Starting phenix.real_space_refine on Sun Aug 9 01:45:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8glw_40221/08_2026/8glw_40221.cif Found real_map, /net/cci-nas-00/data/ceres_data/8glw_40221/08_2026/8glw_40221.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8glw_40221/08_2026/8glw_40221.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8glw_40221/08_2026/8glw_40221.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8glw_40221/08_2026/8glw_40221.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8glw_40221/08_2026/8glw_40221.map" } resolution = 3.51 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= 1.000 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 116 5.49 5 Mg 7 5.21 5 S 110 5.16 5 C 20032 2.51 5 N 5763 2.21 5 O 6144 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32174 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 3865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3865 Classifications: {'peptide': 483} Link IDs: {'PTRANS': 19, 'TRANS': 463} Chain: "B" Number of atoms: 3865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3865 Classifications: {'peptide': 483} Link IDs: {'PTRANS': 19, 'TRANS': 463} Chain: "C" Number of atoms: 3116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3116 Classifications: {'peptide': 391} Link IDs: {'PTRANS': 14, 'TRANS': 376} Chain breaks: 1 Chain: "Y" Number of atoms: 2515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2515 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 15, 'TRANS': 293} Chain: "D" Number of atoms: 3865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3865 Classifications: {'peptide': 483} Link IDs: {'PTRANS': 19, 'TRANS': 463} Chain: "E" Number of atoms: 3860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3860 Classifications: {'peptide': 482} Link IDs: {'PTRANS': 19, 'TRANS': 462} Chain: "F" Number of atoms: 3203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 3203 Classifications: {'peptide': 403} Link IDs: {'PTRANS': 14, 'TRANS': 388} Chain: "G" Number of atoms: 3106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3106 Classifications: {'peptide': 390} Link IDs: {'PTRANS': 14, 'TRANS': 375} Chain breaks: 1 Chain: "X" Number of atoms: 2523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2523 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 15, 'TRANS': 294} Chain: "H" Number of atoms: 1029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1029 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain: "I" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1021 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 2, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 11841 SG CYS Y 124 22.426 82.153 113.979 1.00 30.69 S ATOM 11862 SG CYS Y 127 21.756 85.923 114.327 1.00 28.39 S ATOM 12080 SG CYS Y 152 21.386 83.567 117.422 1.00 37.35 S ATOM 28390 SG CYS X 124 56.103 58.710 57.504 1.00 23.91 S ATOM 28411 SG CYS X 127 59.005 56.222 57.959 1.00 17.16 S ATOM 28629 SG CYS X 152 59.380 59.097 55.468 1.00 19.28 S Time building chain proxies: 7.29, per 1000 atoms: 0.23 Number of scatterers: 32174 At special positions: 0 Unit cell: (182.97, 169.29, 197.505, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 110 16.00 P 116 15.00 Mg 7 11.99 O 6144 8.00 N 5763 7.00 C 20032 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: 2.91 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN X 601 " pdb="ZN ZN X 601 " - pdb=" ND1 HIS X 155 " pdb="ZN ZN X 601 " - pdb=" SG CYS X 127 " pdb="ZN ZN X 601 " - pdb=" SG CYS X 152 " pdb="ZN ZN X 601 " - pdb=" SG CYS X 124 " pdb=" ZN Y 601 " pdb="ZN ZN Y 601 " - pdb=" NE2 HIS Y 155 " pdb="ZN ZN Y 601 " - pdb=" SG CYS Y 124 " pdb="ZN ZN Y 601 " - pdb=" SG CYS Y 152 " pdb="ZN ZN Y 601 " - pdb=" SG CYS Y 127 " Number of angles added : 6 7424 Ramachandran restraints generated. 3712 Oldfield, 0 Emsley, 3712 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7030 Finding SS restraints... Secondary structure from input PDB file: 205 helices and 19 sheets defined 55.3% alpha, 4.2% beta 48 base pairs and 83 stacking pairs defined. Time for finding SS restraints: 3.70 Creating SS restraints... Processing helix chain 'A' and resid 15 through 19 removed outlier: 3.627A pdb=" N TYR A 18 " --> pdb=" O VAL A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 26 Processing helix chain 'A' and resid 35 through 40 removed outlier: 3.663A pdb=" N SER A 39 " --> pdb=" O ASN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 64 Processing helix chain 'A' and resid 73 through 90 removed outlier: 3.728A pdb=" N LEU A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY A 90 " --> pdb=" O MET A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 115 Processing helix chain 'A' and resid 141 through 150 removed outlier: 3.952A pdb=" N ARG A 148 " --> pdb=" O THR A 144 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU A 150 " --> pdb=" O LEU A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 196 Processing helix chain 'A' and resid 199 through 204 Processing helix chain 'A' and resid 209 through 225 removed outlier: 3.609A pdb=" N ALA A 215 " --> pdb=" O GLU A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 237 removed outlier: 3.579A pdb=" N LEU A 237 " --> pdb=" O ILE A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 260 removed outlier: 3.691A pdb=" N ASN A 250 " --> pdb=" O GLN A 246 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY A 260 " --> pdb=" O VAL A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 280 removed outlier: 4.092A pdb=" N PHE A 275 " --> pdb=" O ALA A 271 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ALA A 277 " --> pdb=" O GLU A 273 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N ASP A 278 " --> pdb=" O ILE A 274 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 287 removed outlier: 4.025A pdb=" N GLY A 287 " --> pdb=" O ARG A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 317 removed outlier: 3.823A pdb=" N ILE A 309 " --> pdb=" O ASN A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 341 Processing helix chain 'A' and resid 344 through 362 removed outlier: 3.613A pdb=" N GLY A 362 " --> pdb=" O ALA A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 379 Processing helix chain 'A' and resid 382 through 392 Processing helix chain 'A' and resid 393 through 398 removed outlier: 3.710A pdb=" N ALA A 398 " --> pdb=" O PRO A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 420 removed outlier: 3.920A pdb=" N ALA A 420 " --> pdb=" O GLN A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 434 removed outlier: 3.644A pdb=" N LYS A 430 " --> pdb=" O THR A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 447 removed outlier: 4.195A pdb=" N TYR A 444 " --> pdb=" O GLN A 440 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU A 445 " --> pdb=" O ARG A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 464 Proline residue: A 458 - end of helix Processing helix chain 'A' and resid 465 through 467 No H-bonds generated for 'chain 'A' and resid 465 through 467' Processing helix chain 'A' and resid 475 through 482 removed outlier: 4.451A pdb=" N VAL A 479 " --> pdb=" O LEU A 475 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU A 480 " --> pdb=" O LEU A 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 19 removed outlier: 3.518A pdb=" N TYR B 18 " --> pdb=" O VAL B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 26 Processing helix chain 'B' and resid 36 through 41 Processing helix chain 'B' and resid 48 through 52 removed outlier: 3.561A pdb=" N LEU B 51 " --> pdb=" O SER B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 64 Processing helix chain 'B' and resid 64 through 69 Processing helix chain 'B' and resid 74 through 90 removed outlier: 4.256A pdb=" N LEU B 78 " --> pdb=" O GLY B 74 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY B 90 " --> pdb=" O MET B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 114 removed outlier: 3.946A pdb=" N HIS B 104 " --> pdb=" O ASP B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 150 removed outlier: 3.599A pdb=" N ILE B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU B 150 " --> pdb=" O LEU B 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 145 through 150' Processing helix chain 'B' and resid 179 through 196 removed outlier: 3.640A pdb=" N ILE B 183 " --> pdb=" O SER B 179 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU B 185 " --> pdb=" O LYS B 181 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N PHE B 187 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N PHE B 188 " --> pdb=" O CYS B 184 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG B 189 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA B 194 " --> pdb=" O ALA B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 204 Processing helix chain 'B' and resid 209 through 224 removed outlier: 3.557A pdb=" N MET B 217 " --> pdb=" O MET B 213 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N SER B 218 " --> pdb=" O LEU B 214 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN B 219 " --> pdb=" O ALA B 215 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN B 222 " --> pdb=" O SER B 218 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA B 223 " --> pdb=" O GLN B 219 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N HIS B 224 " --> pdb=" O ILE B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 238 removed outlier: 4.003A pdb=" N LEU B 237 " --> pdb=" O GLU B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 259 Processing helix chain 'B' and resid 268 through 270 No H-bonds generated for 'chain 'B' and resid 268 through 270' Processing helix chain 'B' and resid 271 through 276 removed outlier: 3.749A pdb=" N PHE B 275 " --> pdb=" O ALA B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 286 Processing helix chain 'B' and resid 305 through 315 Processing helix chain 'B' and resid 316 through 319 Processing helix chain 'B' and resid 329 through 341 Processing helix chain 'B' and resid 343 through 362 removed outlier: 3.843A pdb=" N VAL B 347 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N VAL B 348 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS B 349 " --> pdb=" O ASP B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 379 removed outlier: 3.689A pdb=" N LEU B 379 " --> pdb=" O TYR B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 392 removed outlier: 3.550A pdb=" N GLY B 392 " --> pdb=" O ALA B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 401 removed outlier: 3.713A pdb=" N TYR B 400 " --> pdb=" O ARG B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 423 Processing helix chain 'B' and resid 426 through 428 No H-bonds generated for 'chain 'B' and resid 426 through 428' Processing helix chain 'B' and resid 429 through 435 removed outlier: 3.866A pdb=" N LEU B 435 " --> pdb=" O ALA B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 447 Processing helix chain 'B' and resid 455 through 467 removed outlier: 3.665A pdb=" N ILE B 460 " --> pdb=" O LEU B 456 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN B 467 " --> pdb=" O ALA B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 485 removed outlier: 4.145A pdb=" N LEU B 478 " --> pdb=" O LYS B 474 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU B 485 " --> pdb=" O GLN B 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 19 Processing helix chain 'C' and resid 21 through 27 removed outlier: 3.774A pdb=" N LEU C 27 " --> pdb=" O PHE C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 41 removed outlier: 4.375A pdb=" N SER C 39 " --> pdb=" O ASN C 35 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU C 40 " --> pdb=" O SER C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 53 removed outlier: 3.522A pdb=" N GLN C 52 " --> pdb=" O SER C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 63 removed outlier: 3.505A pdb=" N ILE C 62 " --> pdb=" O ARG C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 90 removed outlier: 4.159A pdb=" N LEU C 77 " --> pdb=" O LEU C 73 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU C 78 " --> pdb=" O GLY C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 95 removed outlier: 4.094A pdb=" N ASN C 95 " --> pdb=" O VAL C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 115 removed outlier: 3.764A pdb=" N HIS C 104 " --> pdb=" O ASP C 100 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN C 106 " --> pdb=" O GLN C 102 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU C 110 " --> pdb=" O GLN C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 151 Processing helix chain 'C' and resid 185 through 192 removed outlier: 3.549A pdb=" N ASP C 192 " --> pdb=" O PHE C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 204 Processing helix chain 'C' and resid 209 through 224 removed outlier: 4.252A pdb=" N ALA C 215 " --> pdb=" O GLU C 211 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N SER C 218 " --> pdb=" O LEU C 214 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N HIS C 224 " --> pdb=" O ILE C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 238 removed outlier: 3.704A pdb=" N HIS C 236 " --> pdb=" O GLU C 233 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER C 238 " --> pdb=" O GLN C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 258 removed outlier: 4.673A pdb=" N MET C 248 " --> pdb=" O GLY C 244 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL C 253 " --> pdb=" O LEU C 249 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL C 256 " --> pdb=" O PHE C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 274 Processing helix chain 'C' and resid 305 through 317 Processing helix chain 'C' and resid 329 through 341 Processing helix chain 'C' and resid 343 through 362 removed outlier: 3.642A pdb=" N PHE C 351 " --> pdb=" O VAL C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 379 Processing helix chain 'C' and resid 382 through 392 removed outlier: 3.610A pdb=" N GLY C 392 " --> pdb=" O ALA C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 399 Processing helix chain 'Y' and resid 12 through 24 removed outlier: 3.730A pdb=" N GLN Y 24 " --> pdb=" O ALA Y 20 " (cutoff:3.500A) Processing helix chain 'Y' and resid 28 through 37 removed outlier: 3.574A pdb=" N LEU Y 32 " --> pdb=" O SER Y 28 " (cutoff:3.500A) Processing helix chain 'Y' and resid 51 through 59 removed outlier: 4.079A pdb=" N ILE Y 55 " --> pdb=" O HIS Y 51 " (cutoff:3.500A) Processing helix chain 'Y' and resid 66 through 73 removed outlier: 3.901A pdb=" N LEU Y 70 " --> pdb=" O ALA Y 66 " (cutoff:3.500A) Processing helix chain 'Y' and resid 76 through 80 removed outlier: 3.545A pdb=" N LEU Y 79 " --> pdb=" O LEU Y 76 " (cutoff:3.500A) Processing helix chain 'Y' and resid 85 through 98 removed outlier: 3.681A pdb=" N GLU Y 91 " --> pdb=" O GLU Y 87 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR Y 98 " --> pdb=" O ARG Y 94 " (cutoff:3.500A) Processing helix chain 'Y' and resid 101 through 109 removed outlier: 3.905A pdb=" N HIS Y 105 " --> pdb=" O GLN Y 101 " (cutoff:3.500A) Processing helix chain 'Y' and resid 109 through 114 Processing helix chain 'Y' and resid 124 through 135 removed outlier: 3.743A pdb=" N ALA Y 129 " --> pdb=" O PRO Y 125 " (cutoff:3.500A) Processing helix chain 'Y' and resid 190 through 204 Proline residue: Y 201 - end of helix removed outlier: 3.875A pdb=" N ASP Y 204 " --> pdb=" O ALA Y 200 " (cutoff:3.500A) Processing helix chain 'Y' and resid 205 through 210 removed outlier: 3.839A pdb=" N GLN Y 209 " --> pdb=" O PRO Y 206 " (cutoff:3.500A) Processing helix chain 'Y' and resid 214 through 229 Processing helix chain 'Y' and resid 240 through 250 Processing helix chain 'Y' and resid 251 through 258 Processing helix chain 'Y' and resid 269 through 275 removed outlier: 3.509A pdb=" N SER Y 273 " --> pdb=" O CYS Y 269 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N PHE Y 275 " --> pdb=" O LEU Y 271 " (cutoff:3.500A) Processing helix chain 'Y' and resid 283 through 295 Processing helix chain 'Y' and resid 299 through 309 Processing helix chain 'D' and resid 15 through 19 Processing helix chain 'D' and resid 29 through 31 No H-bonds generated for 'chain 'D' and resid 29 through 31' Processing helix chain 'D' and resid 32 through 37 Processing helix chain 'D' and resid 47 through 51 Processing helix chain 'D' and resid 54 through 64 removed outlier: 3.591A pdb=" N ARG D 64 " --> pdb=" O HIS D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 90 removed outlier: 3.768A pdb=" N LEU D 77 " --> pdb=" O LEU D 73 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU D 78 " --> pdb=" O GLY D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 113 removed outlier: 3.780A pdb=" N HIS D 104 " --> pdb=" O ASP D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 129 Processing helix chain 'D' and resid 142 through 147 Processing helix chain 'D' and resid 179 through 196 removed outlier: 3.648A pdb=" N ILE D 183 " --> pdb=" O SER D 179 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N CYS D 184 " --> pdb=" O LEU D 180 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE D 188 " --> pdb=" O CYS D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 204 removed outlier: 3.997A pdb=" N ARG D 202 " --> pdb=" O ASN D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 224 Processing helix chain 'D' and resid 233 through 237 Processing helix chain 'D' and resid 244 through 260 removed outlier: 3.529A pdb=" N MET D 248 " --> pdb=" O GLY D 244 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLY D 260 " --> pdb=" O VAL D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 273 removed outlier: 3.698A pdb=" N GLU D 273 " --> pdb=" O PRO D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 281 Processing helix chain 'D' and resid 305 through 317 Processing helix chain 'D' and resid 329 through 339 removed outlier: 3.692A pdb=" N TRP D 336 " --> pdb=" O VAL D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 362 removed outlier: 3.833A pdb=" N LEU D 350 " --> pdb=" O ILE D 346 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN D 355 " --> pdb=" O PHE D 351 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU D 356 " --> pdb=" O VAL D 352 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA D 360 " --> pdb=" O LEU D 356 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY D 362 " --> pdb=" O ALA D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 379 Processing helix chain 'D' and resid 382 through 392 Processing helix chain 'D' and resid 393 through 400 Processing helix chain 'D' and resid 407 through 421 removed outlier: 3.970A pdb=" N ARG D 411 " --> pdb=" O GLU D 407 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA D 421 " --> pdb=" O LEU D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 435 removed outlier: 3.863A pdb=" N LEU D 432 " --> pdb=" O GLU D 428 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLN D 433 " --> pdb=" O GLU D 429 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLU D 434 " --> pdb=" O LYS D 430 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU D 435 " --> pdb=" O ALA D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 440 through 448 removed outlier: 3.846A pdb=" N TYR D 444 " --> pdb=" O GLN D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 467 Processing helix chain 'D' and resid 471 through 485 Proline residue: D 477 - end of helix Processing helix chain 'E' and resid 15 through 19 removed outlier: 3.771A pdb=" N ARG E 19 " --> pdb=" O GLU E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 26 Processing helix chain 'E' and resid 47 through 51 removed outlier: 3.651A pdb=" N LEU E 51 " --> pdb=" O SER E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 63 Processing helix chain 'E' and resid 75 through 90 removed outlier: 4.009A pdb=" N LEU E 79 " --> pdb=" O THR E 75 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY E 90 " --> pdb=" O MET E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 95 removed outlier: 3.987A pdb=" N ASN E 95 " --> pdb=" O VAL E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 113 removed outlier: 4.097A pdb=" N HIS E 104 " --> pdb=" O ASP E 100 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN E 113 " --> pdb=" O TYR E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 151 removed outlier: 3.785A pdb=" N ARG E 148 " --> pdb=" O THR E 144 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ILE E 149 " --> pdb=" O SER E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 182 removed outlier: 3.703A pdb=" N GLU E 182 " --> pdb=" O SER E 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 179 through 182' Processing helix chain 'E' and resid 183 through 195 removed outlier: 3.802A pdb=" N PHE E 188 " --> pdb=" O CYS E 184 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARG E 193 " --> pdb=" O ARG E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 203 Processing helix chain 'E' and resid 209 through 224 removed outlier: 4.205A pdb=" N SER E 218 " --> pdb=" O LEU E 214 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLN E 219 " --> pdb=" O ALA E 215 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE E 220 " --> pdb=" O LEU E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 237 Processing helix chain 'E' and resid 253 through 257 Processing helix chain 'E' and resid 279 through 284 Processing helix chain 'E' and resid 305 through 317 removed outlier: 3.883A pdb=" N ILE E 309 " --> pdb=" O ASN E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 341 Processing helix chain 'E' and resid 343 through 362 removed outlier: 3.675A pdb=" N VAL E 348 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS E 349 " --> pdb=" O ASP E 345 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU E 359 " --> pdb=" O GLN E 355 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA E 360 " --> pdb=" O LEU E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 378 Processing helix chain 'E' and resid 382 through 392 removed outlier: 3.541A pdb=" N LEU E 386 " --> pdb=" O VAL E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 393 through 400 Processing helix chain 'E' and resid 407 through 422 removed outlier: 4.090A pdb=" N ARG E 411 " --> pdb=" O GLU E 407 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE E 422 " --> pdb=" O ASP E 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 429 through 435 Processing helix chain 'E' and resid 437 through 448 Processing helix chain 'E' and resid 455 through 467 Processing helix chain 'E' and resid 471 through 485 removed outlier: 3.804A pdb=" N LEU E 476 " --> pdb=" O ARG E 472 " (cutoff:3.500A) Proline residue: E 477 - end of helix Processing helix chain 'F' and resid 21 through 26 Processing helix chain 'F' and resid 34 through 38 removed outlier: 3.613A pdb=" N ALA F 37 " --> pdb=" O VAL F 34 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA F 38 " --> pdb=" O ASN F 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 34 through 38' Processing helix chain 'F' and resid 56 through 61 Processing helix chain 'F' and resid 64 through 69 Processing helix chain 'F' and resid 73 through 76 removed outlier: 3.673A pdb=" N HIS F 76 " --> pdb=" O LEU F 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 73 through 76' Processing helix chain 'F' and resid 77 through 90 removed outlier: 3.642A pdb=" N ARG F 88 " --> pdb=" O SER F 84 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY F 90 " --> pdb=" O MET F 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 114 Processing helix chain 'F' and resid 143 through 150 Processing helix chain 'F' and resid 151 through 153 No H-bonds generated for 'chain 'F' and resid 151 through 153' Processing helix chain 'F' and resid 185 through 192 Processing helix chain 'F' and resid 199 through 204 Processing helix chain 'F' and resid 209 through 216 Processing helix chain 'F' and resid 234 through 238 removed outlier: 3.511A pdb=" N LEU F 237 " --> pdb=" O ILE F 234 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER F 238 " --> pdb=" O GLN F 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 234 through 238' Processing helix chain 'F' and resid 248 through 260 removed outlier: 3.862A pdb=" N VAL F 253 " --> pdb=" O LEU F 249 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLY F 260 " --> pdb=" O VAL F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 276 removed outlier: 3.774A pdb=" N PHE F 275 " --> pdb=" O ALA F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 278 through 286 Processing helix chain 'F' and resid 307 through 316 removed outlier: 3.944A pdb=" N ASN F 314 " --> pdb=" O ALA F 310 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU F 315 " --> pdb=" O PHE F 311 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 319 No H-bonds generated for 'chain 'F' and resid 317 through 319' Processing helix chain 'F' and resid 329 through 341 Processing helix chain 'F' and resid 343 through 346 Processing helix chain 'F' and resid 347 through 362 Processing helix chain 'F' and resid 367 through 379 Processing helix chain 'F' and resid 382 through 392 Processing helix chain 'F' and resid 393 through 398 Processing helix chain 'G' and resid 47 through 51 removed outlier: 3.694A pdb=" N LEU G 51 " --> pdb=" O SER G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 54 through 61 Processing helix chain 'G' and resid 64 through 69 Processing helix chain 'G' and resid 73 through 89 removed outlier: 4.077A pdb=" N LEU G 77 " --> pdb=" O LEU G 73 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU G 78 " --> pdb=" O GLY G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 95 removed outlier: 3.966A pdb=" N ASN G 95 " --> pdb=" O VAL G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 115 removed outlier: 3.572A pdb=" N GLN G 106 " --> pdb=" O GLN G 102 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASN G 107 " --> pdb=" O LYS G 103 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY G 108 " --> pdb=" O HIS G 104 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR G 109 " --> pdb=" O LEU G 105 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLU G 110 " --> pdb=" O GLN G 106 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG G 111 " --> pdb=" O ASN G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 192 Processing helix chain 'G' and resid 209 through 224 removed outlier: 3.690A pdb=" N MET G 217 " --> pdb=" O MET G 213 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER G 218 " --> pdb=" O LEU G 214 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASN G 222 " --> pdb=" O SER G 218 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N HIS G 224 " --> pdb=" O ILE G 220 " (cutoff:3.500A) Processing helix chain 'G' and resid 233 through 238 Processing helix chain 'G' and resid 243 through 258 removed outlier: 3.593A pdb=" N MET G 248 " --> pdb=" O GLY G 244 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N LEU G 249 " --> pdb=" O SER G 245 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL G 253 " --> pdb=" O LEU G 249 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N VAL G 256 " --> pdb=" O PHE G 252 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASN G 257 " --> pdb=" O VAL G 253 " (cutoff:3.500A) Processing helix chain 'G' and resid 268 through 273 removed outlier: 3.982A pdb=" N GLU G 273 " --> pdb=" O LYS G 270 " (cutoff:3.500A) Processing helix chain 'G' and resid 305 through 316 Processing helix chain 'G' and resid 329 through 341 Processing helix chain 'G' and resid 343 through 362 Processing helix chain 'G' and resid 367 through 379 Processing helix chain 'G' and resid 382 through 392 Processing helix chain 'G' and resid 393 through 399 removed outlier: 4.143A pdb=" N ARG G 399 " --> pdb=" O GLU G 395 " (cutoff:3.500A) Processing helix chain 'X' and resid 12 through 23 Processing helix chain 'X' and resid 28 through 37 Processing helix chain 'X' and resid 54 through 59 Processing helix chain 'X' and resid 66 through 74 Processing helix chain 'X' and resid 80 through 85 removed outlier: 4.202A pdb=" N GLY X 85 " --> pdb=" O ALA X 81 " (cutoff:3.500A) Processing helix chain 'X' and resid 86 through 98 removed outlier: 3.928A pdb=" N GLU X 97 " --> pdb=" O ILE X 93 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N TYR X 98 " --> pdb=" O ARG X 94 " (cutoff:3.500A) Processing helix chain 'X' and resid 100 through 108 removed outlier: 3.896A pdb=" N VAL X 104 " --> pdb=" O ALA X 100 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU X 108 " --> pdb=" O VAL X 104 " (cutoff:3.500A) Processing helix chain 'X' and resid 124 through 135 removed outlier: 3.775A pdb=" N ALA X 129 " --> pdb=" O PRO X 125 " (cutoff:3.500A) Processing helix chain 'X' and resid 189 through 200 Processing helix chain 'X' and resid 201 through 203 No H-bonds generated for 'chain 'X' and resid 201 through 203' Processing helix chain 'X' and resid 205 through 209 Processing helix chain 'X' and resid 214 through 230 Processing helix chain 'X' and resid 240 through 250 Processing helix chain 'X' and resid 251 through 258 Processing helix chain 'X' and resid 271 through 276 removed outlier: 4.022A pdb=" N PHE X 275 " --> pdb=" O LEU X 271 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG X 276 " --> pdb=" O LYS X 272 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 271 through 276' Processing helix chain 'X' and resid 283 through 295 removed outlier: 3.593A pdb=" N HIS X 287 " --> pdb=" O SER X 283 " (cutoff:3.500A) Processing helix chain 'X' and resid 299 through 310 removed outlier: 3.517A pdb=" N LEU X 310 " --> pdb=" O GLN X 306 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 7 removed outlier: 5.940A pdb=" N ILE A 6 " --> pdb=" O TYR A 158 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 169 through 173 removed outlier: 7.008A pdb=" N LEU A 170 " --> pdb=" O VAL A 230 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N ASP A 232 " --> pdb=" O LEU A 170 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE A 172 " --> pdb=" O ASP A 232 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU A 229 " --> pdb=" O MET A 264 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N ILE A 266 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ILE A 231 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEU A 133 " --> pdb=" O ILE A 291 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N TRP A 293 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N ILE A 135 " --> pdb=" O TRP A 293 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 299 through 300 Processing sheet with id=AA4, first strand: chain 'B' and resid 171 through 173 removed outlier: 6.753A pdb=" N ILE B 172 " --> pdb=" O ASP B 232 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LEU B 132 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N GLY B 267 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N LEU B 134 " --> pdb=" O GLY B 267 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N LEU B 133 " --> pdb=" O ILE B 291 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N TRP B 293 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ILE B 135 " --> pdb=" O TRP B 293 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 157 through 158 Processing sheet with id=AA6, first strand: chain 'C' and resid 6 through 7 removed outlier: 6.235A pdb=" N ILE C 6 " --> pdb=" O TYR C 158 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 170 through 173 removed outlier: 6.529A pdb=" N LEU C 170 " --> pdb=" O VAL C 230 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ASP C 232 " --> pdb=" O LEU C 170 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ILE C 172 " --> pdb=" O ASP C 232 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU C 229 " --> pdb=" O MET C 264 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N ILE C 266 " --> pdb=" O LEU C 229 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE C 231 " --> pdb=" O ILE C 266 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY C 136 " --> pdb=" O GLY C 267 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N SER C 131 " --> pdb=" O GLY C 289 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N ILE C 291 " --> pdb=" O SER C 131 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEU C 133 " --> pdb=" O ILE C 291 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N TRP C 293 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE C 135 " --> pdb=" O TRP C 293 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'Y' and resid 151 through 152 Processing sheet with id=AA9, first strand: chain 'D' and resid 6 through 7 removed outlier: 6.774A pdb=" N ILE D 6 " --> pdb=" O TYR D 158 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 170 through 172 removed outlier: 5.755A pdb=" N LEU D 132 " --> pdb=" O LEU D 265 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N GLY D 267 " --> pdb=" O LEU D 132 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N LEU D 134 " --> pdb=" O GLY D 267 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE D 291 " --> pdb=" O LEU D 133 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 299 through 300 Processing sheet with id=AB3, first strand: chain 'E' and resid 5 through 7 removed outlier: 6.393A pdb=" N ILE E 6 " --> pdb=" O TYR E 158 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'E' and resid 132 through 135 removed outlier: 6.115A pdb=" N LEU E 132 " --> pdb=" O LEU E 265 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N GLY E 267 " --> pdb=" O LEU E 132 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU E 134 " --> pdb=" O GLY E 267 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 6 through 7 removed outlier: 5.979A pdb=" N ILE F 6 " --> pdb=" O TYR F 158 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 170 through 173 removed outlier: 6.262A pdb=" N LEU F 229 " --> pdb=" O MET F 264 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ILE F 266 " --> pdb=" O LEU F 229 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE F 231 " --> pdb=" O ILE F 266 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 299 through 300 Processing sheet with id=AB8, first strand: chain 'G' and resid 6 through 7 removed outlier: 6.495A pdb=" N ILE G 6 " --> pdb=" O TYR G 158 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'G' and resid 169 through 173 removed outlier: 6.490A pdb=" N LEU G 229 " --> pdb=" O MET G 264 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N ILE G 266 " --> pdb=" O LEU G 229 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE G 231 " --> pdb=" O ILE G 266 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY G 136 " --> pdb=" O GLY G 267 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N SER G 131 " --> pdb=" O GLY G 289 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N ILE G 291 " --> pdb=" O SER G 131 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU G 133 " --> pdb=" O ILE G 291 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N TRP G 293 " --> pdb=" O LEU G 133 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILE G 135 " --> pdb=" O TRP G 293 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'X' and resid 232 through 233 1153 hydrogen bonds defined for protein. 3300 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 122 hydrogen bonds 244 hydrogen bond angles 0 basepair planarities 48 basepair parallelities 83 stacking parallelities Total time for adding SS restraints: 6.09 Time building geometry restraints manager: 3.79 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: 9304 1.34 - 1.45: 5645 1.45 - 1.57: 17645 1.57 - 1.69: 224 1.69 - 1.81: 184 Bond restraints: 33002 Sorted by residual: bond pdb=" C3' DG I 39 " pdb=" C2' DG I 39 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.86e+00 bond pdb=" C3' DT I 27 " pdb=" C2' DT I 27 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.37e+00 bond pdb=" C3' DT I 25 " pdb=" C2' DT I 25 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.27e+00 bond pdb=" C3' DC H 19 " pdb=" C2' DC H 19 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.58e+00 bond pdb=" C3' DG H 21 " pdb=" C2' DG H 21 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 7.17e+00 ... (remaining 32997 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 44400 2.36 - 4.72: 608 4.72 - 7.08: 120 7.08 - 9.43: 10 9.43 - 11.79: 2 Bond angle restraints: 45140 Sorted by residual: angle pdb=" O4' DG H 28 " pdb=" C4' DG H 28 " pdb=" C3' DG H 28 " ideal model delta sigma weight residual 106.00 103.30 2.70 6.00e-01 2.78e+00 2.02e+01 angle pdb=" N3 DT H 27 " pdb=" C4 DT H 27 " pdb=" O4 DT H 27 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.94e+01 angle pdb=" N3 DT H 23 " pdb=" C4 DT H 23 " pdb=" O4 DT H 23 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.94e+01 angle pdb=" N3 DT I 14 " pdb=" C4 DT I 14 " pdb=" O4 DT I 14 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.90e+01 angle pdb=" CA PRO X 125 " pdb=" N PRO X 125 " pdb=" CD PRO X 125 " ideal model delta sigma weight residual 112.00 105.90 6.10 1.40e+00 5.10e-01 1.90e+01 ... (remaining 45135 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.45: 18729 32.45 - 64.90: 980 64.90 - 97.35: 53 97.35 - 129.80: 3 129.80 - 162.25: 6 Dihedral angle restraints: 19771 sinusoidal: 8887 harmonic: 10884 Sorted by residual: dihedral pdb=" C5' ADP D 601 " pdb=" O5' ADP D 601 " pdb=" PA ADP D 601 " pdb=" O2A ADP D 601 " ideal model delta sinusoidal sigma weight residual -60.00 102.26 -162.25 1 2.00e+01 2.50e-03 4.69e+01 dihedral pdb=" C5' ADP B 601 " pdb=" O5' ADP B 601 " pdb=" PA ADP B 601 " pdb=" O2A ADP B 601 " ideal model delta sinusoidal sigma weight residual -60.00 102.20 -162.19 1 2.00e+01 2.50e-03 4.69e+01 dihedral pdb=" C5' ADP E 601 " pdb=" O5' ADP E 601 " pdb=" PA ADP E 601 " pdb=" O2A ADP E 601 " ideal model delta sinusoidal sigma weight residual 300.00 143.69 156.32 1 2.00e+01 2.50e-03 4.60e+01 ... (remaining 19768 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 3615 0.043 - 0.086: 1123 0.086 - 0.129: 299 0.129 - 0.172: 34 0.172 - 0.215: 6 Chirality restraints: 5077 Sorted by residual: chirality pdb=" CA HIS B 383 " pdb=" N HIS B 383 " pdb=" C HIS B 383 " pdb=" CB HIS B 383 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CB ILE F 346 " pdb=" CA ILE F 346 " pdb=" CG1 ILE F 346 " pdb=" CG2 ILE F 346 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.20 2.00e-01 2.50e+01 9.93e-01 chirality pdb=" CA ARG X 114 " pdb=" N ARG X 114 " pdb=" C ARG X 114 " pdb=" CB ARG X 114 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.42e-01 ... (remaining 5074 not shown) Planarity restraints: 5440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS X 124 " 0.081 5.00e-02 4.00e+02 1.19e-01 2.26e+01 pdb=" N PRO X 125 " -0.205 5.00e-02 4.00e+02 pdb=" CA PRO X 125 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO X 125 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU X 149 " 0.055 5.00e-02 4.00e+02 8.47e-02 1.15e+01 pdb=" N PRO X 150 " -0.147 5.00e-02 4.00e+02 pdb=" CA PRO X 150 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO X 150 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP D 402 " 0.013 2.00e-02 2.50e+03 2.56e-02 6.56e+00 pdb=" CG ASP D 402 " -0.044 2.00e-02 2.50e+03 pdb=" OD1 ASP D 402 " 0.016 2.00e-02 2.50e+03 pdb=" OD2 ASP D 402 " 0.015 2.00e-02 2.50e+03 ... (remaining 5437 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 215 2.60 - 3.18: 26217 3.18 - 3.75: 48666 3.75 - 4.33: 64961 4.33 - 4.90: 107377 Nonbonded interactions: 247436 Sorted by model distance: nonbonded pdb="MG MG E 603 " pdb=" O1B ADP F 601 " model vdw 2.028 2.170 nonbonded pdb=" OG1 THR C 143 " pdb="MG MG C 602 " model vdw 2.029 2.170 nonbonded pdb=" O1B ADP E 601 " pdb="MG MG E 602 " model vdw 2.038 2.170 nonbonded pdb=" O3B ADP B 601 " pdb="MG MG B 602 " model vdw 2.045 2.170 nonbonded pdb=" O2G ATP C 601 " pdb="MG MG C 602 " model vdw 2.054 2.170 ... (remaining 247431 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 4 through 602) selection = (chain 'B' and resid 4 through 602) selection = (chain 'D' and resid 4 through 602) selection = (chain 'E' and resid 4 through 602) } ncs_group { reference = (chain 'C' and resid 3 through 403) selection = (chain 'F' and (resid 3 through 275 or resid 288 through 403)) selection = (chain 'G' and resid 3 through 403) } ncs_group { reference = (chain 'X' and (resid 1 through 309 or resid 601)) selection = chain 'Y' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.240 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: 0.830 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 35.680 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.010 Internal consistency checks: 0.000 Total: 45.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 33010 Z= 0.238 Angle : 0.706 11.792 45146 Z= 0.403 Chirality : 0.044 0.215 5077 Planarity : 0.005 0.119 5440 Dihedral : 17.624 162.253 12741 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.01 % Favored : 94.96 % Rotamer: Outliers : 0.03 % Allowed : 0.43 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.13), residues: 3712 helix: -0.30 (0.12), residues: 1821 sheet: 0.67 (0.38), residues: 199 loop : -1.32 (0.14), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 126 TYR 0.018 0.001 TYR D 337 PHE 0.030 0.002 PHE B 351 TRP 0.023 0.001 TRP B 336 HIS 0.011 0.001 HIS C 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.24 (33002) covalent geometry : angle 0.70614 / 0.40 (45140) hydrogen bonds : bond 0.16621 / 10.84 ( 1275) hydrogen bonds : angle 6.07692 / 4.44 ( 3544) metal coordination : bond 0.00900 / 0.52 ( 8) metal coordination : angle 1.29786 / 0.56 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7424 Ramachandran restraints generated. 3712 Oldfield, 0 Emsley, 3712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7424 Ramachandran restraints generated. 3712 Oldfield, 0 Emsley, 3712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 3239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 370 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 64 ARG cc_start: 0.7037 (ttm170) cc_final: 0.6644 (ttm170) REVERT: B 446 MET cc_start: 0.4426 (mpp) cc_final: 0.3673 (mpp) REVERT: D 31 GLN cc_start: 0.8035 (mp10) cc_final: 0.7827 (mp10) REVERT: E 213 MET cc_start: 0.7900 (mtm) cc_final: 0.7683 (mtm) REVERT: F 255 MET cc_start: 0.8250 (ttp) cc_final: 0.8048 (ttm) REVERT: G 357 ARG cc_start: 0.6719 (ttt180) cc_final: 0.6502 (ttt180) outliers start: 1 outliers final: 0 residues processed: 370 average time/residue: 0.2056 time to fit residues: 123.6616 Evaluate side-chains 264 residues out of total 3239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 0.8980 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 481 GLN C 219 GLN C 297 GLN C 306 GLN ** C 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 383 HIS ** Y 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 355 GLN D 376 GLN ** E 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 341 GLN ** G 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 383 HIS X 305 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.221988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.200954 restraints weight = 40081.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.198195 restraints weight = 73986.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.195528 restraints weight = 66052.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.194535 restraints weight = 66855.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.193442 restraints weight = 57439.258| |-----------------------------------------------------------------------------| r_work (final): 0.4207 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4207 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4207 r_free = 0.4207 target_work(ls_wunit_k1) = 0.190 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4207 r_free = 0.4207 target_work(ls_wunit_k1) = 0.190 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.4207 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.1110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.110 33010 Z= 0.278 Angle : 0.758 12.990 45146 Z= 0.383 Chirality : 0.046 0.229 5077 Planarity : 0.006 0.081 5440 Dihedral : 17.360 172.827 5355 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.90 % Favored : 95.02 % Rotamer: Outliers : 1.11 % Allowed : 9.26 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.13), residues: 3712 helix: -0.32 (0.12), residues: 1836 sheet: 0.09 (0.39), residues: 176 loop : -1.50 (0.14), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 357 TYR 0.028 0.002 TYR E 337 PHE 0.025 0.003 PHE Y 4 TRP 0.018 0.002 TRP E 336 HIS 0.009 0.002 HIS F 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00669 / 0.28 (33002) covalent geometry : angle 0.75823 / 0.38 (45140) hydrogen bonds : bond 0.05470 / 3.68 ( 1275) hydrogen bonds : angle 4.97170 / 3.62 ( 3544) metal coordination : bond 0.01447 / 0.93 ( 8) metal coordination : angle 1.06861 / 0.63 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7424 Ramachandran restraints generated. 3712 Oldfield, 0 Emsley, 3712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7424 Ramachandran restraints generated. 3712 Oldfield, 0 Emsley, 3712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 3239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 290 time to evaluate : 0.800 Fit side-chains REVERT: B 61 THR cc_start: 0.7499 (t) cc_final: 0.7178 (m) REVERT: B 470 MET cc_start: -0.0548 (ptp) cc_final: -0.0767 (pmm) REVERT: C 192 ASP cc_start: 0.7546 (p0) cc_final: 0.7343 (p0) REVERT: D 444 TYR cc_start: 0.5098 (t80) cc_final: 0.4822 (t80) REVERT: D 484 MET cc_start: 0.3837 (mpp) cc_final: 0.2259 (tmm) REVERT: E 222 ASN cc_start: 0.7427 (OUTLIER) cc_final: 0.7108 (m-40) REVERT: E 470 MET cc_start: 0.1614 (OUTLIER) cc_final: 0.1020 (ptt) REVERT: G 357 ARG cc_start: 0.6805 (ttt180) cc_final: 0.6566 (ttt180) outliers start: 36 outliers final: 24 residues processed: 309 average time/residue: 0.2016 time to fit residues: 100.8461 Evaluate side-chains 283 residues out of total 3239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 257 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain Y residue 45 THR Chi-restraints excluded: chain Y residue 159 VAL Chi-restraints excluded: chain D residue 137 CYS Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 222 ASN Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 329 SER Chi-restraints excluded: chain E residue 336 TRP Chi-restraints excluded: chain E residue 401 SER Chi-restraints excluded: chain E residue 470 MET Chi-restraints excluded: chain E residue 475 LEU Chi-restraints excluded: chain F residue 248 MET Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain X residue 45 THR Chi-restraints excluded: chain X residue 177 HIS Chi-restraints excluded: chain X residue 193 THR Chi-restraints excluded: chain X residue 295 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 227 optimal weight: 0.6980 chunk 360 optimal weight: 0.9990 chunk 259 optimal weight: 30.0000 chunk 313 optimal weight: 4.9990 chunk 87 optimal weight: 0.0980 chunk 35 optimal weight: 20.0000 chunk 357 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 280 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 152 optimal weight: 4.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 7 GLN C 236 HIS C 297 GLN C 306 GLN ** C 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 440 GLN ** E 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 305 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.226326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.207535 restraints weight = 39961.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.204219 restraints weight = 68549.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.202318 restraints weight = 71929.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.201530 restraints weight = 70557.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.200627 restraints weight = 64883.883| |-----------------------------------------------------------------------------| r_work (final): 0.4302 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4302 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4302 r_free = 0.4302 target_work(ls_wunit_k1) = 0.200 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4302 r_free = 0.4302 target_work(ls_wunit_k1) = 0.200 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4302 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 33010 Z= 0.118 Angle : 0.598 9.067 45146 Z= 0.302 Chirality : 0.040 0.187 5077 Planarity : 0.004 0.059 5440 Dihedral : 17.144 179.802 5355 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.72 % Favored : 96.23 % Rotamer: Outliers : 1.48 % Allowed : 11.42 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.14), residues: 3712 helix: -0.01 (0.13), residues: 1822 sheet: 0.30 (0.39), residues: 180 loop : -1.35 (0.14), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 357 TYR 0.030 0.002 TYR A 158 PHE 0.015 0.001 PHE B 351 TRP 0.015 0.001 TRP E 336 HIS 0.009 0.001 HIS G 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (33002) covalent geometry : angle 0.59764 / 0.30 (45140) hydrogen bonds : bond 0.03919 / 2.60 ( 1275) hydrogen bonds : angle 4.57040 / 3.33 ( 3544) metal coordination : bond 0.00556 / 0.36 ( 8) metal coordination : angle 0.69155 / 0.42 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7424 Ramachandran restraints generated. 3712 Oldfield, 0 Emsley, 3712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7424 Ramachandran restraints generated. 3712 Oldfield, 0 Emsley, 3712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 3239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 288 time to evaluate : 1.166 Fit side-chains revert: symmetry clash REVERT: A 77 LEU cc_start: 0.5257 (OUTLIER) cc_final: 0.5046 (tp) REVERT: B 61 THR cc_start: 0.7502 (t) cc_final: 0.7179 (m) REVERT: B 470 MET cc_start: -0.0571 (ptp) cc_final: -0.0788 (pmm) REVERT: C 192 ASP cc_start: 0.7329 (p0) cc_final: 0.7051 (p0) REVERT: D 444 TYR cc_start: 0.5054 (t80) cc_final: 0.4749 (t80) REVERT: E 470 MET cc_start: 0.1835 (OUTLIER) cc_final: 0.1371 (ptt) REVERT: G 357 ARG cc_start: 0.6793 (ttt180) cc_final: 0.6556 (ttt180) outliers start: 48 outliers final: 29 residues processed: 321 average time/residue: 0.1967 time to fit residues: 104.1530 Evaluate side-chains 293 residues out of total 3239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 262 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain Y residue 159 VAL Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 329 SER Chi-restraints excluded: chain E residue 336 TRP Chi-restraints excluded: chain E residue 401 SER Chi-restraints excluded: chain E residue 446 MET Chi-restraints excluded: chain E residue 470 MET Chi-restraints excluded: chain F residue 248 MET Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 403 LEU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain X residue 45 THR Chi-restraints excluded: chain X residue 177 HIS Chi-restraints excluded: chain X residue 295 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 332 optimal weight: 0.4980 chunk 21 optimal weight: 10.0000 chunk 209 optimal weight: 9.9990 chunk 264 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 chunk 43 optimal weight: 20.0000 chunk 300 optimal weight: 9.9990 chunk 245 optimal weight: 10.0000 chunk 47 optimal weight: 20.0000 chunk 347 optimal weight: 3.9990 chunk 295 optimal weight: 0.6980 overall best weight: 3.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 7 GLN C 222 ASN C 297 GLN ** C 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 355 GLN F 208 HIS ** G 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 305 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.219663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.199276 restraints weight = 39814.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.195404 restraints weight = 65891.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.192549 restraints weight = 72150.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.191747 restraints weight = 70422.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.190217 restraints weight = 61934.009| |-----------------------------------------------------------------------------| r_work (final): 0.4175 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4175 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4175 r_free = 0.4175 target_work(ls_wunit_k1) = 0.187 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4175 r_free = 0.4175 target_work(ls_wunit_k1) = 0.187 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4175 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.075 33010 Z= 0.311 Angle : 0.767 13.421 45146 Z= 0.387 Chirality : 0.047 0.250 5077 Planarity : 0.005 0.058 5440 Dihedral : 17.407 172.902 5355 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.79 % Favored : 94.13 % Rotamer: Outliers : 2.10 % Allowed : 14.05 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.13), residues: 3712 helix: -0.28 (0.12), residues: 1850 sheet: -0.32 (0.38), residues: 176 loop : -1.62 (0.14), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 82 TYR 0.034 0.003 TYR A 91 PHE 0.028 0.003 PHE Y 4 TRP 0.019 0.002 TRP E 336 HIS 0.010 0.002 HIS G 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00764 / 0.31 (33002) covalent geometry : angle 0.76708 / 0.39 (45140) hydrogen bonds : bond 0.05134 / 3.47 ( 1275) hydrogen bonds : angle 4.76038 / 3.45 ( 3544) metal coordination : bond 0.02176 / 1.34 ( 8) metal coordination : angle 2.13073 / 1.23 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7424 Ramachandran restraints generated. 3712 Oldfield, 0 Emsley, 3712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7424 Ramachandran restraints generated. 3712 Oldfield, 0 Emsley, 3712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 3239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 270 time to evaluate : 1.266 Fit side-chains REVERT: C 192 ASP cc_start: 0.7783 (p0) cc_final: 0.7449 (p0) REVERT: C 220 ILE cc_start: 0.8524 (OUTLIER) cc_final: 0.8262 (tp) REVERT: C 344 MET cc_start: 0.6493 (mmm) cc_final: 0.6226 (mmt) REVERT: D 444 TYR cc_start: 0.5372 (t80) cc_final: 0.4885 (t80) REVERT: D 484 MET cc_start: 0.3728 (mpp) cc_final: 0.2133 (tmm) REVERT: E 470 MET cc_start: 0.1849 (OUTLIER) cc_final: 0.1350 (ptt) REVERT: F 361 LEU cc_start: 0.7531 (OUTLIER) cc_final: 0.7075 (mp) REVERT: G 161 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7636 (mm-30) REVERT: G 357 ARG cc_start: 0.6793 (ttt180) cc_final: 0.6554 (ttt180) outliers start: 68 outliers final: 40 residues processed: 314 average time/residue: 0.2007 time to fit residues: 103.3237 Evaluate side-chains 300 residues out of total 3239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 257 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain B residue 224 HIS Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain Y residue 159 VAL Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 329 SER Chi-restraints excluded: chain E residue 336 TRP Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 401 SER Chi-restraints excluded: chain E residue 413 ILE Chi-restraints excluded: chain E residue 470 MET Chi-restraints excluded: chain E residue 475 LEU Chi-restraints excluded: chain F residue 248 MET Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 231 ILE Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 261 VAL Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain X residue 45 THR Chi-restraints excluded: chain X residue 95 LEU Chi-restraints excluded: chain X residue 177 HIS Chi-restraints excluded: chain X residue 193 THR Chi-restraints excluded: chain X residue 300 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 195 optimal weight: 0.5980 chunk 369 optimal weight: 6.9990 chunk 222 optimal weight: 0.1980 chunk 122 optimal weight: 0.8980 chunk 20 optimal weight: 8.9990 chunk 185 optimal weight: 3.9990 chunk 38 optimal weight: 8.9990 chunk 322 optimal weight: 1.9990 chunk 204 optimal weight: 4.9990 chunk 269 optimal weight: 0.5980 chunk 143 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 222 ASN C 297 GLN ** C 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 GLN E 355 GLN ** F 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 305 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4780 r_free = 0.4780 target = 0.235746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.216283 restraints weight = 40858.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.213528 restraints weight = 70459.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.211820 restraints weight = 57833.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.209897 restraints weight = 68400.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.207686 restraints weight = 66390.082| |-----------------------------------------------------------------------------| r_work (final): 0.4519 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4519 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4519 r_free = 0.4519 target_work(ls_wunit_k1) = 0.207 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4519 r_free = 0.4519 target_work(ls_wunit_k1) = 0.207 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4519 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 33010 Z= 0.124 Angle : 0.610 11.384 45146 Z= 0.307 Chirality : 0.041 0.214 5077 Planarity : 0.004 0.057 5440 Dihedral : 17.155 166.627 5355 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.88 % Favored : 96.07 % Rotamer: Outliers : 1.91 % Allowed : 15.25 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.14), residues: 3712 helix: -0.02 (0.13), residues: 1834 sheet: -0.02 (0.39), residues: 180 loop : -1.45 (0.14), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 239 TYR 0.030 0.001 TYR A 91 PHE 0.014 0.001 PHE X 161 TRP 0.017 0.001 TRP E 336 HIS 0.005 0.001 HIS G 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (33002) covalent geometry : angle 0.60979 / 0.31 (45140) hydrogen bonds : bond 0.03738 / 2.49 ( 1275) hydrogen bonds : angle 4.48379 / 3.27 ( 3544) metal coordination : bond 0.00718 / 0.44 ( 8) metal coordination : angle 1.10688 / 0.66 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7424 Ramachandran restraints generated. 3712 Oldfield, 0 Emsley, 3712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7424 Ramachandran restraints generated. 3712 Oldfield, 0 Emsley, 3712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 3239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 288 time to evaluate : 1.203 Fit side-chains revert: symmetry clash REVERT: A 408 ILE cc_start: 0.4961 (tp) cc_final: 0.4411 (tt) REVERT: B 61 THR cc_start: 0.7595 (t) cc_final: 0.7253 (m) REVERT: B 470 MET cc_start: 0.0131 (pmm) cc_final: -0.0752 (pmm) REVERT: C 192 ASP cc_start: 0.7483 (p0) cc_final: 0.7193 (p0) REVERT: D 61 THR cc_start: 0.4901 (m) cc_final: 0.4622 (m) REVERT: D 220 ILE cc_start: 0.7804 (mt) cc_final: 0.7578 (mt) REVERT: D 444 TYR cc_start: 0.5329 (t80) cc_final: 0.4894 (t80) REVERT: D 484 MET cc_start: 0.3994 (mpp) cc_final: 0.2214 (tmm) REVERT: E 470 MET cc_start: 0.1899 (OUTLIER) cc_final: 0.1407 (ptt) REVERT: G 357 ARG cc_start: 0.6794 (ttt180) cc_final: 0.6569 (ttt180) outliers start: 62 outliers final: 39 residues processed: 331 average time/residue: 0.2043 time to fit residues: 111.2384 Evaluate side-chains 306 residues out of total 3239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 266 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain B residue 224 HIS Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 213 MET Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain Y residue 159 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 329 SER Chi-restraints excluded: chain E residue 336 TRP Chi-restraints excluded: chain E residue 355 GLN Chi-restraints excluded: chain E residue 401 SER Chi-restraints excluded: chain E residue 470 MET Chi-restraints excluded: chain F residue 248 MET Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 403 LEU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain X residue 16 THR Chi-restraints excluded: chain X residue 45 THR Chi-restraints excluded: chain X residue 60 HIS Chi-restraints excluded: chain X residue 95 LEU Chi-restraints excluded: chain X residue 177 HIS Chi-restraints excluded: chain X residue 300 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 192 optimal weight: 6.9990 chunk 378 optimal weight: 20.0000 chunk 268 optimal weight: 2.9990 chunk 121 optimal weight: 0.1980 chunk 27 optimal weight: 3.9990 chunk 377 optimal weight: 10.0000 chunk 276 optimal weight: 0.5980 chunk 290 optimal weight: 3.9990 chunk 189 optimal weight: 8.9990 chunk 182 optimal weight: 20.0000 chunk 104 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 71 GLN C 222 ASN C 297 GLN C 306 GLN ** C 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 355 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4763 r_free = 0.4763 target = 0.233658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.213466 restraints weight = 40621.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.210829 restraints weight = 76830.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.208960 restraints weight = 64131.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.207404 restraints weight = 68816.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.205687 restraints weight = 66832.144| |-----------------------------------------------------------------------------| r_work (final): 0.4498 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4498 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4498 r_free = 0.4498 target_work(ls_wunit_k1) = 0.205 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4498 r_free = 0.4498 target_work(ls_wunit_k1) = 0.205 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4498 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.157 33010 Z= 0.191 Angle : 0.651 12.481 45146 Z= 0.327 Chirality : 0.042 0.184 5077 Planarity : 0.004 0.057 5440 Dihedral : 17.172 163.671 5355 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.01 % Favored : 94.94 % Rotamer: Outliers : 2.07 % Allowed : 15.71 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.14), residues: 3712 helix: -0.06 (0.13), residues: 1843 sheet: -0.09 (0.39), residues: 174 loop : -1.47 (0.14), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 239 TYR 0.026 0.002 TYR A 91 PHE 0.019 0.002 PHE E 351 TRP 0.019 0.001 TRP E 336 HIS 0.008 0.001 HIS X 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.19 (33002) covalent geometry : angle 0.65046 / 0.33 (45140) hydrogen bonds : bond 0.04099 / 2.75 ( 1275) hydrogen bonds : angle 4.49889 / 3.27 ( 3544) metal coordination : bond 0.01266 / 0.77 ( 8) metal coordination : angle 1.58222 / 0.93 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7424 Ramachandran restraints generated. 3712 Oldfield, 0 Emsley, 3712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7424 Ramachandran restraints generated. 3712 Oldfield, 0 Emsley, 3712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 276 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 408 ILE cc_start: 0.4967 (tp) cc_final: 0.4450 (tt) REVERT: B 50 ASP cc_start: 0.4776 (OUTLIER) cc_final: 0.4538 (t0) REVERT: B 61 THR cc_start: 0.7630 (t) cc_final: 0.7292 (m) REVERT: B 470 MET cc_start: 0.0082 (pmm) cc_final: -0.0685 (pmm) REVERT: C 102 GLN cc_start: 0.7566 (OUTLIER) cc_final: 0.7362 (mt0) REVERT: C 192 ASP cc_start: 0.7561 (p0) cc_final: 0.7288 (p0) REVERT: D 61 THR cc_start: 0.4936 (m) cc_final: 0.4656 (m) REVERT: D 220 ILE cc_start: 0.7873 (mt) cc_final: 0.7638 (mt) REVERT: D 444 TYR cc_start: 0.5341 (t80) cc_final: 0.4881 (t80) REVERT: E 52 GLN cc_start: 0.7502 (OUTLIER) cc_final: 0.7160 (pt0) REVERT: E 470 MET cc_start: 0.2023 (OUTLIER) cc_final: 0.1561 (ptt) REVERT: F 361 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.6913 (mp) REVERT: G 357 ARG cc_start: 0.6793 (ttt180) cc_final: 0.6567 (ttt180) outliers start: 67 outliers final: 49 residues processed: 322 average time/residue: 0.2051 time to fit residues: 108.3811 Evaluate side-chains 321 residues out of total 3239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 267 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain B residue 224 HIS Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 102 GLN Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 213 MET Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain Y residue 45 THR Chi-restraints excluded: chain Y residue 96 MET Chi-restraints excluded: chain Y residue 130 LEU Chi-restraints excluded: chain Y residue 159 VAL Chi-restraints excluded: chain Y residue 162 ASP Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain E residue 52 GLN Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 329 SER Chi-restraints excluded: chain E residue 336 TRP Chi-restraints excluded: chain E residue 401 SER Chi-restraints excluded: chain E residue 470 MET Chi-restraints excluded: chain E residue 475 LEU Chi-restraints excluded: chain F residue 248 MET Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 346 ILE Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain F residue 403 LEU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 231 ILE Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain X residue 16 THR Chi-restraints excluded: chain X residue 45 THR Chi-restraints excluded: chain X residue 60 HIS Chi-restraints excluded: chain X residue 95 LEU Chi-restraints excluded: chain X residue 177 HIS Chi-restraints excluded: chain X residue 300 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 102 optimal weight: 0.0010 chunk 352 optimal weight: 2.9990 chunk 169 optimal weight: 7.9990 chunk 133 optimal weight: 6.9990 chunk 279 optimal weight: 0.8980 chunk 161 optimal weight: 8.9990 chunk 339 optimal weight: 10.0000 chunk 136 optimal weight: 1.9990 chunk 220 optimal weight: 0.6980 chunk 45 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 overall best weight: 1.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4774 r_free = 0.4774 target = 0.235042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.215011 restraints weight = 40936.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.211529 restraints weight = 73681.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.209153 restraints weight = 72882.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.208415 restraints weight = 72441.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.207589 restraints weight = 60368.471| |-----------------------------------------------------------------------------| r_work (final): 0.4519 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4519 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4519 r_free = 0.4519 target_work(ls_wunit_k1) = 0.207 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4519 r_free = 0.4519 target_work(ls_wunit_k1) = 0.207 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4519 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 33010 Z= 0.140 Angle : 0.615 11.633 45146 Z= 0.309 Chirality : 0.041 0.177 5077 Planarity : 0.004 0.057 5440 Dihedral : 17.085 166.529 5355 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.15 % Favored : 95.77 % Rotamer: Outliers : 2.04 % Allowed : 16.58 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.14), residues: 3712 helix: 0.04 (0.13), residues: 1838 sheet: 0.03 (0.39), residues: 176 loop : -1.39 (0.14), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 201 TYR 0.028 0.001 TYR D 337 PHE 0.017 0.001 PHE X 221 TRP 0.018 0.001 TRP E 336 HIS 0.011 0.001 HIS Y 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (33002) covalent geometry : angle 0.61465 / 0.31 (45140) hydrogen bonds : bond 0.03691 / 2.46 ( 1275) hydrogen bonds : angle 4.41232 / 3.20 ( 3544) metal coordination : bond 0.00823 / 0.49 ( 8) metal coordination : angle 1.27275 / 0.75 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7424 Ramachandran restraints generated. 3712 Oldfield, 0 Emsley, 3712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7424 Ramachandran restraints generated. 3712 Oldfield, 0 Emsley, 3712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 3239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 278 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 408 ILE cc_start: 0.4974 (tp) cc_final: 0.4489 (tt) REVERT: B 50 ASP cc_start: 0.4727 (OUTLIER) cc_final: 0.4484 (t0) REVERT: B 61 THR cc_start: 0.7600 (t) cc_final: 0.7259 (m) REVERT: B 470 MET cc_start: -0.0085 (pmm) cc_final: -0.0744 (pmm) REVERT: C 102 GLN cc_start: 0.7470 (OUTLIER) cc_final: 0.7262 (mt0) REVERT: C 192 ASP cc_start: 0.7490 (p0) cc_final: 0.7207 (p0) REVERT: D 61 THR cc_start: 0.4863 (m) cc_final: 0.4599 (m) REVERT: D 220 ILE cc_start: 0.7864 (mt) cc_final: 0.7637 (mt) REVERT: D 444 TYR cc_start: 0.5324 (t80) cc_final: 0.4825 (t80) REVERT: E 52 GLN cc_start: 0.7494 (OUTLIER) cc_final: 0.7154 (pt0) REVERT: E 470 MET cc_start: 0.1960 (OUTLIER) cc_final: 0.1536 (ptt) REVERT: E 475 LEU cc_start: 0.2069 (OUTLIER) cc_final: 0.1675 (tp) REVERT: G 357 ARG cc_start: 0.6783 (ttt180) cc_final: 0.6573 (ttt180) outliers start: 66 outliers final: 49 residues processed: 321 average time/residue: 0.2065 time to fit residues: 109.0520 Evaluate side-chains 323 residues out of total 3239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 269 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 470 MET Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain B residue 224 HIS Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 102 GLN Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 213 MET Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain Y residue 45 THR Chi-restraints excluded: chain Y residue 130 LEU Chi-restraints excluded: chain Y residue 159 VAL Chi-restraints excluded: chain Y residue 162 ASP Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain E residue 52 GLN Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 329 SER Chi-restraints excluded: chain E residue 336 TRP Chi-restraints excluded: chain E residue 401 SER Chi-restraints excluded: chain E residue 470 MET Chi-restraints excluded: chain E residue 475 LEU Chi-restraints excluded: chain F residue 248 MET Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 403 LEU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 231 ILE Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 397 ILE Chi-restraints excluded: chain X residue 16 THR Chi-restraints excluded: chain X residue 45 THR Chi-restraints excluded: chain X residue 60 HIS Chi-restraints excluded: chain X residue 95 LEU Chi-restraints excluded: chain X residue 177 HIS Chi-restraints excluded: chain X residue 239 HIS Chi-restraints excluded: chain X residue 300 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 366 optimal weight: 5.9990 chunk 170 optimal weight: 9.9990 chunk 10 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 chunk 342 optimal weight: 2.9990 chunk 304 optimal weight: 10.0000 chunk 167 optimal weight: 0.9990 chunk 59 optimal weight: 6.9990 chunk 79 optimal weight: 0.9980 chunk 260 optimal weight: 20.0000 chunk 23 optimal weight: 7.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 319 GLN C 297 GLN ** C 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 GLN F 198 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4732 r_free = 0.4732 target = 0.230357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.211868 restraints weight = 40758.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.207496 restraints weight = 105467.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.203400 restraints weight = 52535.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.201555 restraints weight = 51957.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.201415 restraints weight = 31749.629| |-----------------------------------------------------------------------------| r_work (final): 0.4415 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4414 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4414 r_free = 0.4414 target_work(ls_wunit_k1) = 0.196 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4414 r_free = 0.4414 target_work(ls_wunit_k1) = 0.196 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4414 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 33010 Z= 0.271 Angle : 0.741 14.318 45146 Z= 0.372 Chirality : 0.046 0.229 5077 Planarity : 0.005 0.062 5440 Dihedral : 17.324 161.977 5355 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.95 % Favored : 93.97 % Rotamer: Outliers : 2.62 % Allowed : 16.73 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.13), residues: 3712 helix: -0.17 (0.12), residues: 1821 sheet: -0.43 (0.38), residues: 179 loop : -1.59 (0.14), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 201 TYR 0.029 0.002 TYR D 337 PHE 0.026 0.002 PHE Y 4 TRP 0.032 0.002 TRP A 336 HIS 0.010 0.001 HIS G 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00661 / 0.27 (33002) covalent geometry : angle 0.74072 / 0.37 (45140) hydrogen bonds : bond 0.04845 / 3.26 ( 1275) hydrogen bonds : angle 4.66308 / 3.37 ( 3544) metal coordination : bond 0.02110 / 1.29 ( 8) metal coordination : angle 2.50158 / 1.47 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7424 Ramachandran restraints generated. 3712 Oldfield, 0 Emsley, 3712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7424 Ramachandran restraints generated. 3712 Oldfield, 0 Emsley, 3712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 3239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 271 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 408 ILE cc_start: 0.5228 (tp) cc_final: 0.4727 (tt) REVERT: B 50 ASP cc_start: 0.5049 (OUTLIER) cc_final: 0.4655 (t0) REVERT: B 61 THR cc_start: 0.7786 (t) cc_final: 0.7444 (m) REVERT: C 102 GLN cc_start: 0.7735 (OUTLIER) cc_final: 0.7507 (mt0) REVERT: C 220 ILE cc_start: 0.8566 (OUTLIER) cc_final: 0.8300 (tp) REVERT: D 61 THR cc_start: 0.5027 (m) cc_final: 0.4736 (m) REVERT: D 484 MET cc_start: 0.4764 (mpp) cc_final: 0.2457 (tpt) REVERT: E 44 LEU cc_start: 0.7370 (OUTLIER) cc_final: 0.6815 (mp) REVERT: E 52 GLN cc_start: 0.7593 (OUTLIER) cc_final: 0.7204 (pt0) REVERT: E 470 MET cc_start: 0.2170 (OUTLIER) cc_final: 0.1541 (ptt) REVERT: E 475 LEU cc_start: 0.2539 (OUTLIER) cc_final: 0.1971 (tp) REVERT: F 314 ASN cc_start: 0.7386 (t0) cc_final: 0.7096 (t0) REVERT: F 361 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7058 (mp) REVERT: G 357 ARG cc_start: 0.6796 (ttt180) cc_final: 0.6566 (ttt180) outliers start: 85 outliers final: 60 residues processed: 331 average time/residue: 0.2125 time to fit residues: 114.8123 Evaluate side-chains 323 residues out of total 3239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 255 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 95 ASN Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain B residue 224 HIS Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 102 GLN Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 213 MET Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain Y residue 45 THR Chi-restraints excluded: chain Y residue 96 MET Chi-restraints excluded: chain Y residue 130 LEU Chi-restraints excluded: chain Y residue 159 VAL Chi-restraints excluded: chain Y residue 162 ASP Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 52 GLN Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 327 LEU Chi-restraints excluded: chain E residue 329 SER Chi-restraints excluded: chain E residue 336 TRP Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 401 SER Chi-restraints excluded: chain E residue 413 ILE Chi-restraints excluded: chain E residue 470 MET Chi-restraints excluded: chain E residue 475 LEU Chi-restraints excluded: chain F residue 248 MET Chi-restraints excluded: chain F residue 254 THR Chi-restraints excluded: chain F residue 261 VAL Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 231 ILE Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 367 THR Chi-restraints excluded: chain X residue 16 THR Chi-restraints excluded: chain X residue 45 THR Chi-restraints excluded: chain X residue 60 HIS Chi-restraints excluded: chain X residue 95 LEU Chi-restraints excluded: chain X residue 177 HIS Chi-restraints excluded: chain X residue 193 THR Chi-restraints excluded: chain X residue 239 HIS Chi-restraints excluded: chain X residue 300 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 34 optimal weight: 8.9990 chunk 301 optimal weight: 1.9990 chunk 181 optimal weight: 4.9990 chunk 251 optimal weight: 0.9990 chunk 338 optimal weight: 5.9990 chunk 89 optimal weight: 9.9990 chunk 331 optimal weight: 3.9990 chunk 355 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 chunk 121 optimal weight: 0.6980 chunk 106 optimal weight: 4.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 306 GLN ** C 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 198 ASN ** F 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4760 r_free = 0.4760 target = 0.237682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.216999 restraints weight = 41053.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.213042 restraints weight = 105104.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.209463 restraints weight = 48871.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.207320 restraints weight = 52365.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.207435 restraints weight = 29755.561| |-----------------------------------------------------------------------------| r_work (final): 0.4408 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4408 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4408 r_free = 0.4408 target_work(ls_wunit_k1) = 0.196 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4408 r_free = 0.4408 target_work(ls_wunit_k1) = 0.196 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4408 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 33010 Z= 0.216 Angle : 0.699 13.344 45146 Z= 0.352 Chirality : 0.044 0.201 5077 Planarity : 0.005 0.058 5440 Dihedral : 17.249 161.688 5355 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.28 % Favored : 94.67 % Rotamer: Outliers : 2.28 % Allowed : 17.44 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.13), residues: 3712 helix: -0.17 (0.12), residues: 1836 sheet: -0.43 (0.38), residues: 181 loop : -1.55 (0.14), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 201 TYR 0.029 0.002 TYR A 337 PHE 0.021 0.002 PHE Y 4 TRP 0.025 0.002 TRP D 336 HIS 0.008 0.001 HIS E 442 Details of bonding type rmsd/Z covalent geometry : bond 0.00524 / 0.22 (33002) covalent geometry : angle 0.69850 / 0.35 (45140) hydrogen bonds : bond 0.04380 / 2.95 ( 1275) hydrogen bonds : angle 4.62756 / 3.35 ( 3544) metal coordination : bond 0.01592 / 0.99 ( 8) metal coordination : angle 2.04011 / 1.20 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7424 Ramachandran restraints generated. 3712 Oldfield, 0 Emsley, 3712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7424 Ramachandran restraints generated. 3712 Oldfield, 0 Emsley, 3712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 263 time to evaluate : 1.267 Fit side-chains revert: symmetry clash REVERT: A 344 MET cc_start: 0.4913 (mmt) cc_final: 0.3870 (tpp) REVERT: A 408 ILE cc_start: 0.5301 (tp) cc_final: 0.4824 (tt) REVERT: B 50 ASP cc_start: 0.5171 (OUTLIER) cc_final: 0.4769 (t0) REVERT: B 61 THR cc_start: 0.7913 (t) cc_final: 0.7577 (m) REVERT: B 484 MET cc_start: 0.5391 (mpp) cc_final: 0.2583 (mtp) REVERT: C 102 GLN cc_start: 0.7634 (OUTLIER) cc_final: 0.7420 (mt0) REVERT: D 61 THR cc_start: 0.5158 (m) cc_final: 0.4880 (m) REVERT: D 268 THR cc_start: 0.6928 (OUTLIER) cc_final: 0.6657 (t) REVERT: D 444 TYR cc_start: 0.5369 (t80) cc_final: 0.4946 (t80) REVERT: D 484 MET cc_start: 0.4790 (mpp) cc_final: 0.2475 (tpt) REVERT: E 44 LEU cc_start: 0.7369 (OUTLIER) cc_final: 0.6910 (mp) REVERT: E 52 GLN cc_start: 0.7598 (OUTLIER) cc_final: 0.7219 (pt0) REVERT: E 470 MET cc_start: 0.2236 (OUTLIER) cc_final: 0.1625 (ptt) REVERT: E 475 LEU cc_start: 0.2632 (OUTLIER) cc_final: 0.2132 (tp) REVERT: F 361 LEU cc_start: 0.7496 (OUTLIER) cc_final: 0.7007 (mp) REVERT: G 357 ARG cc_start: 0.6818 (ttt180) cc_final: 0.6583 (ttt180) outliers start: 74 outliers final: 56 residues processed: 315 average time/residue: 0.2023 time to fit residues: 104.7619 Evaluate side-chains 320 residues out of total 3239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 256 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain B residue 224 HIS Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 102 GLN Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 213 MET Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain Y residue 45 THR Chi-restraints excluded: chain Y residue 96 MET Chi-restraints excluded: chain Y residue 159 VAL Chi-restraints excluded: chain Y residue 162 ASP Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 52 GLN Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 327 LEU Chi-restraints excluded: chain E residue 329 SER Chi-restraints excluded: chain E residue 336 TRP Chi-restraints excluded: chain E residue 401 SER Chi-restraints excluded: chain E residue 470 MET Chi-restraints excluded: chain E residue 475 LEU Chi-restraints excluded: chain F residue 248 MET Chi-restraints excluded: chain F residue 254 THR Chi-restraints excluded: chain F residue 261 VAL Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 343 VAL Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 231 ILE Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 367 THR Chi-restraints excluded: chain X residue 16 THR Chi-restraints excluded: chain X residue 45 THR Chi-restraints excluded: chain X residue 60 HIS Chi-restraints excluded: chain X residue 95 LEU Chi-restraints excluded: chain X residue 177 HIS Chi-restraints excluded: chain X residue 193 THR Chi-restraints excluded: chain X residue 239 HIS Chi-restraints excluded: chain X residue 300 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 8 optimal weight: 4.9990 chunk 379 optimal weight: 40.0000 chunk 107 optimal weight: 5.9990 chunk 367 optimal weight: 10.0000 chunk 201 optimal weight: 0.3980 chunk 286 optimal weight: 0.8980 chunk 245 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 288 optimal weight: 0.9990 chunk 135 optimal weight: 0.9990 chunk 301 optimal weight: 1.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 7 GLN C 297 GLN C 306 GLN ** C 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 198 ASN ** F 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 305 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4749 r_free = 0.4749 target = 0.232279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.212741 restraints weight = 40823.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.208912 restraints weight = 72929.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.206463 restraints weight = 74498.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.205595 restraints weight = 75858.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.204879 restraints weight = 58826.806| |-----------------------------------------------------------------------------| r_work (final): 0.4491 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4491 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4491 r_free = 0.4491 target_work(ls_wunit_k1) = 0.204 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4491 r_free = 0.4491 target_work(ls_wunit_k1) = 0.204 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4491 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.174 33010 Z= 0.190 Angle : 0.795 59.197 45146 Z= 0.418 Chirality : 0.043 0.182 5077 Planarity : 0.005 0.057 5440 Dihedral : 17.245 162.031 5355 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.36 % Favored : 94.56 % Rotamer: Outliers : 2.25 % Allowed : 17.57 % Favored : 80.18 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.13), residues: 3712 helix: -0.15 (0.12), residues: 1836 sheet: -0.41 (0.38), residues: 181 loop : -1.55 (0.14), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG B 272 TYR 0.027 0.002 TYR A 337 PHE 0.020 0.002 PHE Y 4 TRP 0.023 0.001 TRP D 336 HIS 0.006 0.001 HIS G 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.19 (33002) covalent geometry : angle 0.79486 / 0.42 (45140) hydrogen bonds : bond 0.04293 / 2.89 ( 1275) hydrogen bonds : angle 4.63051 / 3.35 ( 3544) metal coordination : bond 0.01401 / 0.86 ( 8) metal coordination : angle 2.08802 / 1.23 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7424 Ramachandran restraints generated. 3712 Oldfield, 0 Emsley, 3712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7424 Ramachandran restraints generated. 3712 Oldfield, 0 Emsley, 3712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 3239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 256 time to evaluate : 1.210 Fit side-chains revert: symmetry clash REVERT: A 344 MET cc_start: 0.4755 (mmt) cc_final: 0.3917 (tpp) REVERT: A 408 ILE cc_start: 0.5070 (tp) cc_final: 0.4612 (tt) REVERT: B 50 ASP cc_start: 0.4831 (OUTLIER) cc_final: 0.4446 (t0) REVERT: B 61 THR cc_start: 0.7747 (t) cc_final: 0.7411 (m) REVERT: B 484 MET cc_start: 0.5209 (mpp) cc_final: 0.2431 (mtp) REVERT: C 102 GLN cc_start: 0.7611 (OUTLIER) cc_final: 0.7384 (mt0) REVERT: D 61 THR cc_start: 0.5097 (m) cc_final: 0.4838 (m) REVERT: D 268 THR cc_start: 0.6899 (OUTLIER) cc_final: 0.6618 (t) REVERT: D 444 TYR cc_start: 0.5188 (t80) cc_final: 0.4763 (t80) REVERT: D 484 MET cc_start: 0.4417 (mpp) cc_final: 0.2582 (tpt) REVERT: E 52 GLN cc_start: 0.7542 (OUTLIER) cc_final: 0.7168 (pt0) REVERT: E 446 MET cc_start: 0.4619 (OUTLIER) cc_final: 0.3748 (mtm) REVERT: E 470 MET cc_start: 0.2026 (OUTLIER) cc_final: 0.1554 (ptt) REVERT: E 475 LEU cc_start: 0.2163 (OUTLIER) cc_final: 0.1795 (tp) REVERT: F 185 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8394 (mp) REVERT: F 361 LEU cc_start: 0.7472 (OUTLIER) cc_final: 0.6990 (mp) REVERT: G 357 ARG cc_start: 0.6814 (ttt180) cc_final: 0.6580 (ttt180) outliers start: 73 outliers final: 60 residues processed: 305 average time/residue: 0.2006 time to fit residues: 100.7787 Evaluate side-chains 325 residues out of total 3239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 256 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 95 ASN Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain B residue 224 HIS Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 102 GLN Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 213 MET Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain Y residue 45 THR Chi-restraints excluded: chain Y residue 96 MET Chi-restraints excluded: chain Y residue 159 VAL Chi-restraints excluded: chain Y residue 162 ASP Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain E residue 52 GLN Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 327 LEU Chi-restraints excluded: chain E residue 329 SER Chi-restraints excluded: chain E residue 336 TRP Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 401 SER Chi-restraints excluded: chain E residue 413 ILE Chi-restraints excluded: chain E residue 446 MET Chi-restraints excluded: chain E residue 470 MET Chi-restraints excluded: chain E residue 475 LEU Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 198 ASN Chi-restraints excluded: chain F residue 248 MET Chi-restraints excluded: chain F residue 254 THR Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 343 VAL Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 231 ILE Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 367 THR Chi-restraints excluded: chain X residue 16 THR Chi-restraints excluded: chain X residue 45 THR Chi-restraints excluded: chain X residue 60 HIS Chi-restraints excluded: chain X residue 95 LEU Chi-restraints excluded: chain X residue 177 HIS Chi-restraints excluded: chain X residue 191 GLN Chi-restraints excluded: chain X residue 193 THR Chi-restraints excluded: chain X residue 239 HIS Chi-restraints excluded: chain X residue 258 LEU Chi-restraints excluded: chain X residue 300 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 250 optimal weight: 0.8980 chunk 298 optimal weight: 0.9980 chunk 44 optimal weight: 8.9990 chunk 212 optimal weight: 6.9990 chunk 40 optimal weight: 10.0000 chunk 129 optimal weight: 0.6980 chunk 42 optimal weight: 7.9990 chunk 364 optimal weight: 0.8980 chunk 151 optimal weight: 5.9990 chunk 257 optimal weight: 0.9990 chunk 276 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 198 ASN ** F 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4752 r_free = 0.4752 target = 0.232518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.213323 restraints weight = 40665.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.209625 restraints weight = 72282.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.207682 restraints weight = 71521.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.206923 restraints weight = 68179.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.205034 restraints weight = 62071.046| |-----------------------------------------------------------------------------| r_work (final): 0.4492 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4492 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4492 r_free = 0.4492 target_work(ls_wunit_k1) = 0.204 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4492 r_free = 0.4492 target_work(ls_wunit_k1) = 0.204 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4492 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.255 33010 Z= 0.209 Angle : 0.861 59.199 45146 Z= 0.475 Chirality : 0.044 0.609 5077 Planarity : 0.005 0.067 5440 Dihedral : 17.245 162.197 5355 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.39 % Favored : 94.53 % Rotamer: Outliers : 2.28 % Allowed : 17.54 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.13), residues: 3712 helix: -0.12 (0.13), residues: 1830 sheet: -0.39 (0.38), residues: 181 loop : -1.54 (0.14), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 201 TYR 0.025 0.002 TYR A 337 PHE 0.019 0.002 PHE Y 4 TRP 0.021 0.001 TRP D 336 HIS 0.006 0.001 HIS G 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.21 (33002) covalent geometry : angle 0.86112 / 0.47 (45140) hydrogen bonds : bond 0.04254 / 2.86 ( 1275) hydrogen bonds : angle 4.62863 / 3.35 ( 3544) metal coordination : bond 0.01312 / 0.80 ( 8) metal coordination : angle 2.08298 / 1.23 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5289.49 seconds wall clock time: 92 minutes 21.84 seconds (5541.84 seconds total)