mtt-85) REVERT: E 59 MET cc_start: 0.7098 (tmm) cc_final: 0.6888 (tmm) REVERT: E 204 GLU cc_start: 0.3255 (mm-30) cc_final: 0.2785 (mm-30) REVERT: E 306 MET cc_start: 0.8305 (tpp) cc_final: 0.7952 (tpp) REVERT: E 385 TYR cc_start: 0.6802 (t80) cc_final: 0.6495 (t80) REVERT: E 428 GLU cc_start: 0.7278 (pp20) cc_final: 0.6447 (tp30) REVERT: E 435 PHE cc_start: 0.7389 (m-80) cc_final: 0.7037 (m-80) REVERT: F 57 GLN cc_start: 0.6789 (pm20) cc_final: 0.6224 (tm-30) REVERT: F 269 LEU cc_start: 0.8313 (tp) cc_final: 0.7927 (tp) REVERT: F 299 GLN cc_start: 0.7769 (pm20) cc_final: 0.7388 (pm20) REVERT: F 411 ASP cc_start: 0.7515 (t70) cc_final: 0.6932 (t0) REVERT: F 462 LEU cc_start: 0.6479 (mt) cc_final: 0.5968 (pp) REVERT: e 105 LYS cc_start: 0.7380 (mtmt) cc_final: 0.6853 (mtmm) REVERT: g 74 ARG cc_start: 0.6336 (mmt180) cc_final: 0.5783 (ttp80) REVERT: g 135 ASN cc_start: 0.6557 (m-40) cc_final: 0.5534 (t0) REVERT: g 236 LYS cc_start: 0.6271 (ptpp) cc_final: 0.5637 (mmtm) REVERT: g 270 MET cc_start: 0.3639 (tpt) cc_final: 0.2909 (mmm) REVERT: g 323 MET cc_start: 0.7369 (mmp) cc_final: 0.7020 (mmp) REVERT: I 58 GLN cc_start: 0.6000 (tp40) cc_final: 0.4787 (pt0) REVERT: I 134 GLN cc_start: 0.6328 (mm110) cc_final: 0.5931 (tp40) REVERT: I 153 LEU cc_start: 0.7219 (tt) cc_final: 0.6852 (mt) REVERT: I 175 MET cc_start: 0.5942 (mtp) cc_final: 0.5383 (mtm) REVERT: J 116 MET cc_start: 0.3828 (mmt) cc_final: 0.3244 (mmt) REVERT: J 169 GLU cc_start: 0.5128 (tt0) cc_final: 0.4759 (mm-30) REVERT: J 182 GLU cc_start: 0.8406 (mp0) cc_final: 0.8065 (mp0) REVERT: N 57 LEU cc_start: 0.7555 (mt) cc_final: 0.7159 (mt) REVERT: P 50 ARG cc_start: 0.2635 (mtt-85) cc_final: 0.1189 (mtp-110) REVERT: P 60 MET cc_start: 0.3856 (mtt) cc_final: 0.1290 (tpp) REVERT: T 60 MET cc_start: 0.2913 (tpp) cc_final: 0.2487 (tpp) REVERT: W 37 GLU cc_start: 0.6095 (tt0) cc_final: 0.5244 (tp30) REVERT: X 64 THR cc_start: 0.4435 (m) cc_final: 0.4156 (p) REVERT: Y 68 LEU cc_start: 0.3942 (tp) cc_final: 0.3488 (mm) REVERT: Z 59 PHE cc_start: 0.3878 (m-10) cc_final: 0.3597 (m-10) REVERT: Z 60 MET cc_start: 0.5615 (ttm) cc_final: 0.5297 (ttm) outliers start: 3 outliers final: 0 residues processed: 731 average time/residue: 0.2387 time to fit residues: 290.0158 Evaluate side-chains 557 residues out of total 4091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 556 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 440 optimal weight: 2.9990 chunk 231 optimal weight: 0.5980 chunk 367 optimal weight: 0.9980 chunk 482 optimal weight: 3.9990 chunk 311 optimal weight: 3.9990 chunk 414 optimal weight: 8.9990 chunk 106 optimal weight: 0.9990 chunk 293 optimal weight: 0.0570 chunk 347 optimal weight: 0.9990 chunk 365 optimal weight: 0.9990 chunk 403 optimal weight: 0.9990 overall best weight: 0.7302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 HIS D 226 ASN ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 187 ASN ** F 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 238 GLN ** g 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 135 ASN ** a 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.116970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.099986 restraints weight = 131840.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.099055 restraints weight = 124635.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.100028 restraints weight = 96445.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.100086 restraints weight = 72531.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.100205 restraints weight = 63221.839| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6666 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 39707 Z= 0.145 Angle : 0.678 18.872 53855 Z= 0.334 Chirality : 0.044 0.256 6440 Planarity : 0.005 0.088 6944 Dihedral : 6.138 135.294 5581 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.77 % Favored : 95.19 % Rotamer: Outliers : 0.02 % Allowed : 3.23 % Favored : 96.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.12 % Twisted Proline : 0.49 % 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: -1.19 (0.11), residues: 5133 helix: 0.31 (0.09), residues: 2829 sheet: -2.15 (0.20), residues: 520 loop : -2.08 (0.14), residues: 1784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 284 TYR 0.030 0.002 TYR O 66 PHE 0.031 0.002 PHE a 222 TRP 0.017 0.002 TRP e 57 HIS 0.006 0.001 HIS a 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (39707) covalent geometry : angle 0.67772 / 0.33 (53855) hydrogen bonds : bond 0.04092 / 2.78 ( 2308) hydrogen bonds : angle 4.72153 / 3.27 ( 6864) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10266 Ramachandran restraints generated. 5133 Oldfield, 0 Emsley, 5133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10266 Ramachandran restraints generated. 5133 Oldfield, 0 Emsley, 5133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 739 residues out of total 4091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 738 time to evaluate : 1.534 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 68 GLU cc_start: 0.7114 (mm-30) cc_final: 0.6890 (mm-30) REVERT: A 82 MET cc_start: 0.7971 (mmp) cc_final: 0.7650 (mmm) REVERT: A 219 MET cc_start: 0.8114 (tpp) cc_final: 0.7813 (tpp) REVERT: A 344 PHE cc_start: 0.6910 (m-80) cc_final: 0.6351 (m-80) REVERT: B 266 LYS cc_start: 0.7336 (mmmm) cc_final: 0.6878 (mmmt) REVERT: B 387 LEU cc_start: 0.8341 (mt) cc_final: 0.8122 (tt) REVERT: B 436 MET cc_start: 0.7888 (ptp) cc_final: 0.6952 (ptp) REVERT: B 457 TYR cc_start: 0.7066 (t80) cc_final: 0.6706 (t80) REVERT: C 57 GLU cc_start: 0.6448 (mm-30) cc_final: 0.6160 (mm-30) REVERT: C 81 LEU cc_start: 0.7086 (mt) cc_final: 0.6345 (mt) REVERT: C 154 ILE cc_start: 0.9061 (mm) cc_final: 0.8800 (mm) REVERT: C 208 GLN cc_start: 0.7831 (mt0) cc_final: 0.7614 (mt0) REVERT: C 285 GLU cc_start: 0.7207 (mp0) cc_final: 0.6563 (mp0) REVERT: C 358 ILE cc_start: 0.9005 (mm) cc_final: 0.8649 (tt) REVERT: C 470 PRO cc_start: 0.7143 (Cg_endo) cc_final: 0.6809 (Cg_exo) REVERT: D 110 ILE cc_start: 0.8244 (mm) cc_final: 0.7876 (mt) REVERT: D 239 MET cc_start: 0.7735 (mtt) cc_final: 0.7335 (mtp) REVERT: D 429 ARG cc_start: 0.6594 (mpt-90) cc_final: 0.6319 (mtt-85) REVERT: E 204 GLU cc_start: 0.3249 (mm-30) cc_final: 0.2716 (mm-30) REVERT: E 306 MET cc_start: 0.8262 (tpp) cc_final: 0.7997 (tpt) REVERT: F 57 GLN cc_start: 0.6740 (pm20) cc_final: 0.6272 (tm-30) REVERT: F 269 LEU cc_start: 0.8369 (tp) cc_final: 0.7970 (tp) REVERT: F 299 GLN cc_start: 0.7714 (pm20) cc_final: 0.7390 (pm20) REVERT: F 411 ASP cc_start: 0.7380 (t70) cc_final: 0.6911 (t0) REVERT: F 462 LEU cc_start: 0.6368 (mt) cc_final: 0.5929 (pp) REVERT: e 105 LYS cc_start: 0.7255 (mtmt) cc_final: 0.6752 (mtmm) REVERT: g 74 ARG cc_start: 0.6314 (mmt180) cc_final: 0.5898 (ttp80) REVERT: g 135 ASN cc_start: 0.6492 (m-40) cc_final: 0.5506 (t0) REVERT: g 320 MET cc_start: 0.7277 (tmm) cc_final: 0.6991 (tmm) REVERT: g 323 MET cc_start: 0.7357 (mmp) cc_final: 0.6973 (mmp) REVERT: I 58 GLN cc_start: 0.6208 (tp40) cc_final: 0.5080 (pt0) REVERT: I 96 ARG cc_start: 0.2905 (tpt-90) cc_final: 0.1752 (mtm-85) REVERT: I 134 GLN cc_start: 0.6326 (mm110) cc_final: 0.5952 (tp40) REVERT: J 116 MET cc_start: 0.3732 (mmt) cc_final: 0.3225 (mmt) REVERT: J 148 MET cc_start: -0.0738 (mmp) cc_final: -0.0955 (mmm) REVERT: J 169 GLU cc_start: 0.4932 (tt0) cc_final: 0.4554 (mm-30) REVERT: N 57 LEU cc_start: 0.7494 (mt) cc_final: 0.7141 (mt) REVERT: P 37 GLU cc_start: 0.4977 (mt-10) cc_final: 0.4629 (tp30) REVERT: P 50 ARG cc_start: 0.2821 (mtt-85) cc_final: 0.1509 (mtp-110) REVERT: P 60 MET cc_start: 0.4017 (mtt) cc_final: 0.2346 (ttp) REVERT: W 37 GLU cc_start: 0.6011 (tt0) cc_final: 0.5242 (tp30) REVERT: X 64 THR cc_start: 0.4323 (m) cc_final: 0.4071 (p) REVERT: Y 68 LEU cc_start: 0.3983 (tp) cc_final: 0.3531 (mm) REVERT: Z 59 PHE cc_start: 0.4175 (m-10) cc_final: 0.3912 (m-10) REVERT: Z 60 MET cc_start: 0.5566 (ttm) cc_final: 0.5295 (ttm) outliers start: 1 outliers final: 0 residues processed: 738 average time/residue: 0.2324 time to fit residues: 286.2049 Evaluate side-chains 557 residues out of total 4091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 557 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 426 optimal weight: 0.0050 chunk 225 optimal weight: 0.2980 chunk 40 optimal weight: 0.7980 chunk 406 optimal weight: 5.9990 chunk 247 optimal weight: 2.9990 chunk 344 optimal weight: 0.0980 chunk 213 optimal weight: 0.5980 chunk 93 optimal weight: 0.8980 chunk 266 optimal weight: 0.3980 chunk 260 optimal weight: 0.6980 chunk 465 optimal weight: 6.9990 overall best weight: 0.2794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 186 ASN A 273 GLN A 423 GLN ** B 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 HIS ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 GLN F 66 GLN ** g 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.118294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.101422 restraints weight = 131600.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.100251 restraints weight = 121769.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.100896 restraints weight = 95505.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.101341 restraints weight = 71014.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.101576 restraints weight = 63381.087| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6621 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 39707 Z= 0.131 Angle : 0.668 19.155 53855 Z= 0.328 Chirality : 0.043 0.182 6440 Planarity : 0.004 0.079 6944 Dihedral : 5.878 129.776 5581 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.66 % Favored : 95.30 % Rotamer: Outliers : 0.02 % Allowed : 2.84 % Favored : 97.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.12 % Twisted Proline : 0.98 % 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: -0.91 (0.11), residues: 5133 helix: 0.53 (0.10), residues: 2824 sheet: -1.94 (0.21), residues: 509 loop : -1.98 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 284 TYR 0.029 0.002 TYR O 66 PHE 0.038 0.002 PHE E 343 TRP 0.018 0.001 TRP e 57 HIS 0.004 0.001 HIS E 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (39707) covalent geometry : angle 0.66773 / 0.33 (53855) hydrogen bonds : bond 0.03892 / 2.64 ( 2308) hydrogen bonds : angle 4.58953 / 3.18 ( 6864) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10266 Ramachandran restraints generated. 5133 Oldfield, 0 Emsley, 5133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10266 Ramachandran restraints generated. 5133 Oldfield, 0 Emsley, 5133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 757 residues out of total 4091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 756 time to evaluate : 1.474 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: A 68 GLU cc_start: 0.7176 (mm-30) cc_final: 0.6945 (mm-30) REVERT: A 82 MET cc_start: 0.7849 (mmp) cc_final: 0.7610 (mmm) REVERT: A 166 GLU cc_start: 0.7909 (tp30) cc_final: 0.7692 (tp30) REVERT: A 219 MET cc_start: 0.8131 (tpp) cc_final: 0.7828 (tpp) REVERT: A 344 PHE cc_start: 0.7104 (m-80) cc_final: 0.6778 (m-80) REVERT: B 194 CYS cc_start: 0.7918 (m) cc_final: 0.7515 (m) REVERT: B 199 ILE cc_start: 0.9074 (mt) cc_final: 0.8825 (mt) REVERT: B 251 MET cc_start: 0.6782 (ppp) cc_final: 0.6473 (ppp) REVERT: B 266 LYS cc_start: 0.7373 (mmmm) cc_final: 0.6867 (mmmt) REVERT: B 309 LEU cc_start: 0.8650 (mm) cc_final: 0.8191 (mt) REVERT: B 382 LYS cc_start: 0.6647 (mmtp) cc_final: 0.6399 (mmtp) REVERT: B 436 MET cc_start: 0.7844 (ptp) cc_final: 0.7469 (ptp) REVERT: B 457 TYR cc_start: 0.7015 (t80) cc_final: 0.6690 (t80) REVERT: C 57 GLU cc_start: 0.6518 (mm-30) cc_final: 0.6145 (mm-30) REVERT: C 81 LEU cc_start: 0.6975 (mt) cc_final: 0.6364 (mt) REVERT: C 154 ILE cc_start: 0.9004 (mm) cc_final: 0.8736 (mm) REVERT: C 285 GLU cc_start: 0.7172 (mp0) cc_final: 0.6789 (mm-30) REVERT: C 294 LEU cc_start: 0.8776 (tp) cc_final: 0.8575 (tp) REVERT: C 358 ILE cc_start: 0.8964 (mm) cc_final: 0.8633 (tt) REVERT: C 470 PRO cc_start: 0.7116 (Cg_endo) cc_final: 0.6785 (Cg_exo) REVERT: D 110 ILE cc_start: 0.8307 (mm) cc_final: 0.8001 (mt) REVERT: D 239 MET cc_start: 0.7713 (mtt) cc_final: 0.7415 (mtp) REVERT: D 332 ASP cc_start: 0.7875 (m-30) cc_final: 0.7384 (m-30) REVERT: E 306 MET cc_start: 0.8288 (tpp) cc_final: 0.7894 (tpp) REVERT: F 57 GLN cc_start: 0.6561 (pm20) cc_final: 0.5985 (tm-30) REVERT: F 299 GLN cc_start: 0.7848 (pm20) cc_final: 0.7557 (pm20) REVERT: F 411 ASP cc_start: 0.7354 (t70) cc_final: 0.6904 (t0) REVERT: F 462 LEU cc_start: 0.6379 (mt) cc_final: 0.5942 (pp) REVERT: e 45 ASP cc_start: 0.7244 (p0) cc_final: 0.6879 (p0) REVERT: e 105 LYS cc_start: 0.7137 (mtmt) cc_final: 0.6633 (mtmm) REVERT: g 74 ARG cc_start: 0.6366 (mmt180) cc_final: 0.5945 (ttp80) REVERT: g 121 MET cc_start: 0.6941 (ptp) cc_final: 0.6411 (ptm) REVERT: g 135 ASN cc_start: 0.6335 (m-40) cc_final: 0.5360 (t0) REVERT: g 220 LEU cc_start: 0.7477 (mt) cc_final: 0.6199 (pt) REVERT: I 54 ASP cc_start: 0.3783 (t70) cc_final: 0.3131 (t70) REVERT: I 58 GLN cc_start: 0.6242 (tp40) cc_final: 0.5091 (pt0) REVERT: I 96 ARG cc_start: 0.2896 (tpt-90) cc_final: 0.1694 (mtm-85) REVERT: I 134 GLN cc_start: 0.6179 (mm110) cc_final: 0.5936 (tp40) REVERT: I 153 LEU cc_start: 0.7027 (tt) cc_final: 0.6703 (mt) REVERT: J 169 GLU cc_start: 0.4893 (tt0) cc_final: 0.4558 (mm-30) REVERT: N 57 LEU cc_start: 0.7365 (mt) cc_final: 0.7095 (mt) REVERT: T 60 MET cc_start: 0.2735 (mmt) cc_final: 0.2065 (mmm) REVERT: W 37 GLU cc_start: 0.6111 (tt0) cc_final: 0.5289 (tp30) REVERT: Y 68 LEU cc_start: 0.4075 (tp) cc_final: 0.3687 (mm) outliers start: 1 outliers final: 1 residues processed: 757 average time/residue: 0.2332 time to fit residues: 296.0822 Evaluate side-chains 579 residues out of total 4091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 578 time to evaluate : 1.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 321 optimal weight: 2.9990 chunk 122 optimal weight: 0.0060 chunk 378 optimal weight: 6.9990 chunk 166 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 426 optimal weight: 2.9990 chunk 371 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 403 optimal weight: 3.9990 chunk 332 optimal weight: 1.9990 overall best weight: 1.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 186 ASN ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 423 GLN ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 389 GLN ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 HIS E 310 GLN E 325 GLN F 25 GLN ** g 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 42 GLN P 28 GLN U 28 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.115863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.098696 restraints weight = 132644.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.097739 restraints weight = 114613.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.097938 restraints weight = 97720.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.098233 restraints weight = 83109.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.098346 restraints weight = 71813.495| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6749 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 39707 Z= 0.200 Angle : 0.742 17.985 53855 Z= 0.368 Chirality : 0.046 0.213 6440 Planarity : 0.005 0.081 6944 Dihedral : 6.088 129.137 5581 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.00 % Favored : 93.96 % Rotamer: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.12 % Twisted Proline : 0.49 % 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: -1.06 (0.11), residues: 5133 helix: 0.40 (0.10), residues: 2818 sheet: -1.97 (0.21), residues: 499 loop : -2.02 (0.14), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 172 TYR 0.033 0.002 TYR a 164 PHE 0.035 0.002 PHE D 111 TRP 0.015 0.002 TRP e 57 HIS 0.005 0.001 HIS a 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.20 (39707) covalent geometry : angle 0.74193 / 0.37 (53855) hydrogen bonds : bond 0.04298 / 2.92 ( 2308) hydrogen bonds : angle 4.78779 / 3.31 ( 6864) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10266 Ramachandran restraints generated. 5133 Oldfield, 0 Emsley, 5133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10266 Ramachandran restraints generated. 5133 Oldfield, 0 Emsley, 5133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 4091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 696 time to evaluate : 1.441 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: A 68 GLU cc_start: 0.7425 (mm-30) cc_final: 0.7126 (mm-30) REVERT: A 251 MET cc_start: 0.7492 (ttp) cc_final: 0.6982 (ttp) REVERT: A 344 PHE cc_start: 0.7231 (m-80) cc_final: 0.6770 (m-80) REVERT: B 251 MET cc_start: 0.6767 (ppp) cc_final: 0.6564 (ppp) REVERT: B 382 LYS cc_start: 0.6763 (mmtp) cc_final: 0.6554 (mmtp) REVERT: B 436 MET cc_start: 0.8019 (ptp) cc_final: 0.7485 (ptp) REVERT: B 457 TYR cc_start: 0.7062 (t80) cc_final: 0.6801 (t80) REVERT: C 81 LEU cc_start: 0.7049 (mt) cc_final: 0.6532 (mt) REVERT: C 154 ILE cc_start: 0.9085 (mm) cc_final: 0.8831 (mm) REVERT: C 358 ILE cc_start: 0.9033 (mm) cc_final: 0.8650 (tt) REVERT: C 470 PRO cc_start: 0.7235 (Cg_endo) cc_final: 0.6923 (Cg_exo) REVERT: D 110 ILE cc_start: 0.8229 (mm) cc_final: 0.7867 (mt) REVERT: D 239 MET cc_start: 0.7757 (mtt) cc_final: 0.7472 (mtp) REVERT: E 306 MET cc_start: 0.8510 (tpp) cc_final: 0.7715 (tpp) REVERT: F 57 GLN cc_start: 0.6837 (pm20) cc_final: 0.6337 (tm-30) REVERT: F 246 ARG cc_start: 0.7513 (mpp80) cc_final: 0.7044 (mpp80) REVERT: F 299 GLN cc_start: 0.7823 (pm20) cc_final: 0.7435 (pm20) REVERT: F 411 ASP cc_start: 0.7407 (t70) cc_final: 0.6873 (t0) REVERT: F 462 LEU cc_start: 0.6458 (mt) cc_final: 0.5885 (pp) REVERT: d 234 ASP cc_start: 0.5828 (p0) cc_final: 0.5307 (p0) REVERT: e 45 ASP cc_start: 0.7154 (p0) cc_final: 0.6797 (p0) REVERT: e 105 LYS cc_start: 0.7265 (mtmt) cc_final: 0.6718 (mtmm) REVERT: e 125 ARG cc_start: 0.6893 (mtp85) cc_final: 0.5761 (mtp85) REVERT: g 74 ARG cc_start: 0.6351 (mmt180) cc_final: 0.5928 (ttp80) REVERT: g 107 VAL cc_start: 0.7128 (t) cc_final: 0.6824 (m) REVERT: g 121 MET cc_start: 0.6926 (ptp) cc_final: 0.6596 (ptm) REVERT: g 135 ASN cc_start: 0.6333 (m-40) cc_final: 0.5394 (t0) REVERT: g 160 ILE cc_start: 0.6209 (mp) cc_final: 0.5242 (tt) REVERT: g 212 MET cc_start: 0.6607 (mmm) cc_final: 0.6396 (mmt) REVERT: g 220 LEU cc_start: 0.7413 (mt) cc_final: 0.6126 (pt) REVERT: g 328 ASP cc_start: 0.6694 (t70) cc_final: 0.6467 (t70) REVERT: g 343 ARG cc_start: 0.6572 (mtp180) cc_final: 0.5875 (mtm180) REVERT: I 58 GLN cc_start: 0.6324 (tp40) cc_final: 0.5319 (pt0) REVERT: I 153 LEU cc_start: 0.7119 (tt) cc_final: 0.6807 (mt) REVERT: I 175 MET cc_start: 0.6143 (mtm) cc_final: 0.5864 (mtp) REVERT: J 162 MET cc_start: 0.3591 (ppp) cc_final: 0.3382 (ppp) REVERT: J 169 GLU cc_start: 0.4937 (tt0) cc_final: 0.4383 (mm-30) REVERT: N 57 LEU cc_start: 0.7410 (mt) cc_final: 0.7072 (mt) REVERT: P 60 MET cc_start: 0.4241 (mtt) cc_final: 0.1644 (tpp) REVERT: P 61 GLU cc_start: 0.5628 (mm-30) cc_final: 0.5288 (mm-30) REVERT: Q 60 MET cc_start: 0.1381 (mtp) cc_final: -0.0245 (tpt) REVERT: R 42 GLN cc_start: 0.4699 (tt0) cc_final: 0.4413 (mt0) REVERT: R 61 GLU cc_start: 0.3308 (mm-30) cc_final: 0.2565 (mt-10) REVERT: T 60 MET cc_start: 0.2768 (mmt) cc_final: 0.2177 (mmm) REVERT: W 37 GLU cc_start: 0.6281 (tt0) cc_final: 0.5404 (tp30) REVERT: Y 68 LEU cc_start: 0.4129 (tp) cc_final: 0.3726 (mm) outliers start: 0 outliers final: 0 residues processed: 696 average time/residue: 0.2282 time to fit residues: 269.4505 Evaluate side-chains 544 residues out of total 4091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 544 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 216 optimal weight: 0.9990 chunk 319 optimal weight: 2.9990 chunk 455 optimal weight: 10.0000 chunk 59 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 403 optimal weight: 0.9980 chunk 163 optimal weight: 0.9980 chunk 200 optimal weight: 2.9990 chunk 257 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 186 ASN ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 423 GLN ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 310 GLN E 187 ASN ** g 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 301 ASN ** I 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 227 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.116266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.098891 restraints weight = 131809.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.097702 restraints weight = 131546.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.098512 restraints weight = 99295.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.098738 restraints weight = 77875.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.098840 restraints weight = 71071.704| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6728 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 39707 Z= 0.171 Angle : 0.718 18.264 53855 Z= 0.354 Chirality : 0.045 0.216 6440 Planarity : 0.005 0.079 6944 Dihedral : 6.022 128.320 5581 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.61 % Favored : 94.35 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.12 % Twisted Proline : 0.49 % 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: -0.98 (0.11), residues: 5133 helix: 0.45 (0.10), residues: 2822 sheet: -1.96 (0.21), residues: 514 loop : -1.95 (0.14), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 312 TYR 0.027 0.002 TYR O 66 PHE 0.027 0.002 PHE R 59 TRP 0.019 0.002 TRP e 57 HIS 0.003 0.001 HIS a 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 (39707) covalent geometry : angle 0.71783 / 0.35 (53855) hydrogen bonds : bond 0.04165 / 2.83 ( 2308) hydrogen bonds : angle 4.72675 / 3.26 ( 6864) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10266 Ramachandran restraints generated. 5133 Oldfield, 0 Emsley, 5133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10266 Ramachandran restraints generated. 5133 Oldfield, 0 Emsley, 5133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 709 residues out of total 4091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 709 time to evaluate : 1.687 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 68 GLU cc_start: 0.7316 (mm-30) cc_final: 0.6937 (mm-30) REVERT: A 251 MET cc_start: 0.7607 (ttp) cc_final: 0.6471 (ttp) REVERT: A 344 PHE cc_start: 0.7202 (m-80) cc_final: 0.6727 (m-80) REVERT: B 199 ILE cc_start: 0.9076 (mt) cc_final: 0.8858 (mt) REVERT: B 436 MET cc_start: 0.7997 (ptp) cc_final: 0.7532 (ptp) REVERT: B 457 TYR cc_start: 0.7022 (t80) cc_final: 0.6736 (t80) REVERT: C 49 MET cc_start: 0.5481 (tpt) cc_final: 0.4992 (tpt) REVERT: C 81 LEU cc_start: 0.7031 (mt) cc_final: 0.6397 (mt) REVERT: C 154 ILE cc_start: 0.9040 (mm) cc_final: 0.8790 (mm) REVERT: C 358 ILE cc_start: 0.9020 (mm) cc_final: 0.8624 (tt) REVERT: C 470 PRO cc_start: 0.7250 (Cg_endo) cc_final: 0.6928 (Cg_exo) REVERT: D 59 MET cc_start: 0.6441 (ppp) cc_final: 0.6191 (ppp) REVERT: D 110 ILE cc_start: 0.8268 (mm) cc_final: 0.7949 (mt) REVERT: D 239 MET cc_start: 0.7733 (mtt) cc_final: 0.7489 (mtp) REVERT: E 306 MET cc_start: 0.8264 (tpp) cc_final: 0.7842 (tpp) REVERT: F 57 GLN cc_start: 0.6814 (pm20) cc_final: 0.6215 (tm-30) REVERT: F 299 GLN cc_start: 0.7786 (pm20) cc_final: 0.7317 (pm20) REVERT: F 411 ASP cc_start: 0.7443 (t70) cc_final: 0.6867 (t0) REVERT: F 462 LEU cc_start: 0.6418 (mt) cc_final: 0.5865 (pp) REVERT: d 234 ASP cc_start: 0.5937 (p0) cc_final: 0.5353 (p0) REVERT: e 45 ASP cc_start: 0.7187 (p0) cc_final: 0.6841 (p0) REVERT: e 105 LYS cc_start: 0.7280 (mtmt) cc_final: 0.6741 (mtmm) REVERT: g 74 ARG cc_start: 0.6342 (mmt180) cc_final: 0.6042 (ttp80) REVERT: g 107 VAL cc_start: 0.7198 (t) cc_final: 0.6872 (m) REVERT: g 135 ASN cc_start: 0.6341 (m-40) cc_final: 0.5423 (t0) REVERT: g 160 ILE cc_start: 0.6312 (mp) cc_final: 0.5244 (tt) REVERT: g 220 LEU cc_start: 0.7297 (mt) cc_final: 0.6058 (pt) REVERT: g 320 MET cc_start: 0.7364 (tmm) cc_final: 0.7159 (tmm) REVERT: g 328 ASP cc_start: 0.6713 (t70) cc_final: 0.6456 (t70) REVERT: g 343 ARG cc_start: 0.6680 (mtp180) cc_final: 0.5965 (mtm180) REVERT: I 58 GLN cc_start: 0.6359 (tp40) cc_final: 0.5367 (pt0) REVERT: I 90 MET cc_start: 0.2157 (tpt) cc_final: 0.1869 (tpt) REVERT: I 96 ARG cc_start: 0.2515 (tpt-90) cc_final: 0.0996 (mtm180) REVERT: I 153 LEU cc_start: 0.7161 (tt) cc_final: 0.6818 (mt) REVERT: J 162 MET cc_start: 0.3610 (ppp) cc_final: 0.3323 (ppp) REVERT: J 169 GLU cc_start: 0.4891 (tt0) cc_final: 0.4334 (mm-30) REVERT: N 57 LEU cc_start: 0.7364 (mt) cc_final: 0.7023 (mt) REVERT: P 60 MET cc_start: 0.4142 (mtt) cc_final: 0.1376 (tpp) REVERT: Q 60 MET cc_start: 0.1453 (mtp) cc_final: 0.0565 (tpp) REVERT: R 42 GLN cc_start: 0.4604 (tt0) cc_final: 0.4401 (mt0) REVERT: R 61 GLU cc_start: 0.3414 (mm-30) cc_final: 0.2675 (mt-10) REVERT: T 53 LEU cc_start: 0.5638 (tp) cc_final: 0.5360 (tt) REVERT: T 60 MET cc_start: 0.2917 (mmt) cc_final: 0.2359 (mmm) REVERT: W 37 GLU cc_start: 0.6293 (tt0) cc_final: 0.5385 (tp30) REVERT: Y 68 LEU cc_start: 0.4104 (tp) cc_final: 0.3694 (mm) outliers start: 0 outliers final: 0 residues processed: 709 average time/residue: 0.2301 time to fit residues: 275.3792 Evaluate side-chains 551 residues out of total 4091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 551 time to evaluate : 1.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 21 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 422 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 304 optimal weight: 6.9990 chunk 279 optimal weight: 0.0980 chunk 107 optimal weight: 4.9990 chunk 89 optimal weight: 0.5980 chunk 59 optimal weight: 0.9990 chunk 474 optimal weight: 8.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 186 ASN ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 423 GLN ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 187 ASN F 238 GLN ** g 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 301 ASN ** I 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.117435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.099880 restraints weight = 132302.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.099199 restraints weight = 126547.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.099764 restraints weight = 93484.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.100022 restraints weight = 73794.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.100218 restraints weight = 69069.389| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6672 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 39707 Z= 0.143 Angle : 0.703 19.768 53855 Z= 0.344 Chirality : 0.044 0.202 6440 Planarity : 0.004 0.076 6944 Dihedral : 5.844 126.703 5581 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.24 % Favored : 94.72 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.12 % Twisted Proline : 0.98 % 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: -0.81 (0.12), residues: 5133 helix: 0.58 (0.10), residues: 2818 sheet: -1.88 (0.21), residues: 520 loop : -1.85 (0.14), residues: 1795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 416 TYR 0.041 0.002 TYR J 109 PHE 0.029 0.002 PHE W 59 TRP 0.021 0.002 TRP e 57 HIS 0.003 0.001 HIS F 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (39707) covalent geometry : angle 0.70321 / 0.34 (53855) hydrogen bonds : bond 0.04011 / 2.71 ( 2308) hydrogen bonds : angle 4.64130 / 3.21 ( 6864) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10266 Ramachandran restraints generated. 5133 Oldfield, 0 Emsley, 5133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10266 Ramachandran restraints generated. 5133 Oldfield, 0 Emsley, 5133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 706 residues out of total 4091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 706 time to evaluate : 1.703 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 68 GLU cc_start: 0.7314 (mm-30) cc_final: 0.7093 (mm-30) REVERT: A 172 ARG cc_start: 0.7666 (tmm160) cc_final: 0.7106 (ptt90) REVERT: A 251 MET cc_start: 0.7484 (ttp) cc_final: 0.6397 (ttp) REVERT: A 344 PHE cc_start: 0.7141 (m-80) cc_final: 0.6651 (m-80) REVERT: B 199 ILE cc_start: 0.9034 (mt) cc_final: 0.8796 (mt) REVERT: B 436 MET cc_start: 0.7845 (ptp) cc_final: 0.7400 (ptp) REVERT: B 457 TYR cc_start: 0.6997 (t80) cc_final: 0.6709 (t80) REVERT: C 49 MET cc_start: 0.5535 (tpt) cc_final: 0.5184 (tpt) REVERT: C 81 LEU cc_start: 0.6809 (mt) cc_final: 0.6311 (mt) REVERT: C 154 ILE cc_start: 0.9003 (mm) cc_final: 0.8720 (mm) REVERT: C 358 ILE cc_start: 0.8933 (mm) cc_final: 0.8527 (tt) REVERT: C 390 PHE cc_start: 0.6828 (t80) cc_final: 0.6607 (t80) REVERT: C 470 PRO cc_start: 0.7123 (Cg_endo) cc_final: 0.6777 (Cg_exo) REVERT: D 110 ILE cc_start: 0.8219 (mm) cc_final: 0.7918 (mt) REVERT: E 306 MET cc_start: 0.8182 (tpp) cc_final: 0.7752 (tpp) REVERT: F 57 GLN cc_start: 0.6696 (pm20) cc_final: 0.6115 (tm-30) REVERT: F 299 GLN cc_start: 0.7915 (pm20) cc_final: 0.7631 (pm20) REVERT: F 411 ASP cc_start: 0.7462 (t70) cc_final: 0.7003 (t0) REVERT: F 462 LEU cc_start: 0.6443 (mt) cc_final: 0.5902 (pp) REVERT: e 45 ASP cc_start: 0.7018 (p0) cc_final: 0.6657 (p0) REVERT: e 105 LYS cc_start: 0.7287 (mtmt) cc_final: 0.6760 (mtmm) REVERT: g 107 VAL cc_start: 0.7237 (t) cc_final: 0.6848 (m) REVERT: g 135 ASN cc_start: 0.6315 (m-40) cc_final: 0.5402 (t0) REVERT: g 220 LEU cc_start: 0.7289 (mt) cc_final: 0.6092 (pt) REVERT: g 328 ASP cc_start: 0.6664 (t70) cc_final: 0.6420 (t70) REVERT: I 58 GLN cc_start: 0.6409 (tp40) cc_final: 0.5438 (pt0) REVERT: I 90 MET cc_start: 0.2080 (tpt) cc_final: 0.1800 (tpt) REVERT: I 96 ARG cc_start: 0.2735 (tpt-90) cc_final: 0.1165 (mtm180) REVERT: I 153 LEU cc_start: 0.7164 (tt) cc_final: 0.6819 (mt) REVERT: I 175 MET cc_start: 0.6134 (mtm) cc_final: 0.5418 (mtm) REVERT: J 162 MET cc_start: 0.3577 (ppp) cc_final: 0.3100 (ppp) REVERT: J 169 GLU cc_start: 0.4952 (tt0) cc_final: 0.4396 (mm-30) REVERT: a 87 ILE cc_start: 0.5079 (mm) cc_final: 0.4871 (mm) REVERT: N 57 LEU cc_start: 0.7351 (mt) cc_final: 0.6954 (mt) REVERT: P 50 ARG cc_start: 0.3277 (mtt-85) cc_final: 0.1890 (mtp-110) REVERT: P 60 MET cc_start: 0.4185 (mtt) cc_final: 0.1316 (tpp) REVERT: Q 60 MET cc_start: 0.1431 (mtp) cc_final: -0.0420 (tpt) REVERT: R 61 GLU cc_start: 0.3286 (mm-30) cc_final: 0.2643 (mt-10) REVERT: T 60 MET cc_start: 0.3046 (mmt) cc_final: 0.2568 (mmm) REVERT: W 37 GLU cc_start: 0.6265 (tt0) cc_final: 0.5416 (tp30) REVERT: Y 68 LEU cc_start: 0.4253 (tp) cc_final: 0.3828 (mm) REVERT: Z 37 GLU cc_start: 0.3165 (tp30) cc_final: 0.2539 (tm-30) outliers start: 0 outliers final: 0 residues processed: 706 average time/residue: 0.2319 time to fit residues: 276.6268 Evaluate side-chains 548 residues out of total 4091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 548 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 48 optimal weight: 0.6980 chunk 97 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 chunk 113 optimal weight: 0.4980 chunk 274 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 460 optimal weight: 6.9990 chunk 386 optimal weight: 3.9990 chunk 361 optimal weight: 0.6980 chunk 453 optimal weight: 0.8980 chunk 356 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 186 ASN ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 423 GLN ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 299 GLN D 310 GLN E 187 ASN E 310 GLN ** g 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 301 ASN ** I 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 86 GLN ** N 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 28 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.117430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.100134 restraints weight = 131444.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.099165 restraints weight = 126718.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.099758 restraints weight = 93419.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.099926 restraints weight = 72581.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.100047 restraints weight = 71259.554| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6692 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 39707 Z= 0.143 Angle : 0.703 19.845 53855 Z= 0.345 Chirality : 0.044 0.221 6440 Planarity : 0.005 0.077 6944 Dihedral : 5.749 125.686 5581 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.16 % Favored : 94.80 % Rotamer: Outliers : 0.02 % Allowed : 0.46 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.12 % Twisted Proline : 0.49 % 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: -0.73 (0.12), residues: 5133 helix: 0.63 (0.10), residues: 2818 sheet: -1.84 (0.21), residues: 531 loop : -1.79 (0.14), residues: 1784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 378 TYR 0.033 0.002 TYR D 162 PHE 0.046 0.002 PHE a 222 TRP 0.022 0.002 TRP e 57 HIS 0.003 0.001 HIS F 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (39707) covalent geometry : angle 0.70251 / 0.34 (53855) hydrogen bonds : bond 0.03951 / 2.66 ( 2308) hydrogen bonds : angle 4.61717 / 3.19 ( 6864) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10266 Ramachandran restraints generated. 5133 Oldfield, 0 Emsley, 5133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10266 Ramachandran restraints generated. 5133 Oldfield, 0 Emsley, 5133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 707 residues out of total 4091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 706 time to evaluate : 1.463 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 68 GLU cc_start: 0.7334 (mm-30) cc_final: 0.7042 (mm-30) REVERT: A 130 ILE cc_start: 0.8253 (pt) cc_final: 0.7990 (pt) REVERT: A 172 ARG cc_start: 0.7829 (tmm160) cc_final: 0.7264 (ptt90) REVERT: A 251 MET cc_start: 0.7533 (ttp) cc_final: 0.6470 (ttp) REVERT: A 344 PHE cc_start: 0.7157 (m-80) cc_final: 0.6665 (m-80) REVERT: B 199 ILE cc_start: 0.9059 (mt) cc_final: 0.8806 (mt) REVERT: B 436 MET cc_start: 0.7894 (ptp) cc_final: 0.7485 (ptp) REVERT: B 457 TYR cc_start: 0.7018 (t80) cc_final: 0.6740 (t80) REVERT: C 81 LEU cc_start: 0.6860 (mt) cc_final: 0.6545 (mt) REVERT: C 154 ILE cc_start: 0.9013 (mm) cc_final: 0.8762 (mm) REVERT: C 358 ILE cc_start: 0.8878 (mm) cc_final: 0.8488 (tt) REVERT: C 470 PRO cc_start: 0.7116 (Cg_endo) cc_final: 0.6772 (Cg_exo) REVERT: D 110 ILE cc_start: 0.8341 (mm) cc_final: 0.8018 (mt) REVERT: E 204 GLU cc_start: 0.3055 (mm-30) cc_final: 0.2507 (mm-30) REVERT: E 306 MET cc_start: 0.8254 (tpp) cc_final: 0.7866 (tpp) REVERT: F 57 GLN cc_start: 0.6804 (pm20) cc_final: 0.6201 (tm-30) REVERT: F 299 GLN cc_start: 0.7861 (pm20) cc_final: 0.7507 (pm20) REVERT: F 411 ASP cc_start: 0.7463 (t70) cc_final: 0.6931 (t0) REVERT: F 462 LEU cc_start: 0.6426 (mt) cc_final: 0.5846 (pp) REVERT: e 45 ASP cc_start: 0.6976 (p0) cc_final: 0.6654 (p0) REVERT: e 105 LYS cc_start: 0.7169 (mtmt) cc_final: 0.6642 (mtmm) REVERT: g 135 ASN cc_start: 0.6199 (m-40) cc_final: 0.5316 (t0) REVERT: g 220 LEU cc_start: 0.7189 (mt) cc_final: 0.6911 (mt) REVERT: g 320 MET cc_start: 0.7434 (tmm) cc_final: 0.7145 (tmm) REVERT: g 328 ASP cc_start: 0.6690 (t70) cc_final: 0.6474 (t70) REVERT: I 58 GLN cc_start: 0.6464 (tp40) cc_final: 0.5509 (pt0) REVERT: I 90 MET cc_start: 0.2132 (tpt) cc_final: 0.1875 (tpt) REVERT: I 153 LEU cc_start: 0.7418 (tt) cc_final: 0.7092 (mt) REVERT: J 101 MET cc_start: -0.0290 (mtp) cc_final: -0.0738 (mtp) REVERT: J 162 MET cc_start: 0.3574 (ppp) cc_final: 0.3024 (ppp) REVERT: J 169 GLU cc_start: 0.4983 (tt0) cc_final: 0.4407 (mm-30) REVERT: a 195 LEU cc_start: 0.5773 (tp) cc_final: 0.5535 (tt) REVERT: N 57 LEU cc_start: 0.7336 (mt) cc_final: 0.7000 (mt) REVERT: P 50 ARG cc_start: 0.3252 (mtt-85) cc_final: 0.1897 (mtp-110) REVERT: P 60 MET cc_start: 0.4106 (mtt) cc_final: 0.1182 (tpp) REVERT: Q 60 MET cc_start: 0.1514 (mtp) cc_final: -0.0348 (tpt) REVERT: R 61 GLU cc_start: 0.2951 (mm-30) cc_final: 0.2316 (mt-10) REVERT: T 60 MET cc_start: 0.3312 (mmt) cc_final: 0.2849 (mmm) REVERT: W 37 GLU cc_start: 0.6306 (tt0) cc_final: 0.5432 (tp30) REVERT: Y 68 LEU cc_start: 0.4150 (tp) cc_final: 0.3814 (mm) REVERT: Z 37 GLU cc_start: 0.3119 (tp30) cc_final: 0.2506 (tm-30) outliers start: 1 outliers final: 0 residues processed: 707 average time/residue: 0.2258 time to fit residues: 269.8276 Evaluate side-chains 552 residues out of total 4091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 552 time to evaluate : 1.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 309 optimal weight: 2.9990 chunk 457 optimal weight: 4.9990 chunk 467 optimal weight: 8.9990 chunk 492 optimal weight: 0.8980 chunk 271 optimal weight: 0.9980 chunk 311 optimal weight: 4.9990 chunk 169 optimal weight: 4.9990 chunk 217 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 315 optimal weight: 0.8980 chunk 331 optimal weight: 0.0970 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 186 ASN ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 423 GLN ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 301 ASN ** I 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 86 GLN ** N 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 78 ASN P 28 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.117362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.099842 restraints weight = 132120.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.098916 restraints weight = 128652.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.099466 restraints weight = 101923.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.099695 restraints weight = 83676.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.099863 restraints weight = 71800.047| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6678 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 39707 Z= 0.143 Angle : 0.699 18.513 53855 Z= 0.343 Chirality : 0.044 0.172 6440 Planarity : 0.004 0.068 6944 Dihedral : 5.684 125.131 5581 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.30 % Favored : 94.66 % Rotamer: Outliers : 0.02 % Allowed : 0.44 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.12 % Twisted Proline : 0.49 % 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: -0.70 (0.12), residues: 5133 helix: 0.67 (0.10), residues: 2825 sheet: -1.82 (0.20), residues: 529 loop : -1.83 (0.14), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 378 TYR 0.032 0.002 TYR J 109 PHE 0.037 0.002 PHE a 218 TRP 0.023 0.002 TRP e 57 HIS 0.003 0.001 HIS F 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (39707) covalent geometry : angle 0.69932 / 0.34 (53855) hydrogen bonds : bond 0.03947 / 2.66 ( 2308) hydrogen bonds : angle 4.57893 / 3.16 ( 6864) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7177.85 seconds wall clock time: 125 minutes 7.20 seconds (7507.20 seconds total)