Starting phenix.real_space_refine on Mon Aug 10 05:24:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9prt_71813/08_2026/9prt_71813.cif Found real_map, /net/cci-nas-00/data/ceres_data/9prt_71813/08_2026/9prt_71813.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9prt_71813/08_2026/9prt_71813.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9prt_71813/08_2026/9prt_71813.map" model { file = "/net/cci-nas-00/data/ceres_data/9prt_71813/08_2026/9prt_71813.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9prt_71813/08_2026/9prt_71813.cif" } resolution = 3.02 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.012 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 1 6.06 5 P 11 5.49 5 Mg 2 5.21 5 S 224 5.16 5 C 26333 2.51 5 N 7174 2.21 5 O 7859 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.05s 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: 41604 Number of models: 1 Model: "" Number of chains: 21 Chain: "C" Number of atoms: 2912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2912 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 15, 'TRANS': 354} Chain breaks: 1 Chain: "D" Number of atoms: 2935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2935 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 17, 'TRANS': 351} Chain: "E" Number of atoms: 3025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3025 Classifications: {'peptide': 380} Link IDs: {'PTRANS': 17, 'TRANS': 362} Chain: "F" Number of atoms: 2945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2945 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 17, 'TRANS': 358} Chain breaks: 1 Chain: "U" Number of atoms: 6472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 831, 6472 Classifications: {'peptide': 831} Link IDs: {'PTRANS': 31, 'TRANS': 799} Chain breaks: 2 Chain: "V" Number of atoms: 3739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3739 Classifications: {'peptide': 464} Link IDs: {'PTRANS': 18, 'TRANS': 445} Chain breaks: 1 Chain: "W" Number of atoms: 2605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2605 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 310} Chain: "X" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 836 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 100} Chain: "Y" Number of atoms: 3115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 3115 Classifications: {'peptide': 378} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 370} Chain: "Z" Number of atoms: 2290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2290 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 9, 'TRANS': 277} Chain: "a" Number of atoms: 3003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 3003 Classifications: {'peptide': 374} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 361} Chain: "b" Number of atoms: 1449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1449 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 9, 'TRANS': 179} Chain: "c" Number of atoms: 2272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2272 Classifications: {'peptide': 289} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 277} Chain: "d" Number of atoms: 2166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2166 Classifications: {'peptide': 265} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 253} Chain: "e" Number of atoms: 334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 334 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain breaks: 1 Chain: "g" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1383 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 163} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N GLY Z 30 " occ=0.35 ... (2 atoms not shown) pdb=" O GLY Z 30 " occ=0.35 residue: pdb=" N ILE d 156 " occ=0.00 ... (6 atoms not shown) pdb=" CD1 ILE d 156 " occ=0.00 residue: pdb=" N SER d 163 " occ=0.02 ... (4 atoms not shown) pdb=" OG SER d 163 " occ=0.02 residue: pdb=" N MET d 237 " occ=0.39 ... (6 atoms not shown) pdb=" CE MET d 237 " occ=0.39 Time building chain proxies: 7.83, per 1000 atoms: 0.19 Number of scatterers: 41604 At special positions: 0 Unit cell: (185.49, 155.52, 201.69, 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 1 29.99 S 224 16.00 P 11 15.00 Mg 2 11.99 O 7859 8.00 N 7174 7.00 C 26333 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.70 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN c 401 " pdb="ZN ZN c 401 " - pdb=" NE2 HIS g 289 " pdb="ZN ZN c 401 " - pdb=" NE2 HIS c 113 " pdb="ZN ZN c 401 " - pdb=" NE2 HIS c 115 " 10324 Ramachandran restraints generated. 5162 Oldfield, 0 Emsley, 5162 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9862 Finding SS restraints... Secondary structure from input PDB file: 243 helices and 21 sheets defined 61.4% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'C' and resid 20 through 66 removed outlier: 4.188A pdb=" N TYR C 24 " --> pdb=" O LEU C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 139 removed outlier: 3.803A pdb=" N MET C 138 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N MET C 139 " --> pdb=" O SER C 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 135 through 139' Processing helix chain 'C' and resid 154 through 171 removed outlier: 4.157A pdb=" N LEU C 167 " --> pdb=" O GLU C 163 " (cutoff:3.500A) Proline residue: C 168 - end of helix Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 195 through 207 Processing helix chain 'C' and resid 217 through 219 No H-bonds generated for 'chain 'C' and resid 217 through 219' Processing helix chain 'C' and resid 225 through 241 Processing helix chain 'C' and resid 250 through 254 removed outlier: 3.568A pdb=" N SER C 253 " --> pdb=" O GLU C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 281 removed outlier: 3.702A pdb=" N ASP C 281 " --> pdb=" O LEU C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 334 Processing helix chain 'C' and resid 343 through 351 removed outlier: 3.822A pdb=" N ILE C 347 " --> pdb=" O ASN C 343 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N MET C 351 " --> pdb=" O ILE C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 372 Processing helix chain 'C' and resid 379 through 391 Processing helix chain 'D' and resid 40 through 82 Processing helix chain 'D' and resid 155 through 159 Processing helix chain 'D' and resid 163 through 167 removed outlier: 3.661A pdb=" N ILE D 167 " --> pdb=" O TYR D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 181 Processing helix chain 'D' and resid 182 through 187 Processing helix chain 'D' and resid 211 through 223 Processing helix chain 'D' and resid 241 through 258 removed outlier: 4.060A pdb=" N ALA D 258 " --> pdb=" O ALA D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 270 Processing helix chain 'D' and resid 279 through 297 removed outlier: 3.898A pdb=" N VAL D 285 " --> pdb=" O ALA D 281 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN D 286 " --> pdb=" O ASP D 282 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET D 296 " --> pdb=" O LEU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 317 removed outlier: 3.980A pdb=" N THR D 316 " --> pdb=" O ARG D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 323 Processing helix chain 'D' and resid 337 through 350 removed outlier: 3.515A pdb=" N LEU D 343 " --> pdb=" O ARG D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 366 removed outlier: 4.073A pdb=" N ARG D 366 " --> pdb=" O ASP D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 389 Processing helix chain 'D' and resid 395 through 407 removed outlier: 3.600A pdb=" N PHE D 399 " --> pdb=" O LEU D 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 51 removed outlier: 3.613A pdb=" N LEU E 9 " --> pdb=" O ARG E 5 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N GLU E 21 " --> pdb=" O LEU E 17 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ILE E 22 " --> pdb=" O GLU E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 121 Processing helix chain 'E' and resid 138 through 155 removed outlier: 4.682A pdb=" N LEU E 151 " --> pdb=" O GLU E 147 " (cutoff:3.500A) Proline residue: E 152 - end of helix Processing helix chain 'E' and resid 155 through 163 removed outlier: 4.321A pdb=" N PHE E 159 " --> pdb=" O ASN E 155 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL E 162 " --> pdb=" O LEU E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 192 removed outlier: 3.536A pdb=" N ALA E 184 " --> pdb=" O LYS E 180 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER E 189 " --> pdb=" O ARG E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 225 Processing helix chain 'E' and resid 234 through 238 removed outlier: 3.912A pdb=" N ALA E 237 " --> pdb=" O GLU E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 265 Processing helix chain 'E' and resid 281 through 285 removed outlier: 3.870A pdb=" N THR E 284 " --> pdb=" O ARG E 281 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU E 285 " --> pdb=" O PRO E 282 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 281 through 285' Processing helix chain 'E' and resid 305 through 317 Processing helix chain 'E' and resid 327 through 335 Processing helix chain 'E' and resid 339 through 356 Processing helix chain 'E' and resid 357 through 359 No H-bonds generated for 'chain 'E' and resid 357 through 359' Processing helix chain 'E' and resid 363 through 381 removed outlier: 4.811A pdb=" N ARG E 372 " --> pdb=" O MET E 368 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS E 373 " --> pdb=" O LYS E 369 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N ALA E 375 " --> pdb=" O VAL E 371 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 44 removed outlier: 3.905A pdb=" N ILE F 41 " --> pdb=" O SER F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 84 Processing helix chain 'F' and resid 169 through 176 removed outlier: 3.555A pdb=" N GLU F 176 " --> pdb=" O VAL F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 188 Processing helix chain 'F' and resid 191 through 200 Processing helix chain 'F' and resid 202 through 208 Processing helix chain 'F' and resid 208 through 215 removed outlier: 3.744A pdb=" N PHE F 212 " --> pdb=" O HIS F 208 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU F 215 " --> pdb=" O LYS F 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 232 through 244 Processing helix chain 'F' and resid 262 through 278 Processing helix chain 'F' and resid 287 through 291 Processing helix chain 'F' and resid 299 through 318 removed outlier: 4.553A pdb=" N GLN F 307 " --> pdb=" O ASP F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 339 through 344 Processing helix chain 'F' and resid 358 through 371 removed outlier: 3.550A pdb=" N ARG F 371 " --> pdb=" O GLN F 367 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 388 Processing helix chain 'F' and resid 392 through 410 Processing helix chain 'F' and resid 416 through 426 removed outlier: 3.543A pdb=" N GLU F 426 " --> pdb=" O GLU F 422 " (cutoff:3.500A) Processing helix chain 'U' and resid 8 through 14 removed outlier: 3.842A pdb=" N LEU U 12 " --> pdb=" O ILE U 8 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASP U 13 " --> pdb=" O ILE U 9 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU U 14 " --> pdb=" O SER U 10 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 8 through 14' Processing helix chain 'U' and resid 16 through 30 removed outlier: 3.552A pdb=" N VAL U 30 " --> pdb=" O LYS U 26 " (cutoff:3.500A) Processing helix chain 'U' and resid 34 through 39 Processing helix chain 'U' and resid 41 through 51 removed outlier: 3.763A pdb=" N ILE U 45 " --> pdb=" O SER U 41 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU U 50 " --> pdb=" O GLU U 46 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP U 51 " --> pdb=" O VAL U 47 " (cutoff:3.500A) Processing helix chain 'U' and resid 56 through 72 Processing helix chain 'U' and resid 73 through 84 Processing helix chain 'U' and resid 85 through 88 removed outlier: 3.728A pdb=" N PHE U 88 " --> pdb=" O GLY U 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 85 through 88' Processing helix chain 'U' and resid 94 through 117 removed outlier: 4.309A pdb=" N ASP U 117 " --> pdb=" O VAL U 113 " (cutoff:3.500A) Processing helix chain 'U' and resid 127 through 144 Processing helix chain 'U' and resid 146 through 157 Processing helix chain 'U' and resid 160 through 169 Processing helix chain 'U' and resid 172 through 187 Processing helix chain 'U' and resid 190 through 207 removed outlier: 3.603A pdb=" N LYS U 196 " --> pdb=" O GLN U 192 " (cutoff:3.500A) Processing helix chain 'U' and resid 212 through 223 Processing helix chain 'U' and resid 225 through 239 removed outlier: 3.624A pdb=" N VAL U 229 " --> pdb=" O ASP U 225 " (cutoff:3.500A) Processing helix chain 'U' and resid 241 through 256 Processing helix chain 'U' and resid 257 through 269 Processing helix chain 'U' and resid 321 through 330 Processing helix chain 'U' and resid 331 through 345 Processing helix chain 'U' and resid 349 through 358 removed outlier: 3.983A pdb=" N LEU U 353 " --> pdb=" O ASP U 349 " (cutoff:3.500A) Processing helix chain 'U' and resid 362 through 377 removed outlier: 4.423A pdb=" N SER U 374 " --> pdb=" O VAL U 370 " (cutoff:3.500A) Processing helix chain 'U' and resid 383 through 389 removed outlier: 3.569A pdb=" N ASN U 389 " --> pdb=" O PHE U 385 " (cutoff:3.500A) Processing helix chain 'U' and resid 389 through 394 Processing helix chain 'U' and resid 398 through 412 removed outlier: 4.084A pdb=" N LEU U 408 " --> pdb=" O ALA U 404 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N GLY U 409 " --> pdb=" O THR U 405 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL U 410 " --> pdb=" O ALA U 406 " (cutoff:3.500A) Processing helix chain 'U' and resid 418 through 426 Processing helix chain 'U' and resid 434 through 451 Processing helix chain 'U' and resid 456 through 467 removed outlier: 3.963A pdb=" N TYR U 460 " --> pdb=" O ASP U 456 " (cutoff:3.500A) Processing helix chain 'U' and resid 470 through 485 Processing helix chain 'U' and resid 490 through 503 removed outlier: 3.834A pdb=" N LEU U 496 " --> pdb=" O ASP U 492 " (cutoff:3.500A) Processing helix chain 'U' and resid 505 through 520 removed outlier: 4.004A pdb=" N GLU U 510 " --> pdb=" O ALA U 506 " (cutoff:3.500A) Processing helix chain 'U' and resid 525 through 537 Processing helix chain 'U' and resid 541 through 555 removed outlier: 3.576A pdb=" N VAL U 550 " --> pdb=" O ARG U 546 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ALA U 553 " --> pdb=" O ALA U 549 " (cutoff:3.500A) Processing helix chain 'U' and resid 559 through 562 Processing helix chain 'U' and resid 563 through 573 Processing helix chain 'U' and resid 575 through 590 Processing helix chain 'U' and resid 595 through 609 Processing helix chain 'U' and resid 611 through 620 Processing helix chain 'U' and resid 621 through 623 No H-bonds generated for 'chain 'U' and resid 621 through 623' Processing helix chain 'U' and resid 631 through 642 removed outlier: 4.098A pdb=" N SER U 635 " --> pdb=" O GLU U 631 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N LEU U 639 " --> pdb=" O SER U 635 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU U 640 " --> pdb=" O VAL U 636 " (cutoff:3.500A) Processing helix chain 'U' and resid 645 through 660 Processing helix chain 'U' and resid 667 through 673 Processing helix chain 'U' and resid 680 through 695 Processing helix chain 'U' and resid 705 through 718 Processing helix chain 'U' and resid 723 through 738 Processing helix chain 'U' and resid 739 through 742 Processing helix chain 'U' and resid 756 through 767 Processing helix chain 'U' and resid 768 through 771 Processing helix chain 'U' and resid 772 through 781 removed outlier: 3.542A pdb=" N PHE U 778 " --> pdb=" O LEU U 775 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU U 779 " --> pdb=" O SER U 776 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER U 780 " --> pdb=" O HIS U 777 " (cutoff:3.500A) Processing helix chain 'U' and resid 885 through 890 removed outlier: 4.093A pdb=" N LYS U 890 " --> pdb=" O PRO U 886 " (cutoff:3.500A) Processing helix chain 'U' and resid 905 through 909 removed outlier: 3.999A pdb=" N ILE U 908 " --> pdb=" O PRO U 905 " (cutoff:3.500A) Processing helix chain 'V' and resid 30 through 51 Processing helix chain 'V' and resid 59 through 61 No H-bonds generated for 'chain 'V' and resid 59 through 61' Processing helix chain 'V' and resid 62 through 73 removed outlier: 4.230A pdb=" N VAL V 70 " --> pdb=" O GLU V 66 " (cutoff:3.500A) Processing helix chain 'V' and resid 89 through 93 removed outlier: 4.018A pdb=" N ARG V 92 " --> pdb=" O LYS V 89 " (cutoff:3.500A) Processing helix chain 'V' and resid 100 through 121 Processing helix chain 'V' and resid 136 through 140 Processing helix chain 'V' and resid 147 through 157 Processing helix chain 'V' and resid 158 through 165 Processing helix chain 'V' and resid 170 through 189 removed outlier: 3.539A pdb=" N PHE V 174 " --> pdb=" O LEU V 170 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N MET V 176 " --> pdb=" O VAL V 172 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER V 188 " --> pdb=" O ALA V 184 " (cutoff:3.500A) Processing helix chain 'V' and resid 198 through 200 No H-bonds generated for 'chain 'V' and resid 198 through 200' Processing helix chain 'V' and resid 201 through 211 Processing helix chain 'V' and resid 214 through 219 Processing helix chain 'V' and resid 220 through 222 No H-bonds generated for 'chain 'V' and resid 220 through 222' Processing helix chain 'V' and resid 223 through 226 removed outlier: 3.936A pdb=" N VAL V 226 " --> pdb=" O LYS V 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 223 through 226' Processing helix chain 'V' and resid 227 through 241 removed outlier: 3.543A pdb=" N ARG V 241 " --> pdb=" O THR V 237 " (cutoff:3.500A) Processing helix chain 'V' and resid 243 through 261 removed outlier: 3.922A pdb=" N TYR V 261 " --> pdb=" O ASN V 257 " (cutoff:3.500A) Processing helix chain 'V' and resid 263 through 274 Processing helix chain 'V' and resid 281 through 299 removed outlier: 3.553A pdb=" N TRP V 285 " --> pdb=" O ASN V 281 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA V 286 " --> pdb=" O ASN V 282 " (cutoff:3.500A) Processing helix chain 'V' and resid 301 through 315 Processing helix chain 'V' and resid 323 through 340 removed outlier: 3.951A pdb=" N GLY V 340 " --> pdb=" O GLU V 336 " (cutoff:3.500A) Processing helix chain 'V' and resid 357 through 369 Processing helix chain 'V' and resid 371 through 389 removed outlier: 6.078A pdb=" N GLU V 384 " --> pdb=" O ASP V 380 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LYS V 385 " --> pdb=" O GLN V 381 " (cutoff:3.500A) Processing helix chain 'V' and resid 391 through 400 removed outlier: 3.952A pdb=" N HIS V 400 " --> pdb=" O ILE V 396 " (cutoff:3.500A) Processing helix chain 'V' and resid 401 through 414 removed outlier: 3.579A pdb=" N THR V 405 " --> pdb=" O ASN V 401 " (cutoff:3.500A) Processing helix chain 'V' and resid 419 through 426 Processing helix chain 'V' and resid 430 through 445 removed outlier: 3.670A pdb=" N PHE V 436 " --> pdb=" O GLU V 432 " (cutoff:3.500A) Processing helix chain 'V' and resid 470 through 493 removed outlier: 3.567A pdb=" N ALA V 493 " --> pdb=" O MET V 489 " (cutoff:3.500A) Processing helix chain 'W' and resid 141 through 156 Processing helix chain 'W' and resid 158 through 168 removed outlier: 3.667A pdb=" N SER W 164 " --> pdb=" O LYS W 160 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU W 166 " --> pdb=" O ALA W 162 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU W 168 " --> pdb=" O SER W 164 " (cutoff:3.500A) Processing helix chain 'W' and resid 170 through 174 removed outlier: 3.722A pdb=" N THR W 173 " --> pdb=" O GLN W 170 " (cutoff:3.500A) Processing helix chain 'W' and resid 178 through 196 removed outlier: 3.552A pdb=" N ARG W 182 " --> pdb=" O GLU W 178 " (cutoff:3.500A) Processing helix chain 'W' and resid 198 through 206 Processing helix chain 'W' and resid 207 through 209 No H-bonds generated for 'chain 'W' and resid 207 through 209' Processing helix chain 'W' and resid 219 through 237 removed outlier: 3.944A pdb=" N LYS W 225 " --> pdb=" O LYS W 221 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU W 237 " --> pdb=" O LEU W 233 " (cutoff:3.500A) Processing helix chain 'W' and resid 239 through 252 removed outlier: 3.746A pdb=" N ILE W 243 " --> pdb=" O SER W 239 " (cutoff:3.500A) Processing helix chain 'W' and resid 253 through 259 removed outlier: 4.167A pdb=" N GLU W 259 " --> pdb=" O CYS W 255 " (cutoff:3.500A) Processing helix chain 'W' and resid 259 through 277 removed outlier: 3.826A pdb=" N TRP W 263 " --> pdb=" O GLU W 259 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ILE W 275 " --> pdb=" O VAL W 271 " (cutoff:3.500A) Processing helix chain 'W' and resid 280 through 291 Processing helix chain 'W' and resid 293 through 298 removed outlier: 3.510A pdb=" N GLU W 298 " --> pdb=" O LYS W 295 " (cutoff:3.500A) Processing helix chain 'W' and resid 299 through 311 removed outlier: 3.599A pdb=" N PHE W 309 " --> pdb=" O LEU W 305 " (cutoff:3.500A) Processing helix chain 'W' and resid 316 through 330 removed outlier: 6.348A pdb=" N MET W 326 " --> pdb=" O GLU W 322 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N GLU W 327 " --> pdb=" O ASP W 323 " (cutoff:3.500A) Processing helix chain 'W' and resid 338 through 342 removed outlier: 3.931A pdb=" N PHE W 341 " --> pdb=" O THR W 338 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLY W 342 " --> pdb=" O ASP W 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 338 through 342' Processing helix chain 'W' and resid 344 through 370 Processing helix chain 'W' and resid 375 through 382 Processing helix chain 'W' and resid 385 through 399 Processing helix chain 'W' and resid 420 through 456 Processing helix chain 'X' and resid 320 through 339 removed outlier: 3.724A pdb=" N ARG X 337 " --> pdb=" O GLN X 333 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL X 338 " --> pdb=" O ASN X 334 " (cutoff:3.500A) Processing helix chain 'X' and resid 347 through 355 Processing helix chain 'X' and resid 357 through 371 Processing helix chain 'X' and resid 394 through 419 Processing helix chain 'Y' and resid 21 through 28 removed outlier: 3.802A pdb=" N LEU Y 25 " --> pdb=" O GLN Y 21 " (cutoff:3.500A) Processing helix chain 'Y' and resid 36 through 48 removed outlier: 4.942A pdb=" N MET Y 42 " --> pdb=" O ARG Y 38 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N ALA Y 43 " --> pdb=" O ASP Y 39 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ARG Y 46 " --> pdb=" O MET Y 42 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP Y 47 " --> pdb=" O ALA Y 43 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ASN Y 48 " --> pdb=" O ALA Y 44 " (cutoff:3.500A) Processing helix chain 'Y' and resid 52 through 59 removed outlier: 4.113A pdb=" N ALA Y 56 " --> pdb=" O PRO Y 52 " (cutoff:3.500A) Processing helix chain 'Y' and resid 67 through 94 removed outlier: 3.610A pdb=" N LYS Y 72 " --> pdb=" O ASP Y 68 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N MET Y 73 " --> pdb=" O LEU Y 69 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU Y 87 " --> pdb=" O ARG Y 83 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU Y 88 " --> pdb=" O LEU Y 84 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU Y 89 " --> pdb=" O ASP Y 85 " (cutoff:3.500A) Processing helix chain 'Y' and resid 96 through 112 removed outlier: 3.619A pdb=" N ILE Y 100 " --> pdb=" O GLY Y 96 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N MET Y 104 " --> pdb=" O ILE Y 100 " (cutoff:3.500A) Processing helix chain 'Y' and resid 117 through 130 removed outlier: 3.727A pdb=" N LYS Y 130 " --> pdb=" O LYS Y 126 " (cutoff:3.500A) Processing helix chain 'Y' and resid 133 through 151 removed outlier: 3.869A pdb=" N ARG Y 137 " --> pdb=" O ALA Y 133 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP Y 139 " --> pdb=" O GLY Y 135 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE Y 142 " --> pdb=" O LEU Y 138 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU Y 144 " --> pdb=" O ILE Y 140 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU Y 145 " --> pdb=" O VAL Y 141 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE Y 150 " --> pdb=" O ARG Y 146 " (cutoff:3.500A) Processing helix chain 'Y' and resid 154 through 159 removed outlier: 3.912A pdb=" N ARG Y 159 " --> pdb=" O ASP Y 155 " (cutoff:3.500A) Processing helix chain 'Y' and resid 160 through 171 removed outlier: 3.641A pdb=" N GLU Y 170 " --> pdb=" O SER Y 166 " (cutoff:3.500A) Processing helix chain 'Y' and resid 175 through 191 Processing helix chain 'Y' and resid 193 through 204 removed outlier: 3.692A pdb=" N ALA Y 197 " --> pdb=" O ASP Y 193 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP Y 203 " --> pdb=" O GLU Y 199 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR Y 204 " --> pdb=" O LEU Y 200 " (cutoff:3.500A) Processing helix chain 'Y' and resid 215 through 231 removed outlier: 3.713A pdb=" N SER Y 227 " --> pdb=" O THR Y 223 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N MET Y 228 " --> pdb=" O VAL Y 224 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ILE Y 229 " --> pdb=" O TYR Y 225 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA Y 230 " --> pdb=" O VAL Y 226 " (cutoff:3.500A) Processing helix chain 'Y' and resid 232 through 241 removed outlier: 3.874A pdb=" N GLU Y 238 " --> pdb=" O PRO Y 234 " (cutoff:3.500A) Processing helix chain 'Y' and resid 246 through 251 Processing helix chain 'Y' and resid 253 through 265 removed outlier: 3.692A pdb=" N LEU Y 263 " --> pdb=" O TYR Y 259 " (cutoff:3.500A) Processing helix chain 'Y' and resid 267 through 282 Processing helix chain 'Y' and resid 291 through 309 removed outlier: 3.561A pdb=" N TYR Y 295 " --> pdb=" O HIS Y 291 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG Y 297 " --> pdb=" O ARG Y 293 " (cutoff:3.500A) Processing helix chain 'Y' and resid 316 through 324 removed outlier: 3.577A pdb=" N ALA Y 320 " --> pdb=" O LEU Y 316 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLU Y 321 " --> pdb=" O GLY Y 317 " (cutoff:3.500A) Processing helix chain 'Y' and resid 326 through 340 Processing helix chain 'Y' and resid 362 through 388 Processing helix chain 'Z' and resid 12 through 28 removed outlier: 3.587A pdb=" N ILE Z 26 " --> pdb=" O HIS Z 22 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS Z 28 " --> pdb=" O ASN Z 24 " (cutoff:3.500A) Processing helix chain 'Z' and resid 71 through 86 Processing helix chain 'Z' and resid 104 through 114 removed outlier: 3.977A pdb=" N ARG Z 114 " --> pdb=" O GLU Z 110 " (cutoff:3.500A) Processing helix chain 'Z' and resid 165 through 176 Processing helix chain 'Z' and resid 186 through 218 Processing helix chain 'Z' and resid 223 through 234 Processing helix chain 'Z' and resid 242 through 289 removed outlier: 4.026A pdb=" N VAL Z 259 " --> pdb=" O ASP Z 255 " (cutoff:3.500A) Processing helix chain 'a' and resid 4 through 11 Processing helix chain 'a' and resid 20 through 31 Processing helix chain 'a' and resid 33 through 45 Processing helix chain 'a' and resid 55 through 63 Processing helix chain 'a' and resid 67 through 71 Processing helix chain 'a' and resid 72 through 84 Processing helix chain 'a' and resid 89 through 104 removed outlier: 3.910A pdb=" N ALA a 93 " --> pdb=" O ASP a 89 " (cutoff:3.500A) Processing helix chain 'a' and resid 108 through 125 Processing helix chain 'a' and resid 127 through 143 Processing helix chain 'a' and resid 150 through 167 removed outlier: 3.986A pdb=" N ARG a 154 " --> pdb=" O SER a 150 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR a 165 " --> pdb=" O LYS a 161 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY a 167 " --> pdb=" O TYR a 163 " (cutoff:3.500A) Processing helix chain 'a' and resid 168 through 183 Processing helix chain 'a' and resid 189 through 206 Processing helix chain 'a' and resid 213 through 218 Processing helix chain 'a' and resid 230 through 243 removed outlier: 4.152A pdb=" N ILE a 234 " --> pdb=" O ARG a 230 " (cutoff:3.500A) Processing helix chain 'a' and resid 244 through 250 Processing helix chain 'a' and resid 258 through 264 Processing helix chain 'a' and resid 264 through 284 removed outlier: 4.115A pdb=" N LEU a 277 " --> pdb=" O GLN a 273 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N MET a 278 " --> pdb=" O LEU a 274 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ARG a 284 " --> pdb=" O MET a 280 " (cutoff:3.500A) Processing helix chain 'a' and resid 293 through 301 Processing helix chain 'a' and resid 303 through 305 No H-bonds generated for 'chain 'a' and resid 303 through 305' Processing helix chain 'a' and resid 306 through 318 Processing helix chain 'a' and resid 342 through 371 Processing helix chain 'b' and resid 13 through 18 Processing helix chain 'b' and resid 24 through 44 Processing helix chain 'b' and resid 67 through 76 removed outlier: 4.156A pdb=" N ILE b 71 " --> pdb=" O ASP b 67 " (cutoff:3.500A) Processing helix chain 'b' and resid 85 through 99 Processing helix chain 'b' and resid 120 through 134 Processing helix chain 'b' and resid 145 through 161 removed outlier: 3.905A pdb=" N THR b 150 " --> pdb=" O GLU b 146 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N GLU b 151 " --> pdb=" O GLU b 147 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N LYS b 152 " --> pdb=" O VAL b 148 " (cutoff:3.500A) Processing helix chain 'c' and resid 35 through 48 Processing helix chain 'c' and resid 83 through 87 Processing helix chain 'c' and resid 88 through 101 removed outlier: 3.550A pdb=" N GLN c 92 " --> pdb=" O ASP c 88 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLN c 101 " --> pdb=" O ASP c 97 " (cutoff:3.500A) Processing helix chain 'c' and resid 123 through 135 Processing helix chain 'c' and resid 180 through 184 removed outlier: 3.612A pdb=" N HIS c 183 " --> pdb=" O ASN c 180 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU c 184 " --> pdb=" O LEU c 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 180 through 184' Processing helix chain 'c' and resid 188 through 194 removed outlier: 3.558A pdb=" N HIS c 194 " --> pdb=" O GLN c 190 " (cutoff:3.500A) Processing helix chain 'c' and resid 210 through 218 Processing helix chain 'c' and resid 224 through 229 removed outlier: 3.578A pdb=" N GLY c 228 " --> pdb=" O SER c 224 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU c 229 " --> pdb=" O TRP c 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 224 through 229' Processing helix chain 'c' and resid 233 through 264 removed outlier: 3.748A pdb=" N LYS c 239 " --> pdb=" O SER c 235 " (cutoff:3.500A) Processing helix chain 'c' and resid 269 through 274 Processing helix chain 'c' and resid 279 through 309 removed outlier: 3.540A pdb=" N HIS c 283 " --> pdb=" O ASP c 279 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N HIS c 287 " --> pdb=" O HIS c 283 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL c 288 " --> pdb=" O LEU c 284 " (cutoff:3.500A) Processing helix chain 'd' and resid 87 through 103 removed outlier: 3.504A pdb=" N GLY d 93 " --> pdb=" O GLN d 89 " (cutoff:3.500A) Processing helix chain 'd' and resid 108 through 126 removed outlier: 4.901A pdb=" N GLU d 114 " --> pdb=" O SER d 110 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLY d 117 " --> pdb=" O GLY d 113 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU d 125 " --> pdb=" O LEU d 121 " (cutoff:3.500A) Processing helix chain 'd' and resid 137 through 158 removed outlier: 4.063A pdb=" N LEU d 141 " --> pdb=" O THR d 137 " (cutoff:3.500A) Processing helix chain 'd' and resid 160 through 176 removed outlier: 3.548A pdb=" N GLN d 170 " --> pdb=" O ARG d 166 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N CYS d 173 " --> pdb=" O ALA d 169 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR d 174 " --> pdb=" O GLN d 170 " (cutoff:3.500A) Processing helix chain 'd' and resid 187 through 202 Processing helix chain 'd' and resid 204 through 215 removed outlier: 3.831A pdb=" N ARG d 214 " --> pdb=" O THR d 210 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LEU d 215 " --> pdb=" O GLU d 211 " (cutoff:3.500A) Processing helix chain 'd' and resid 216 through 222 removed outlier: 3.908A pdb=" N ILE d 220 " --> pdb=" O PRO d 216 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLN d 221 " --> pdb=" O ALA d 217 " (cutoff:3.500A) Processing helix chain 'd' and resid 223 through 239 Proline residue: d 229 - end of helix Processing helix chain 'd' and resid 240 through 247 Processing helix chain 'd' and resid 248 through 250 No H-bonds generated for 'chain 'd' and resid 248 through 250' Processing helix chain 'd' and resid 253 through 255 No H-bonds generated for 'chain 'd' and resid 253 through 255' Processing helix chain 'd' and resid 256 through 279 removed outlier: 3.522A pdb=" N CYS d 274 " --> pdb=" O GLU d 270 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU d 276 " --> pdb=" O ALA d 272 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LYS d 277 " --> pdb=" O GLY d 273 " (cutoff:3.500A) Processing helix chain 'd' and resid 284 through 291 Processing helix chain 'd' and resid 295 through 305 Processing helix chain 'd' and resid 323 through 327 Processing helix chain 'd' and resid 331 through 345 Processing helix chain 'e' and resid 59 through 69 Processing helix chain 'g' and resid 205 through 212 Processing helix chain 'g' and resid 222 through 226 removed outlier: 3.588A pdb=" N LYS g 226 " --> pdb=" O ASP g 223 " (cutoff:3.500A) Processing helix chain 'g' and resid 274 through 278 Processing sheet with id=AA1, first strand: chain 'C' and resid 94 through 98 removed outlier: 7.414A pdb=" N LYS C 84 " --> pdb=" O ALA C 79 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ALA C 79 " --> pdb=" O LYS C 84 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N LEU C 86 " --> pdb=" O VAL C 77 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 210 through 215 removed outlier: 6.845A pdb=" N THR C 210 " --> pdb=" O ILE C 245 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N PHE C 247 " --> pdb=" O THR C 210 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ILE C 212 " --> pdb=" O PHE C 247 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N ASP C 249 " --> pdb=" O ILE C 212 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N VAL C 214 " --> pdb=" O ASP C 249 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER C 244 " --> pdb=" O ASN C 288 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET C 248 " --> pdb=" O ILE C 292 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL C 186 " --> pdb=" O VAL C 291 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N GLY C 185 " --> pdb=" O ARG C 313 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ILE C 315 " --> pdb=" O GLY C 185 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N LEU C 187 " --> pdb=" O ILE C 315 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 87 through 97 removed outlier: 6.825A pdb=" N ILE D 102 " --> pdb=" O LEU D 93 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N ALA D 95 " --> pdb=" O THR D 100 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N THR D 100 " --> pdb=" O ALA D 95 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER D 109 " --> pdb=" O SER D 105 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 109 through 114 current: chain 'D' and resid 139 through 142 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 139 through 142 current: chain 'E' and resid 68 through 73 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 78 through 83 current: chain 'E' and resid 106 through 110 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 106 through 110 current: chain 'F' and resid 121 through 126 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 131 through 134 current: chain 'F' and resid 160 through 163 Processing sheet with id=AA4, first strand: chain 'D' and resid 227 through 229 removed outlier: 6.646A pdb=" N ILE D 228 " --> pdb=" O PHE D 263 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N ASP D 265 " --> pdb=" O ILE D 228 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ILE D 262 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N ALA D 310 " --> pdb=" O ILE D 262 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ILE D 264 " --> pdb=" O ALA D 310 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N VAL D 202 " --> pdb=" O MET D 309 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N ILE D 331 " --> pdb=" O GLY D 201 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N LEU D 203 " --> pdb=" O ILE D 331 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 195 through 199 removed outlier: 3.603A pdb=" N ASP E 233 " --> pdb=" O VAL E 198 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N CYS E 170 " --> pdb=" O MET E 277 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N THR E 279 " --> pdb=" O CYS E 170 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU E 172 " --> pdb=" O THR E 279 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N GLY E 169 " --> pdb=" O ARG E 297 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N ILE E 299 " --> pdb=" O GLY E 169 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N LEU E 171 " --> pdb=" O ILE E 299 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 247 through 252 removed outlier: 6.969A pdb=" N THR F 247 " --> pdb=" O ILE F 282 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N PHE F 284 " --> pdb=" O THR F 247 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU F 249 " --> pdb=" O PHE F 284 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N ASP F 286 " --> pdb=" O LEU F 249 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N LEU F 251 " --> pdb=" O ASP F 286 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N SER F 281 " --> pdb=" O LYS F 327 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N ILE F 329 " --> pdb=" O SER F 281 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ILE F 283 " --> pdb=" O ILE F 329 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N ALA F 331 " --> pdb=" O ILE F 283 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ILE F 285 " --> pdb=" O ALA F 331 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL F 223 " --> pdb=" O VAL F 328 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR F 332 " --> pdb=" O MET F 225 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'U' and resid 744 through 746 Processing sheet with id=AA8, first strand: chain 'U' and resid 882 through 883 removed outlier: 3.525A pdb=" N ALA U 882 " --> pdb=" O VAL U 788 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N CYS U 787 " --> pdb=" O GLY U 910 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ILE U 912 " --> pdb=" O CYS U 787 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ILE U 789 " --> pdb=" O ILE U 912 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU U 914 " --> pdb=" O ILE U 789 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N LEU U 791 " --> pdb=" O LEU U 914 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ASP U 916 " --> pdb=" O LEU U 791 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'U' and resid 876 through 878 Processing sheet with id=AB1, first strand: chain 'V' and resid 416 through 418 Processing sheet with id=AB2, first strand: chain 'W' and resid 372 through 374 Processing sheet with id=AB3, first strand: chain 'X' and resid 344 through 346 removed outlier: 7.499A pdb=" N ARG Y 312 " --> pdb=" O GLY X 376 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N LEU X 378 " --> pdb=" O ARG Y 312 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N LEU Y 314 " --> pdb=" O LEU X 378 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ARG Y 312 " --> pdb=" O THR Y 356 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'Z' and resid 9 through 11 WARNING: can't find start of bonding for strands! previous: chain 'Z' and resid 9 through 11 current: chain 'Z' and resid 48 through 56 WARNING: can't find start of bonding for strands! previous: chain 'Z' and resid 48 through 56 current: chain 'Z' and resid 120 through 124 Processing sheet with id=AB5, first strand: chain 'Z' and resid 58 through 60 removed outlier: 3.586A pdb=" N ASP Z 59 " --> pdb=" O PHE Z 69 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'a' and resid 290 through 292 removed outlier: 6.997A pdb=" N LYS a 321 " --> pdb=" O THR a 334 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'b' and resid 60 through 65 removed outlier: 5.721A pdb=" N THR b 63 " --> pdb=" O LEU b 51 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LEU b 51 " --> pdb=" O THR b 63 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR b 65 " --> pdb=" O VAL b 49 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N GLU b 4 " --> pdb=" O ASN b 48 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N GLY b 50 " --> pdb=" O GLU b 4 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N THR b 6 " --> pdb=" O GLY b 50 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N ILE b 52 " --> pdb=" O THR b 6 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL b 8 " --> pdb=" O ILE b 52 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N SER b 5 " --> pdb=" O ARG b 108 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ILE b 110 " --> pdb=" O SER b 5 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N MET b 7 " --> pdb=" O ILE b 110 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N PHE b 112 " --> pdb=" O MET b 7 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N CYS b 9 " --> pdb=" O PHE b 112 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASN b 137 " --> pdb=" O MET b 107 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N VAL b 138 " --> pdb=" O HIS b 169 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N VAL b 171 " --> pdb=" O VAL b 138 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE b 140 " --> pdb=" O VAL b 171 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'c' and resid 30 through 34 removed outlier: 7.041A pdb=" N GLN c 30 " --> pdb=" O VAL c 67 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N VAL c 69 " --> pdb=" O GLN c 30 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N TYR c 32 " --> pdb=" O VAL c 69 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ASP c 71 " --> pdb=" O TYR c 32 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N SER c 34 " --> pdb=" O ASP c 71 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N VAL c 69 " --> pdb=" O GLU c 60 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N GLU c 60 " --> pdb=" O VAL c 69 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASP c 71 " --> pdb=" O LEU c 58 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLY c 110 " --> pdb=" O MET c 57 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N GLY c 59 " --> pdb=" O VAL c 108 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N VAL c 108 " --> pdb=" O GLY c 59 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL c 145 " --> pdb=" O HIS c 113 " (cutoff:3.500A) removed outlier: 10.203A pdb=" N ILE c 157 " --> pdb=" O ILE c 205 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE c 205 " --> pdb=" O ILE c 157 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ALA c 159 " --> pdb=" O ILE c 203 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N VAL c 31 " --> pdb=" O ASN c 206 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ARG c 208 " --> pdb=" O VAL c 31 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ILE c 33 " --> pdb=" O ARG c 208 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'd' and resid 281 through 283 removed outlier: 3.827A pdb=" N ILE d 282 " --> pdb=" O TYR d 316 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'g' and resid 124 through 125 Processing sheet with id=AC2, first strand: chain 'g' and resid 130 through 138 removed outlier: 9.813A pdb=" N ILE g 130 " --> pdb=" O PRO g 174 " (cutoff:3.500A) removed outlier: 9.533A pdb=" N LYS g 132 " --> pdb=" O ASN g 172 " (cutoff:3.500A) removed outlier: 9.925A pdb=" N ASN g 172 " --> pdb=" O LYS g 132 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLY g 134 " --> pdb=" O ALA g 170 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ALA g 170 " --> pdb=" O GLY g 134 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU g 166 " --> pdb=" O LEU g 138 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU g 165 " --> pdb=" O VAL g 248 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ASN g 242 " --> pdb=" O PHE g 171 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE g 196 " --> pdb=" O GLN g 216 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLN g 216 " --> pdb=" O ILE g 196 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'g' and resid 157 through 158 2214 hydrogen bonds defined for protein. 6489 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.60 Time building geometry restraints manager: 4.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 13985 1.36 - 1.50: 10421 1.50 - 1.65: 17527 1.65 - 1.80: 270 1.80 - 1.95: 112 Bond restraints: 42315 Sorted by residual: bond pdb=" O2G AGS E 501 " pdb=" PG AGS E 501 " ideal model delta sigma weight residual 1.604 1.508 0.096 2.00e-02 2.50e+03 2.31e+01 bond pdb=" O2G AGS C 501 " pdb=" PG AGS C 501 " ideal model delta sigma weight residual 1.604 1.509 0.095 2.00e-02 2.50e+03 2.25e+01 bond pdb=" O2G AGS D 501 " pdb=" PG AGS D 501 " ideal model delta sigma weight residual 1.604 1.510 0.094 2.00e-02 2.50e+03 2.22e+01 bond pdb=" O3B AGS D 501 " pdb=" PB AGS D 501 " ideal model delta sigma weight residual 1.673 1.599 0.074 2.00e-02 2.50e+03 1.38e+01 bond pdb=" O3B AGS C 501 " pdb=" PB AGS C 501 " ideal model delta sigma weight residual 1.673 1.600 0.073 2.00e-02 2.50e+03 1.35e+01 ... (remaining 42310 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.45: 56131 3.45 - 6.89: 872 6.89 - 10.34: 130 10.34 - 13.79: 21 13.79 - 17.24: 1 Bond angle restraints: 57155 Sorted by residual: angle pdb=" CA VAL c 49 " pdb=" C VAL c 49 " pdb=" N PRO c 50 " ideal model delta sigma weight residual 120.83 124.16 -3.33 6.10e-01 2.69e+00 2.99e+01 angle pdb=" C ARG E 251 " pdb=" N GLU E 252 " pdb=" CA GLU E 252 " ideal model delta sigma weight residual 121.14 112.47 8.67 1.75e+00 3.27e-01 2.45e+01 angle pdb=" N VAL C 376 " pdb=" CA VAL C 376 " pdb=" C VAL C 376 " ideal model delta sigma weight residual 112.83 107.95 4.88 9.90e-01 1.02e+00 2.43e+01 angle pdb=" CA LEU F 348 " pdb=" CB LEU F 348 " pdb=" CG LEU F 348 " ideal model delta sigma weight residual 116.30 133.54 -17.24 3.50e+00 8.16e-02 2.43e+01 angle pdb=" C VAL E 371 " pdb=" N ARG E 372 " pdb=" CA ARG E 372 " ideal model delta sigma weight residual 121.54 130.89 -9.35 1.91e+00 2.74e-01 2.40e+01 ... (remaining 57150 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.86: 25457 34.86 - 69.73: 565 69.73 - 104.59: 76 104.59 - 139.45: 1 139.45 - 174.31: 2 Dihedral angle restraints: 26101 sinusoidal: 10886 harmonic: 15215 Sorted by residual: dihedral pdb=" CA ARG C 310 " pdb=" C ARG C 310 " pdb=" N ILE C 311 " pdb=" CA ILE C 311 " ideal model delta harmonic sigma weight residual 180.00 150.90 29.10 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" CA ARG F 409 " pdb=" C ARG F 409 " pdb=" N ARG F 410 " pdb=" CA ARG F 410 " ideal model delta harmonic sigma weight residual 180.00 151.67 28.33 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CA LYS F 278 " pdb=" C LYS F 278 " pdb=" N ALA F 279 " pdb=" CA ALA F 279 " ideal model delta harmonic sigma weight residual -180.00 -151.72 -28.28 0 5.00e+00 4.00e-02 3.20e+01 ... (remaining 26098 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 5284 0.072 - 0.145: 1052 0.145 - 0.217: 122 0.217 - 0.289: 28 0.289 - 0.361: 9 Chirality restraints: 6495 Sorted by residual: chirality pdb=" CB ILE C 292 " pdb=" CA ILE C 292 " pdb=" CG1 ILE C 292 " pdb=" CG2 ILE C 292 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.27e+00 chirality pdb=" C3' AGS E 501 " pdb=" C2' AGS E 501 " pdb=" C4' AGS E 501 " pdb=" O3' AGS E 501 " both_signs ideal model delta sigma weight residual False -2.37 -2.73 0.35 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" CB VAL C 231 " pdb=" CA VAL C 231 " pdb=" CG1 VAL C 231 " pdb=" CG2 VAL C 231 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.34 2.00e-01 2.50e+01 2.97e+00 ... (remaining 6492 not shown) Planarity restraints: 7357 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG a 352 " -0.280 9.50e-02 1.11e+02 1.25e-01 9.69e+00 pdb=" NE ARG a 352 " 0.018 2.00e-02 2.50e+03 pdb=" CZ ARG a 352 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG a 352 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG a 352 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY F 253 " 0.050 5.00e-02 4.00e+02 7.54e-02 9.10e+00 pdb=" N PRO F 254 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO F 254 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO F 254 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG d 158 " -0.270 9.50e-02 1.11e+02 1.21e-01 9.01e+00 pdb=" NE ARG d 158 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG d 158 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG d 158 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG d 158 " -0.009 2.00e-02 2.50e+03 ... (remaining 7354 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 37 2.60 - 3.18: 34538 3.18 - 3.75: 69352 3.75 - 4.33: 92852 4.33 - 4.90: 148495 Nonbonded interactions: 345274 Sorted by model distance: nonbonded pdb=" O3G AGS D 501 " pdb="MG MG D 502 " model vdw 2.030 2.170 nonbonded pdb=" O1B AGS C 501 " pdb="MG MG C 502 " model vdw 2.044 2.170 nonbonded pdb=" O3G AGS C 501 " pdb="MG MG C 502 " model vdw 2.095 2.170 nonbonded pdb=" O1B AGS D 501 " pdb="MG MG D 502 " model vdw 2.097 2.170 nonbonded pdb=" OD2 ASP c 126 " pdb="ZN ZN c 401 " model vdw 2.120 2.230 ... (remaining 345269 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.460 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: 0.040 Extract box with map and model: 0.850 Check model and map are aligned: 0.130 Set scattering table: 0.120 Process input model: 41.410 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5639 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 : 0.006 0.429 42318 Z= 0.315 Angle : 1.087 17.236 57155 Z= 0.591 Chirality : 0.059 0.361 6495 Planarity : 0.008 0.125 7357 Dihedral : 15.385 174.315 16239 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 0.26 % Allowed : 0.61 % Favored : 99.13 % 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: -2.37 (0.10), residues: 5162 helix: -1.35 (0.08), residues: 2923 sheet: -1.15 (0.26), residues: 395 loop : -1.76 (0.13), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG b 100 TYR 0.033 0.002 TYR W 369 PHE 0.043 0.003 PHE C 235 TRP 0.018 0.002 TRP Z 94 HIS 0.011 0.001 HIS U 475 Details of bonding type rmsd/Z covalent geometry : bond 0.00568 / 0.31 (42315) covalent geometry : angle 1.08687 / 0.59 (57155) hydrogen bonds : bond 0.13839 / 9.13 ( 2214) hydrogen bonds : angle 6.72924 / 4.63 ( 6489) metal coordination : bond 0.25261 / 12.61 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10324 Ramachandran restraints generated. 5162 Oldfield, 0 Emsley, 5162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10324 Ramachandran restraints generated. 5162 Oldfield, 0 Emsley, 5162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1001 residues out of total 4573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 989 time to evaluate : 1.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 121 TYR cc_start: 0.8071 (m-80) cc_final: 0.6615 (p90) REVERT: C 232 ARG cc_start: 0.8416 (ppt170) cc_final: 0.7742 (tmm-80) REVERT: D 85 ILE cc_start: 0.7905 (pt) cc_final: 0.7541 (pt) REVERT: D 170 MET cc_start: 0.4804 (ptt) cc_final: 0.4184 (mmt) REVERT: D 296 MET cc_start: 0.8819 (ppp) cc_final: 0.8560 (ppp) REVERT: E 120 TYR cc_start: 0.8331 (t80) cc_final: 0.7941 (t80) REVERT: E 151 LEU cc_start: 0.8748 (tp) cc_final: 0.8461 (tp) REVERT: E 155 ASN cc_start: 0.7880 (t0) cc_final: 0.7415 (t0) REVERT: E 220 ASN cc_start: 0.9442 (m-40) cc_final: 0.9078 (m-40) REVERT: F 36 MET cc_start: 0.7913 (OUTLIER) cc_final: 0.7707 (tpp) REVERT: F 46 ARG cc_start: 0.8335 (ttp80) cc_final: 0.8071 (tpp-160) REVERT: F 64 HIS cc_start: 0.8644 (m-70) cc_final: 0.8036 (m-70) REVERT: F 79 LYS cc_start: 0.9142 (tptt) cc_final: 0.8877 (pttp) REVERT: F 270 ASP cc_start: 0.8144 (m-30) cc_final: 0.7296 (t70) REVERT: U 13 ASP cc_start: 0.8166 (t0) cc_final: 0.7951 (t0) REVERT: U 41 SER cc_start: 0.8027 (m) cc_final: 0.7820 (p) REVERT: U 325 MET cc_start: 0.8465 (mmm) cc_final: 0.8042 (mmt) REVERT: U 332 GLU cc_start: 0.8255 (tt0) cc_final: 0.7825 (tp30) REVERT: U 370 VAL cc_start: 0.6361 (m) cc_final: 0.5886 (t) REVERT: U 560 MET cc_start: 0.7325 (mmp) cc_final: 0.6997 (mmp) REVERT: U 593 SER cc_start: 0.7665 (m) cc_final: 0.7388 (p) REVERT: U 696 ILE cc_start: 0.5810 (tt) cc_final: 0.5442 (tt) REVERT: U 893 THR cc_start: 0.8473 (m) cc_final: 0.8230 (p) REVERT: U 926 GLU cc_start: 0.9459 (pm20) cc_final: 0.9179 (pm20) REVERT: V 175 MET cc_start: 0.8437 (ppp) cc_final: 0.7676 (ptt) REVERT: V 304 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7613 (tp30) REVERT: V 367 VAL cc_start: 0.5660 (t) cc_final: 0.5419 (t) REVERT: V 471 GLU cc_start: 0.8869 (tp30) cc_final: 0.8588 (tp30) REVERT: W 183 VAL cc_start: 0.9259 (t) cc_final: 0.8662 (t) REVERT: W 185 PHE cc_start: 0.9046 (t80) cc_final: 0.8835 (t80) REVERT: W 190 MET cc_start: 0.8295 (mmp) cc_final: 0.7665 (mmt) REVERT: W 193 CYS cc_start: 0.8741 (m) cc_final: 0.8161 (p) REVERT: W 227 TYR cc_start: 0.8733 (m-80) cc_final: 0.8502 (m-10) REVERT: W 241 LEU cc_start: 0.8953 (tp) cc_final: 0.8493 (mt) REVERT: W 255 CYS cc_start: 0.9364 (t) cc_final: 0.9083 (t) REVERT: W 282 GLU cc_start: 0.9032 (tp30) cc_final: 0.8743 (tm-30) REVERT: W 366 MET cc_start: 0.5333 (mtm) cc_final: 0.5064 (mtt) REVERT: X 360 ASP cc_start: 0.9081 (m-30) cc_final: 0.8819 (t0) REVERT: X 408 SER cc_start: 0.8422 (t) cc_final: 0.8166 (m) REVERT: X 412 ASP cc_start: 0.8539 (m-30) cc_final: 0.8323 (m-30) REVERT: X 413 SER cc_start: 0.7048 (m) cc_final: 0.6374 (t) REVERT: Y 83 ARG cc_start: 0.9798 (mtt180) cc_final: 0.9544 (tpm170) REVERT: Y 228 MET cc_start: 0.6342 (ptt) cc_final: 0.5955 (ptt) REVERT: Z 44 GLN cc_start: 0.8367 (mm-40) cc_final: 0.8152 (mm-40) REVERT: Z 59 ASP cc_start: 0.6358 (t0) cc_final: 0.5695 (t0) REVERT: Z 79 TYR cc_start: 0.7445 (t80) cc_final: 0.7177 (t80) REVERT: Z 131 LEU cc_start: 0.9340 (tp) cc_final: 0.8977 (tp) REVERT: Z 170 VAL cc_start: 0.8220 (t) cc_final: 0.7641 (p) REVERT: a 87 MET cc_start: 0.6322 (mpp) cc_final: 0.5920 (mtm) REVERT: a 375 LEU cc_start: 0.8225 (mt) cc_final: 0.7921 (mt) REVERT: b 1 MET cc_start: 0.7142 (mmt) cc_final: 0.6540 (mmm) REVERT: b 14 GLU cc_start: 0.8282 (mm-30) cc_final: 0.7959 (mm-30) REVERT: b 67 ASP cc_start: 0.7196 (t0) cc_final: 0.6869 (t0) REVERT: b 118 GLU cc_start: 0.8811 (mp0) cc_final: 0.8176 (mp0) REVERT: b 146 GLU cc_start: 0.8164 (pm20) cc_final: 0.7794 (pm20) REVERT: b 181 ASP cc_start: 0.9608 (m-30) cc_final: 0.9271 (p0) REVERT: c 26 ASP cc_start: 0.6372 (t0) cc_final: 0.5988 (t0) REVERT: c 56 LEU cc_start: 0.6411 (mm) cc_final: 0.6161 (mp) REVERT: c 64 ASP cc_start: 0.8436 (m-30) cc_final: 0.7679 (t0) REVERT: c 87 VAL cc_start: 0.8470 (t) cc_final: 0.8115 (t) REVERT: c 145 VAL cc_start: 0.6762 (p) cc_final: 0.6303 (p) REVERT: c 175 ARG cc_start: 0.6926 (mtm180) cc_final: 0.6459 (mtm180) REVERT: c 190 GLN cc_start: 0.8786 (tt0) cc_final: 0.8357 (tp-100) REVERT: c 279 ASP cc_start: 0.8714 (t0) cc_final: 0.8013 (p0) REVERT: c 283 HIS cc_start: 0.7621 (m90) cc_final: 0.7251 (m170) REVERT: c 286 GLU cc_start: 0.8205 (pt0) cc_final: 0.7951 (pt0) REVERT: d 102 TRP cc_start: 0.8396 (t60) cc_final: 0.8038 (t60) REVERT: d 141 LEU cc_start: 0.7524 (mt) cc_final: 0.6970 (mm) REVERT: d 211 GLU cc_start: 0.8614 (tp30) cc_final: 0.8407 (tp30) REVERT: d 347 GLU cc_start: 0.8734 (mm-30) cc_final: 0.8437 (mt-10) REVERT: e 43 TRP cc_start: 0.8355 (t60) cc_final: 0.8148 (t60) REVERT: e 47 ASN cc_start: 0.7883 (t0) cc_final: 0.7678 (t0) REVERT: g 121 LYS cc_start: 0.7523 (ptpt) cc_final: 0.7303 (pttt) REVERT: g 148 ASN cc_start: 0.7845 (m-40) cc_final: 0.7571 (t0) REVERT: g 200 LEU cc_start: 0.7858 (mt) cc_final: 0.7240 (mp) REVERT: g 205 ASP cc_start: 0.5869 (p0) cc_final: 0.5523 (p0) REVERT: g 213 GLU cc_start: 0.9035 (pm20) cc_final: 0.8717 (pm20) REVERT: g 262 TYR cc_start: 0.5836 (t80) cc_final: 0.5624 (t80) REVERT: g 277 ASP cc_start: 0.8801 (m-30) cc_final: 0.8520 (m-30) outliers start: 12 outliers final: 2 residues processed: 996 average time/residue: 0.2630 time to fit residues: 412.5812 Evaluate side-chains 525 residues out of total 4573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 522 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 351 LYS Chi-restraints excluded: chain F residue 36 MET Chi-restraints excluded: chain Y residue 53 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 394 optimal weight: 0.8980 chunk 430 optimal weight: 9.9990 chunk 41 optimal weight: 2.9990 chunk 265 optimal weight: 9.9990 chunk 497 optimal weight: 5.9990 chunk 414 optimal weight: 6.9990 chunk 310 optimal weight: 2.9990 chunk 488 optimal weight: 9.9990 chunk 366 optimal weight: 2.9990 chunk 223 optimal weight: 0.9990 chunk 142 optimal weight: 0.2980 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 48 GLN C 67 GLN ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 GLN D 312 ASN ** E 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 226 GLN F 64 HIS ** F 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 283 ASN W 167 GLN ** W 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 23 HIS a 129 GLN a 273 GLN b 56 ASN ** b 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 176 GLN c 180 ASN c 199 HIS c 219 ASN c 237 HIS c 241 ASN ** c 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 283 HIS c 295 ASN d 189 HIS ** g 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 242 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.091189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.064970 restraints weight = 160728.894| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 4.12 r_work: 0.3192 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3181 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 37 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (12 function evaluations) r_final: 0.3178 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 42318 Z= 0.161 Angle : 0.673 14.113 57155 Z= 0.344 Chirality : 0.043 0.208 6495 Planarity : 0.005 0.053 7357 Dihedral : 8.510 157.416 5771 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.70 % Favored : 96.28 % Rotamer: Outliers : 1.42 % Allowed : 9.21 % Favored : 89.37 % 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: -0.88 (0.11), residues: 5162 helix: -0.02 (0.09), residues: 2988 sheet: -0.76 (0.26), residues: 412 loop : -1.34 (0.14), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG U 572 TYR 0.020 0.002 TYR Y 54 PHE 0.017 0.001 PHE D 263 TRP 0.021 0.002 TRP Y 174 HIS 0.009 0.001 HIS Z 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (42315) covalent geometry : angle 0.67273 / 0.34 (57155) hydrogen bonds : bond 0.04293 / 2.87 ( 2214) hydrogen bonds : angle 4.86298 / 3.34 ( 6489) metal coordination : bond 0.01704 / 0.87 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10324 Ramachandran restraints generated. 5162 Oldfield, 0 Emsley, 5162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10324 Ramachandran restraints generated. 5162 Oldfield, 0 Emsley, 5162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 4573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 536 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 80 MET cc_start: 0.7986 (OUTLIER) cc_final: 0.7687 (mtm) REVERT: C 223 PHE cc_start: 0.8308 (m-80) cc_final: 0.7943 (m-80) REVERT: C 293 MET cc_start: 0.8077 (tpp) cc_final: 0.7800 (tpt) REVERT: C 351 MET cc_start: 0.3775 (pmm) cc_final: 0.3549 (pmm) REVERT: D 120 ASP cc_start: 0.9026 (m-30) cc_final: 0.8140 (p0) REVERT: D 141 ASP cc_start: 0.8738 (t0) cc_final: 0.8490 (t0) REVERT: D 170 MET cc_start: 0.5047 (ptt) cc_final: 0.4137 (mmt) REVERT: D 214 MET cc_start: 0.8375 (ptm) cc_final: 0.8126 (ptm) REVERT: D 296 MET cc_start: 0.8795 (ppp) cc_final: 0.8579 (ppp) REVERT: D 351 LYS cc_start: 0.9017 (pttm) cc_final: 0.8760 (tptp) REVERT: E 40 TYR cc_start: 0.8450 (t80) cc_final: 0.7930 (t80) REVERT: E 66 GLU cc_start: 0.8769 (tp30) cc_final: 0.8291 (tp30) REVERT: E 120 TYR cc_start: 0.8420 (t80) cc_final: 0.7954 (t80) REVERT: E 124 HIS cc_start: 0.8354 (p-80) cc_final: 0.7937 (p90) REVERT: E 151 LEU cc_start: 0.8985 (tp) cc_final: 0.8730 (tp) REVERT: E 155 ASN cc_start: 0.8523 (t0) cc_final: 0.8088 (t0) REVERT: E 207 TYR cc_start: 0.6243 (m-10) cc_final: 0.5974 (m-10) REVERT: E 220 ASN cc_start: 0.9386 (m-40) cc_final: 0.9060 (m110) REVERT: E 275 MET cc_start: 0.8653 (mmm) cc_final: 0.8178 (mpp) REVERT: F 55 MET cc_start: 0.8580 (ptp) cc_final: 0.8248 (ptm) REVERT: F 259 MET cc_start: 0.6074 (tpt) cc_final: 0.5843 (tpt) REVERT: U 13 ASP cc_start: 0.8150 (t0) cc_final: 0.7926 (t0) REVERT: U 332 GLU cc_start: 0.8264 (tt0) cc_final: 0.8008 (tp30) REVERT: U 497 LEU cc_start: 0.9622 (OUTLIER) cc_final: 0.9408 (mm) REVERT: U 556 MET cc_start: 0.9188 (tpt) cc_final: 0.8841 (tpt) REVERT: U 560 MET cc_start: 0.9211 (mmp) cc_final: 0.8973 (mmp) REVERT: U 885 MET cc_start: 0.8133 (mpp) cc_final: 0.7507 (mtp) REVERT: V 66 GLU cc_start: 0.9317 (mm-30) cc_final: 0.8969 (mm-30) REVERT: V 175 MET cc_start: 0.8349 (ppp) cc_final: 0.8061 (ppp) REVERT: V 409 MET cc_start: 0.8674 (tmm) cc_final: 0.8268 (ppp) REVERT: V 471 GLU cc_start: 0.8998 (tp30) cc_final: 0.8678 (tp30) REVERT: W 193 CYS cc_start: 0.9324 (m) cc_final: 0.8733 (p) REVERT: W 212 LYS cc_start: 0.9481 (tppt) cc_final: 0.9056 (tptp) REVERT: X 328 ASP cc_start: 0.9564 (m-30) cc_final: 0.9273 (t0) REVERT: X 394 ASP cc_start: 0.7293 (t0) cc_final: 0.6636 (t0) REVERT: X 398 GLU cc_start: 0.8954 (mt-10) cc_final: 0.8669 (mt-10) REVERT: X 405 GLN cc_start: 0.8318 (tm-30) cc_final: 0.8012 (tm-30) REVERT: X 413 SER cc_start: 0.9338 (m) cc_final: 0.9127 (t) REVERT: Y 83 ARG cc_start: 0.9570 (mtt180) cc_final: 0.9290 (tpm170) REVERT: Y 374 ASP cc_start: 0.8713 (m-30) cc_final: 0.8511 (m-30) REVERT: a 24 ARG cc_start: 0.9513 (tpp-160) cc_final: 0.9172 (mmm-85) REVERT: a 87 MET cc_start: 0.7734 (mpp) cc_final: 0.7216 (mtp) REVERT: b 1 MET cc_start: 0.5530 (mmt) cc_final: 0.5249 (mmm) REVERT: b 57 ASP cc_start: 0.8776 (m-30) cc_final: 0.8558 (t70) REVERT: b 67 ASP cc_start: 0.8940 (t0) cc_final: 0.8376 (t70) REVERT: b 181 ASP cc_start: 0.9582 (m-30) cc_final: 0.9078 (p0) REVERT: c 64 ASP cc_start: 0.9218 (m-30) cc_final: 0.8621 (t0) REVERT: c 208 ARG cc_start: 0.8727 (mmm-85) cc_final: 0.8417 (mmm-85) REVERT: c 279 ASP cc_start: 0.9133 (t0) cc_final: 0.8613 (p0) REVERT: c 282 ARG cc_start: 0.8412 (ttp80) cc_final: 0.7930 (ttp80) REVERT: d 153 GLN cc_start: 0.8574 (mm110) cc_final: 0.7811 (mp10) REVERT: d 207 GLU cc_start: 0.8643 (mp0) cc_final: 0.8405 (mp0) REVERT: e 1 MET cc_start: 0.7378 (mpp) cc_final: 0.6341 (mpp) REVERT: g 204 MET cc_start: 0.8117 (ptm) cc_final: 0.7851 (ptm) REVERT: g 275 MET cc_start: 0.8482 (mmm) cc_final: 0.8243 (tpp) outliers start: 65 outliers final: 29 residues processed: 573 average time/residue: 0.2348 time to fit residues: 221.6775 Evaluate side-chains 462 residues out of total 4573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 431 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 112 CYS Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain F residue 121 CYS Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain U residue 497 LEU Chi-restraints excluded: chain U residue 732 LEU Chi-restraints excluded: chain V residue 157 THR Chi-restraints excluded: chain V residue 251 LEU Chi-restraints excluded: chain W residue 213 PHE Chi-restraints excluded: chain X residue 320 SER Chi-restraints excluded: chain X residue 419 LYS Chi-restraints excluded: chain Z residue 70 LEU Chi-restraints excluded: chain Z residue 180 LYS Chi-restraints excluded: chain a residue 277 LEU Chi-restraints excluded: chain c residue 60 GLU Chi-restraints excluded: chain c residue 176 GLN Chi-restraints excluded: chain c residue 183 HIS Chi-restraints excluded: chain c residue 238 CYS Chi-restraints excluded: chain c residue 248 MET Chi-restraints excluded: chain d residue 119 LEU Chi-restraints excluded: chain d residue 309 VAL Chi-restraints excluded: chain g residue 118 ASP Chi-restraints excluded: chain g residue 167 ILE Chi-restraints excluded: chain g residue 230 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 309 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 507 optimal weight: 8.9990 chunk 510 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 434 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 175 optimal weight: 7.9990 chunk 165 optimal weight: 0.6980 chunk 348 optimal weight: 0.9980 chunk 307 optimal weight: 0.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 241 HIS ** C 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 187 HIS D 390 ASN ** E 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 HIS ** F 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 154 ASN F 315 ASN ** U 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 257 ASN W 210 ASN W 246 HIS ** W 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 388 ASN ** Z 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 23 HIS c 180 ASN ** c 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 295 ASN ** d 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 189 HIS ** g 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.089616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.063293 restraints weight = 160120.521| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 4.05 r_work: 0.3152 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3142 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 37 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 39 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3142 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 42318 Z= 0.135 Angle : 0.617 13.385 57155 Z= 0.313 Chirality : 0.042 0.197 6495 Planarity : 0.004 0.049 7357 Dihedral : 7.670 153.125 5762 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.82 % Favored : 96.16 % Rotamer: Outliers : 1.51 % Allowed : 11.09 % Favored : 87.40 % 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: -0.14 (0.12), residues: 5162 helix: 0.64 (0.09), residues: 2984 sheet: -0.71 (0.26), residues: 419 loop : -1.08 (0.15), residues: 1759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 229 TYR 0.029 0.001 TYR W 226 PHE 0.024 0.001 PHE F 320 TRP 0.020 0.002 TRP a 356 HIS 0.012 0.001 HIS a 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (42315) covalent geometry : angle 0.61698 / 0.31 (57155) hydrogen bonds : bond 0.03873 / 2.60 ( 2214) hydrogen bonds : angle 4.47096 / 3.08 ( 6489) metal coordination : bond 0.01265 / 0.65 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10324 Ramachandran restraints generated. 5162 Oldfield, 0 Emsley, 5162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10324 Ramachandran restraints generated. 5162 Oldfield, 0 Emsley, 5162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 4573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 466 time to evaluate : 1.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 223 PHE cc_start: 0.8399 (m-80) cc_final: 0.8073 (m-80) REVERT: C 273 MET cc_start: 0.7743 (tpp) cc_final: 0.7520 (tpp) REVERT: C 293 MET cc_start: 0.8372 (tpp) cc_final: 0.8131 (tpt) REVERT: D 120 ASP cc_start: 0.9049 (m-30) cc_final: 0.8150 (p0) REVERT: D 141 ASP cc_start: 0.8783 (t0) cc_final: 0.8581 (t0) REVERT: D 170 MET cc_start: 0.5070 (ptt) cc_final: 0.3973 (mmt) REVERT: D 214 MET cc_start: 0.8559 (ptm) cc_final: 0.8330 (ptm) REVERT: D 351 LYS cc_start: 0.9100 (pttm) cc_final: 0.8843 (tptp) REVERT: E 40 TYR cc_start: 0.8197 (t80) cc_final: 0.7897 (t80) REVERT: E 132 TYR cc_start: 0.7863 (t80) cc_final: 0.7258 (m-80) REVERT: E 151 LEU cc_start: 0.8996 (tp) cc_final: 0.8736 (tp) REVERT: E 155 ASN cc_start: 0.8649 (t0) cc_final: 0.8305 (t0) REVERT: E 220 ASN cc_start: 0.9341 (m-40) cc_final: 0.9071 (m110) REVERT: E 275 MET cc_start: 0.8699 (mmm) cc_final: 0.8213 (mpp) REVERT: F 36 MET cc_start: 0.5675 (tpp) cc_final: 0.5438 (tpp) REVERT: U 13 ASP cc_start: 0.8146 (t0) cc_final: 0.7881 (t0) REVERT: U 332 GLU cc_start: 0.8315 (tt0) cc_final: 0.8054 (tp30) REVERT: U 497 LEU cc_start: 0.9610 (OUTLIER) cc_final: 0.9384 (mm) REVERT: U 885 MET cc_start: 0.8264 (mpp) cc_final: 0.7663 (mtp) REVERT: V 66 GLU cc_start: 0.9356 (mm-30) cc_final: 0.8992 (mm-30) REVERT: V 175 MET cc_start: 0.8322 (ppp) cc_final: 0.8045 (ppp) REVERT: V 409 MET cc_start: 0.8713 (tmm) cc_final: 0.8254 (ppp) REVERT: V 471 GLU cc_start: 0.9000 (tp30) cc_final: 0.8690 (tp30) REVERT: V 494 MET cc_start: 0.8725 (mmm) cc_final: 0.8243 (mmm) REVERT: W 193 CYS cc_start: 0.9376 (m) cc_final: 0.8791 (p) REVERT: X 322 HIS cc_start: 0.9134 (m90) cc_final: 0.8932 (m90) REVERT: X 328 ASP cc_start: 0.9561 (m-30) cc_final: 0.9272 (t0) REVERT: X 368 MET cc_start: 0.9064 (ptm) cc_final: 0.8799 (ptm) REVERT: X 394 ASP cc_start: 0.7632 (t0) cc_final: 0.7238 (t0) REVERT: X 405 GLN cc_start: 0.8454 (tm-30) cc_final: 0.8036 (tm-30) REVERT: X 413 SER cc_start: 0.9365 (m) cc_final: 0.9163 (t) REVERT: Y 83 ARG cc_start: 0.9569 (mtt180) cc_final: 0.9290 (tpm170) REVERT: Y 374 ASP cc_start: 0.8763 (m-30) cc_final: 0.8544 (m-30) REVERT: Z 244 GLU cc_start: 0.8788 (mp0) cc_final: 0.8467 (tp30) REVERT: a 24 ARG cc_start: 0.9501 (tpp-160) cc_final: 0.9171 (mmm-85) REVERT: a 87 MET cc_start: 0.7757 (mpp) cc_final: 0.7382 (mtp) REVERT: a 363 MET cc_start: 0.9204 (tpp) cc_final: 0.8818 (tpp) REVERT: b 1 MET cc_start: 0.5592 (mmt) cc_final: 0.5262 (mmm) REVERT: b 16 MET cc_start: 0.9111 (tpp) cc_final: 0.8664 (tpp) REVERT: b 67 ASP cc_start: 0.8960 (t0) cc_final: 0.8419 (t70) REVERT: b 181 ASP cc_start: 0.9586 (m-30) cc_final: 0.9079 (p0) REVERT: c 64 ASP cc_start: 0.9256 (m-30) cc_final: 0.8618 (t0) REVERT: c 279 ASP cc_start: 0.9120 (t0) cc_final: 0.8619 (p0) REVERT: d 153 GLN cc_start: 0.8414 (mm110) cc_final: 0.7788 (mp10) REVERT: d 160 ASP cc_start: 0.8077 (t0) cc_final: 0.6947 (p0) REVERT: d 328 THR cc_start: 0.8016 (p) cc_final: 0.7810 (t) REVERT: g 127 MET cc_start: 0.9043 (mmp) cc_final: 0.8473 (mmp) REVERT: g 204 MET cc_start: 0.8413 (ptm) cc_final: 0.8207 (ptm) REVERT: g 225 ILE cc_start: 0.8693 (pt) cc_final: 0.8467 (pt) REVERT: g 275 MET cc_start: 0.8557 (mmm) cc_final: 0.8310 (tpp) outliers start: 69 outliers final: 42 residues processed: 509 average time/residue: 0.2325 time to fit residues: 195.0388 Evaluate side-chains 468 residues out of total 4573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 425 time to evaluate : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 112 CYS Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain E residue 51 GLN Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain U residue 11 LEU Chi-restraints excluded: chain U residue 497 LEU Chi-restraints excluded: chain U residue 555 VAL Chi-restraints excluded: chain U residue 701 ILE Chi-restraints excluded: chain U residue 720 LYS Chi-restraints excluded: chain U residue 732 LEU Chi-restraints excluded: chain V residue 157 THR Chi-restraints excluded: chain V residue 251 LEU Chi-restraints excluded: chain W residue 213 PHE Chi-restraints excluded: chain X residue 380 GLN Chi-restraints excluded: chain X residue 401 LEU Chi-restraints excluded: chain X residue 419 LYS Chi-restraints excluded: chain Y residue 53 TYR Chi-restraints excluded: chain Z residue 70 LEU Chi-restraints excluded: chain Z residue 170 VAL Chi-restraints excluded: chain Z residue 180 LYS Chi-restraints excluded: chain a residue 277 LEU Chi-restraints excluded: chain a residue 336 VAL Chi-restraints excluded: chain c residue 60 GLU Chi-restraints excluded: chain c residue 95 MET Chi-restraints excluded: chain c residue 96 LEU Chi-restraints excluded: chain c residue 180 ASN Chi-restraints excluded: chain c residue 183 HIS Chi-restraints excluded: chain c residue 248 MET Chi-restraints excluded: chain d residue 119 LEU Chi-restraints excluded: chain d residue 205 VAL Chi-restraints excluded: chain d residue 309 VAL Chi-restraints excluded: chain e residue 65 TYR Chi-restraints excluded: chain g residue 118 ASP Chi-restraints excluded: chain g residue 167 ILE Chi-restraints excluded: chain g residue 230 ILE Chi-restraints excluded: chain g residue 231 VAL Chi-restraints excluded: chain g residue 236 VAL Chi-restraints excluded: chain g residue 266 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 46 optimal weight: 10.0000 chunk 269 optimal weight: 0.9990 chunk 388 optimal weight: 8.9990 chunk 464 optimal weight: 0.9990 chunk 412 optimal weight: 0.7980 chunk 181 optimal weight: 6.9990 chunk 111 optimal weight: 9.9990 chunk 460 optimal weight: 0.6980 chunk 470 optimal weight: 7.9990 chunk 320 optimal weight: 30.0000 chunk 375 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 HIS ** E 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 GLN E 271 HIS ** F 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 185 GLN ** X 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 202 ASN a 12 GLN a 23 HIS a 249 GLN c 176 GLN c 183 HIS ** c 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 283 HIS ** c 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 189 HIS ** g 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.095957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.068068 restraints weight = 129908.848| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 4.35 r_work: 0.3124 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3089 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3089 r_free = 0.3089 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 39 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3089 r_free = 0.3089 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 40 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3089 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 42318 Z= 0.129 Angle : 0.594 13.615 57155 Z= 0.298 Chirality : 0.041 0.184 6495 Planarity : 0.004 0.047 7357 Dihedral : 7.303 148.398 5762 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.68 % Favored : 96.30 % Rotamer: Outliers : 1.84 % Allowed : 12.14 % Favored : 86.03 % 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: 0.23 (0.12), residues: 5162 helix: 0.98 (0.10), residues: 2979 sheet: -0.73 (0.26), residues: 403 loop : -0.97 (0.15), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG V 443 TYR 0.026 0.001 TYR W 226 PHE 0.016 0.001 PHE W 309 TRP 0.028 0.001 TRP a 356 HIS 0.009 0.001 HIS W 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (42315) covalent geometry : angle 0.59444 / 0.30 (57155) hydrogen bonds : bond 0.03698 / 2.48 ( 2214) hydrogen bonds : angle 4.27278 / 2.94 ( 6489) metal coordination : bond 0.00949 / 0.48 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10324 Ramachandran restraints generated. 5162 Oldfield, 0 Emsley, 5162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10324 Ramachandran restraints generated. 5162 Oldfield, 0 Emsley, 5162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 4573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 451 time to evaluate : 1.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 223 PHE cc_start: 0.8450 (m-80) cc_final: 0.8152 (m-80) REVERT: C 273 MET cc_start: 0.7753 (tpp) cc_final: 0.7463 (tpp) REVERT: C 293 MET cc_start: 0.8453 (tpp) cc_final: 0.8250 (tpp) REVERT: D 120 ASP cc_start: 0.9044 (m-30) cc_final: 0.8196 (p0) REVERT: D 141 ASP cc_start: 0.8822 (t0) cc_final: 0.8595 (t0) REVERT: D 214 MET cc_start: 0.8705 (ptm) cc_final: 0.8430 (ptm) REVERT: D 351 LYS cc_start: 0.9172 (pttm) cc_final: 0.8873 (tptp) REVERT: E 40 TYR cc_start: 0.8360 (t80) cc_final: 0.8110 (t80) REVERT: E 66 GLU cc_start: 0.8761 (tp30) cc_final: 0.8490 (tp30) REVERT: E 132 TYR cc_start: 0.7825 (t80) cc_final: 0.7305 (m-80) REVERT: E 151 LEU cc_start: 0.8940 (tp) cc_final: 0.8658 (tp) REVERT: E 155 ASN cc_start: 0.8596 (t0) cc_final: 0.8182 (t0) REVERT: E 220 ASN cc_start: 0.9328 (m-40) cc_final: 0.9077 (m110) REVERT: E 275 MET cc_start: 0.8783 (mmm) cc_final: 0.8319 (mpp) REVERT: F 259 MET cc_start: 0.5807 (tpt) cc_final: 0.5545 (tpt) REVERT: U 13 ASP cc_start: 0.8159 (t0) cc_final: 0.7887 (t0) REVERT: U 176 MET cc_start: 0.8907 (tpp) cc_final: 0.8649 (tpt) REVERT: U 332 GLU cc_start: 0.8456 (tt0) cc_final: 0.8085 (tp30) REVERT: U 497 LEU cc_start: 0.9619 (OUTLIER) cc_final: 0.9405 (mm) REVERT: U 885 MET cc_start: 0.8274 (mpp) cc_final: 0.7640 (mtp) REVERT: V 66 GLU cc_start: 0.9370 (mm-30) cc_final: 0.9005 (mm-30) REVERT: V 139 MET cc_start: 0.9261 (mmm) cc_final: 0.8543 (mpp) REVERT: V 175 MET cc_start: 0.8296 (ppp) cc_final: 0.8027 (ppp) REVERT: V 409 MET cc_start: 0.8760 (tmm) cc_final: 0.8246 (ppp) REVERT: V 448 GLU cc_start: 0.8967 (mm-30) cc_final: 0.8762 (mm-30) REVERT: V 471 GLU cc_start: 0.9009 (tp30) cc_final: 0.8691 (tp30) REVERT: V 494 MET cc_start: 0.8732 (mmm) cc_final: 0.8217 (mmm) REVERT: W 212 LYS cc_start: 0.9470 (tppt) cc_final: 0.9043 (tptp) REVERT: X 328 ASP cc_start: 0.9562 (m-30) cc_final: 0.9213 (t70) REVERT: X 332 GLU cc_start: 0.9115 (tm-30) cc_final: 0.8791 (pp20) REVERT: X 368 MET cc_start: 0.9023 (ptm) cc_final: 0.8758 (ptm) REVERT: X 379 ASP cc_start: 0.8529 (m-30) cc_final: 0.8095 (m-30) REVERT: X 394 ASP cc_start: 0.7609 (t0) cc_final: 0.7272 (t0) REVERT: X 405 GLN cc_start: 0.8543 (tm-30) cc_final: 0.8062 (tm-30) REVERT: Y 83 ARG cc_start: 0.9660 (mtt180) cc_final: 0.9378 (tpm170) REVERT: Y 374 ASP cc_start: 0.8797 (m-30) cc_final: 0.8551 (m-30) REVERT: a 23 HIS cc_start: 0.9123 (OUTLIER) cc_final: 0.8899 (m170) REVERT: a 24 ARG cc_start: 0.9445 (tpp-160) cc_final: 0.9173 (mmm-85) REVERT: a 87 MET cc_start: 0.7842 (mpp) cc_final: 0.7622 (mtp) REVERT: b 7 MET cc_start: 0.8395 (tpp) cc_final: 0.8164 (tpt) REVERT: b 67 ASP cc_start: 0.8989 (t0) cc_final: 0.8448 (t70) REVERT: b 181 ASP cc_start: 0.9608 (m-30) cc_final: 0.9101 (p0) REVERT: c 64 ASP cc_start: 0.9290 (m-30) cc_final: 0.8612 (t0) REVERT: c 107 MET cc_start: 0.8702 (ptm) cc_final: 0.8493 (ptm) REVERT: c 279 ASP cc_start: 0.9143 (t0) cc_final: 0.8641 (p0) REVERT: c 287 HIS cc_start: 0.7707 (m170) cc_final: 0.7496 (m170) REVERT: c 303 MET cc_start: 0.9160 (mmm) cc_final: 0.8724 (mpp) REVERT: d 153 GLN cc_start: 0.8380 (mm110) cc_final: 0.7798 (mp10) REVERT: d 160 ASP cc_start: 0.8379 (t0) cc_final: 0.7293 (p0) REVERT: d 277 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.8047 (pmtt) REVERT: e 67 MET cc_start: 0.9054 (mpp) cc_final: 0.8719 (mpp) REVERT: g 127 MET cc_start: 0.9051 (mmp) cc_final: 0.8494 (mmp) REVERT: g 164 GLN cc_start: 0.7977 (mm110) cc_final: 0.7596 (mm110) REVERT: g 204 MET cc_start: 0.8662 (ptm) cc_final: 0.8199 (ptm) REVERT: g 225 ILE cc_start: 0.8725 (pt) cc_final: 0.8452 (pt) REVERT: g 275 MET cc_start: 0.8558 (mmm) cc_final: 0.8275 (tpp) outliers start: 84 outliers final: 48 residues processed: 505 average time/residue: 0.2505 time to fit residues: 210.3104 Evaluate side-chains 473 residues out of total 4573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 422 time to evaluate : 1.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 112 CYS Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain E residue 19 HIS Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain U residue 69 TYR Chi-restraints excluded: chain U residue 497 LEU Chi-restraints excluded: chain U residue 701 ILE Chi-restraints excluded: chain U residue 732 LEU Chi-restraints excluded: chain V residue 157 THR Chi-restraints excluded: chain V residue 229 SER Chi-restraints excluded: chain W residue 213 PHE Chi-restraints excluded: chain W residue 236 HIS Chi-restraints excluded: chain X residue 380 GLN Chi-restraints excluded: chain X residue 401 LEU Chi-restraints excluded: chain Y residue 47 ASP Chi-restraints excluded: chain Y residue 174 TRP Chi-restraints excluded: chain Y residue 277 VAL Chi-restraints excluded: chain Y residue 302 HIS Chi-restraints excluded: chain Z residue 70 LEU Chi-restraints excluded: chain Z residue 180 LYS Chi-restraints excluded: chain a residue 23 HIS Chi-restraints excluded: chain a residue 277 LEU Chi-restraints excluded: chain b residue 143 PHE Chi-restraints excluded: chain c residue 60 GLU Chi-restraints excluded: chain c residue 96 LEU Chi-restraints excluded: chain c residue 98 MET Chi-restraints excluded: chain c residue 156 VAL Chi-restraints excluded: chain c residue 238 CYS Chi-restraints excluded: chain c residue 248 MET Chi-restraints excluded: chain d residue 87 VAL Chi-restraints excluded: chain d residue 205 VAL Chi-restraints excluded: chain d residue 277 LYS Chi-restraints excluded: chain d residue 309 VAL Chi-restraints excluded: chain e residue 65 TYR Chi-restraints excluded: chain g residue 118 ASP Chi-restraints excluded: chain g residue 167 ILE Chi-restraints excluded: chain g residue 220 LEU Chi-restraints excluded: chain g residue 230 ILE Chi-restraints excluded: chain g residue 231 VAL Chi-restraints excluded: chain g residue 236 VAL Chi-restraints excluded: chain g residue 266 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 61 optimal weight: 10.0000 chunk 96 optimal weight: 3.9990 chunk 373 optimal weight: 0.0000 chunk 222 optimal weight: 1.9990 chunk 151 optimal weight: 0.6980 chunk 326 optimal weight: 40.0000 chunk 236 optimal weight: 5.9990 chunk 89 optimal weight: 0.7980 chunk 310 optimal weight: 5.9990 chunk 398 optimal weight: 6.9990 chunk 264 optimal weight: 8.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 GLN ** F 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 647 HIS ** W 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 12 GLN c 176 GLN c 180 ASN c 256 ASN c 283 HIS ** c 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 189 HIS ** g 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.088332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.061654 restraints weight = 159185.199| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 4.06 r_work: 0.3097 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3091 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 40 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 40 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3091 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 42318 Z= 0.134 Angle : 0.588 13.132 57155 Z= 0.295 Chirality : 0.041 0.308 6495 Planarity : 0.004 0.046 7357 Dihedral : 7.142 146.178 5762 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.72 % Favored : 96.26 % Rotamer: Outliers : 1.66 % Allowed : 13.65 % Favored : 84.69 % 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: 0.43 (0.12), residues: 5162 helix: 1.17 (0.10), residues: 2971 sheet: -0.75 (0.26), residues: 410 loop : -0.88 (0.15), residues: 1781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG W 289 TYR 0.030 0.001 TYR W 226 PHE 0.019 0.001 PHE F 320 TRP 0.026 0.001 TRP a 356 HIS 0.035 0.001 HIS a 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (42315) covalent geometry : angle 0.58816 / 0.29 (57155) hydrogen bonds : bond 0.03663 / 2.45 ( 2214) hydrogen bonds : angle 4.19501 / 2.89 ( 6489) metal coordination : bond 0.01013 / 0.52 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10324 Ramachandran restraints generated. 5162 Oldfield, 0 Emsley, 5162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10324 Ramachandran restraints generated. 5162 Oldfield, 0 Emsley, 5162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 4573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 437 time to evaluate : 1.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 223 PHE cc_start: 0.8458 (m-80) cc_final: 0.8176 (m-80) REVERT: D 64 GLU cc_start: 0.9268 (tp30) cc_final: 0.8908 (tt0) REVERT: D 120 ASP cc_start: 0.9030 (m-30) cc_final: 0.8161 (p0) REVERT: D 141 ASP cc_start: 0.8805 (t0) cc_final: 0.8569 (t0) REVERT: D 214 MET cc_start: 0.8769 (ptm) cc_final: 0.8429 (ptm) REVERT: D 351 LYS cc_start: 0.9254 (pttm) cc_final: 0.8901 (tptp) REVERT: E 66 GLU cc_start: 0.8795 (tp30) cc_final: 0.8339 (tp30) REVERT: E 120 TYR cc_start: 0.8488 (t80) cc_final: 0.8171 (t80) REVERT: E 124 HIS cc_start: 0.8382 (p-80) cc_final: 0.8161 (p90) REVERT: E 132 TYR cc_start: 0.7864 (t80) cc_final: 0.7404 (m-80) REVERT: E 151 LEU cc_start: 0.8949 (tp) cc_final: 0.8674 (tp) REVERT: E 155 ASN cc_start: 0.8602 (t0) cc_final: 0.8207 (t0) REVERT: E 220 ASN cc_start: 0.9330 (m-40) cc_final: 0.9080 (m110) REVERT: E 275 MET cc_start: 0.8844 (mmm) cc_final: 0.8385 (mpp) REVERT: F 259 MET cc_start: 0.6145 (tpt) cc_final: 0.5754 (tpt) REVERT: F 409 ARG cc_start: 0.7203 (OUTLIER) cc_final: 0.6862 (mtt180) REVERT: U 325 MET cc_start: 0.9314 (mtp) cc_final: 0.9000 (tpp) REVERT: U 332 GLU cc_start: 0.8533 (tt0) cc_final: 0.8154 (tp30) REVERT: U 560 MET cc_start: 0.9375 (mmm) cc_final: 0.8966 (mmm) REVERT: U 675 MET cc_start: 0.9570 (OUTLIER) cc_final: 0.9262 (ttp) REVERT: U 885 MET cc_start: 0.8323 (mpp) cc_final: 0.7584 (mpp) REVERT: V 66 GLU cc_start: 0.9398 (mm-30) cc_final: 0.9021 (mm-30) REVERT: V 150 ARG cc_start: 0.8426 (ttm170) cc_final: 0.8146 (ttm170) REVERT: V 175 MET cc_start: 0.8288 (ppp) cc_final: 0.8013 (ppp) REVERT: V 409 MET cc_start: 0.8804 (tmm) cc_final: 0.8267 (ppp) REVERT: V 471 GLU cc_start: 0.9031 (tp30) cc_final: 0.8723 (tp30) REVERT: V 494 MET cc_start: 0.8745 (mmm) cc_final: 0.8227 (mmm) REVERT: W 212 LYS cc_start: 0.9460 (tppt) cc_final: 0.9034 (tptt) REVERT: W 289 ARG cc_start: 0.8365 (mtm110) cc_final: 0.8025 (mtm110) REVERT: X 328 ASP cc_start: 0.9577 (m-30) cc_final: 0.9228 (t70) REVERT: X 332 GLU cc_start: 0.9064 (tm-30) cc_final: 0.8758 (pp20) REVERT: X 368 MET cc_start: 0.9052 (ptm) cc_final: 0.8827 (ptm) REVERT: X 380 GLN cc_start: 0.9033 (OUTLIER) cc_final: 0.8513 (tt0) REVERT: X 382 GLU cc_start: 0.8851 (pm20) cc_final: 0.8620 (pm20) REVERT: X 394 ASP cc_start: 0.7757 (t0) cc_final: 0.7422 (t0) REVERT: X 405 GLN cc_start: 0.8609 (tm-30) cc_final: 0.8121 (tm-30) REVERT: Y 83 ARG cc_start: 0.9612 (mtt180) cc_final: 0.9345 (tpm170) REVERT: Y 374 ASP cc_start: 0.8853 (m-30) cc_final: 0.8599 (m-30) REVERT: Z 90 ARG cc_start: 0.8624 (mtm-85) cc_final: 0.8411 (mtm110) REVERT: Z 138 TYR cc_start: 0.9361 (m-10) cc_final: 0.9075 (m-10) REVERT: Z 177 ARG cc_start: 0.8520 (tpt90) cc_final: 0.8312 (tpt90) REVERT: Z 244 GLU cc_start: 0.8784 (mp0) cc_final: 0.8495 (tp30) REVERT: a 87 MET cc_start: 0.7895 (mpp) cc_final: 0.7663 (mtp) REVERT: b 67 ASP cc_start: 0.8960 (t0) cc_final: 0.8470 (t70) REVERT: b 181 ASP cc_start: 0.9615 (m-30) cc_final: 0.9103 (p0) REVERT: c 64 ASP cc_start: 0.9325 (m-30) cc_final: 0.8648 (t0) REVERT: c 107 MET cc_start: 0.8811 (ptm) cc_final: 0.8603 (ptm) REVERT: c 279 ASP cc_start: 0.9151 (t0) cc_final: 0.8648 (p0) REVERT: c 303 MET cc_start: 0.9190 (mmm) cc_final: 0.8707 (mpp) REVERT: d 153 GLN cc_start: 0.8376 (mm110) cc_final: 0.7810 (mp10) REVERT: d 160 ASP cc_start: 0.8484 (t0) cc_final: 0.7454 (p0) REVERT: d 277 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.8018 (pmtt) REVERT: g 127 MET cc_start: 0.9011 (mmp) cc_final: 0.8496 (mmp) REVERT: g 164 GLN cc_start: 0.7899 (mm110) cc_final: 0.7558 (mm110) REVERT: g 204 MET cc_start: 0.8521 (ptm) cc_final: 0.8247 (ptm) REVERT: g 225 ILE cc_start: 0.8739 (pt) cc_final: 0.8462 (pt) REVERT: g 230 ILE cc_start: 0.7955 (OUTLIER) cc_final: 0.7711 (tp) outliers start: 76 outliers final: 53 residues processed: 485 average time/residue: 0.2428 time to fit residues: 195.1934 Evaluate side-chains 471 residues out of total 4573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 413 time to evaluate : 1.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 112 CYS Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain E residue 19 HIS Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 409 ARG Chi-restraints excluded: chain U residue 69 TYR Chi-restraints excluded: chain U residue 555 VAL Chi-restraints excluded: chain U residue 675 MET Chi-restraints excluded: chain V residue 157 THR Chi-restraints excluded: chain V residue 229 SER Chi-restraints excluded: chain V residue 251 LEU Chi-restraints excluded: chain W residue 193 CYS Chi-restraints excluded: chain W residue 213 PHE Chi-restraints excluded: chain W residue 236 HIS Chi-restraints excluded: chain X residue 380 GLN Chi-restraints excluded: chain X residue 401 LEU Chi-restraints excluded: chain X residue 419 LYS Chi-restraints excluded: chain Y residue 47 ASP Chi-restraints excluded: chain Y residue 174 TRP Chi-restraints excluded: chain Y residue 277 VAL Chi-restraints excluded: chain Y residue 302 HIS Chi-restraints excluded: chain Z residue 18 SER Chi-restraints excluded: chain Z residue 70 LEU Chi-restraints excluded: chain Z residue 120 VAL Chi-restraints excluded: chain Z residue 160 SER Chi-restraints excluded: chain Z residue 180 LYS Chi-restraints excluded: chain a residue 269 LEU Chi-restraints excluded: chain a residue 277 LEU Chi-restraints excluded: chain c residue 60 GLU Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain c residue 96 LEU Chi-restraints excluded: chain c residue 98 MET Chi-restraints excluded: chain c residue 156 VAL Chi-restraints excluded: chain c residue 238 CYS Chi-restraints excluded: chain c residue 248 MET Chi-restraints excluded: chain c residue 283 HIS Chi-restraints excluded: chain d residue 87 VAL Chi-restraints excluded: chain d residue 205 VAL Chi-restraints excluded: chain d residue 277 LYS Chi-restraints excluded: chain d residue 309 VAL Chi-restraints excluded: chain e residue 54 ASN Chi-restraints excluded: chain e residue 65 TYR Chi-restraints excluded: chain g residue 118 ASP Chi-restraints excluded: chain g residue 220 LEU Chi-restraints excluded: chain g residue 230 ILE Chi-restraints excluded: chain g residue 231 VAL Chi-restraints excluded: chain g residue 236 VAL Chi-restraints excluded: chain g residue 266 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 239 optimal weight: 7.9990 chunk 255 optimal weight: 0.9990 chunk 165 optimal weight: 0.0000 chunk 217 optimal weight: 6.9990 chunk 392 optimal weight: 3.9990 chunk 430 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 chunk 135 optimal weight: 50.0000 chunk 26 optimal weight: 20.0000 chunk 167 optimal weight: 0.9980 chunk 287 optimal weight: 0.9990 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 377 HIS ** E 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 GLN F 83 ASN ** U 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 214 HIS Y 273 GLN ** Z 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 35 HIS c 219 ASN ** c 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 189 HIS ** g 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.088790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.062139 restraints weight = 159419.636| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 4.11 r_work: 0.3111 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3098 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 40 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 40 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3098 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 42318 Z= 0.111 Angle : 0.583 13.006 57155 Z= 0.291 Chirality : 0.041 0.204 6495 Planarity : 0.003 0.046 7357 Dihedral : 7.034 144.134 5762 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.80 % Favored : 96.18 % Rotamer: Outliers : 1.73 % Allowed : 14.19 % Favored : 84.08 % 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: 0.56 (0.12), residues: 5162 helix: 1.26 (0.10), residues: 2975 sheet: -0.71 (0.26), residues: 408 loop : -0.81 (0.15), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG a 24 TYR 0.034 0.001 TYR W 226 PHE 0.031 0.001 PHE F 284 TRP 0.020 0.001 TRP a 356 HIS 0.021 0.001 HIS c 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (42315) covalent geometry : angle 0.58275 / 0.29 (57155) hydrogen bonds : bond 0.03520 / 2.36 ( 2214) hydrogen bonds : angle 4.12249 / 2.84 ( 6489) metal coordination : bond 0.00535 / 0.27 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10324 Ramachandran restraints generated. 5162 Oldfield, 0 Emsley, 5162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10324 Ramachandran restraints generated. 5162 Oldfield, 0 Emsley, 5162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 4573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 428 time to evaluate : 1.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 223 PHE cc_start: 0.8443 (m-80) cc_final: 0.8167 (m-80) REVERT: C 351 MET cc_start: 0.3594 (pmm) cc_final: 0.3175 (pmm) REVERT: D 64 GLU cc_start: 0.9263 (tp30) cc_final: 0.8979 (tt0) REVERT: D 120 ASP cc_start: 0.9031 (m-30) cc_final: 0.8205 (p0) REVERT: D 141 ASP cc_start: 0.8777 (t0) cc_final: 0.8556 (t0) REVERT: D 214 MET cc_start: 0.8793 (ptm) cc_final: 0.8435 (ptm) REVERT: D 351 LYS cc_start: 0.9301 (pttm) cc_final: 0.8942 (tptp) REVERT: E 66 GLU cc_start: 0.8771 (tp30) cc_final: 0.8454 (tp30) REVERT: E 120 TYR cc_start: 0.8512 (t80) cc_final: 0.8190 (t80) REVERT: E 124 HIS cc_start: 0.8426 (p-80) cc_final: 0.8223 (p90) REVERT: E 132 TYR cc_start: 0.7846 (t80) cc_final: 0.7422 (m-80) REVERT: E 151 LEU cc_start: 0.8936 (tp) cc_final: 0.8649 (tp) REVERT: E 155 ASN cc_start: 0.8583 (t0) cc_final: 0.7953 (t0) REVERT: E 220 ASN cc_start: 0.9310 (m-40) cc_final: 0.9052 (m110) REVERT: E 275 MET cc_start: 0.8821 (mmm) cc_final: 0.8379 (mpp) REVERT: F 55 MET cc_start: 0.7994 (ptm) cc_final: 0.7399 (ppp) REVERT: F 259 MET cc_start: 0.6180 (tpt) cc_final: 0.5790 (tpt) REVERT: F 386 ARG cc_start: 0.9509 (tpm170) cc_final: 0.9080 (ttp80) REVERT: F 406 ILE cc_start: 0.7888 (OUTLIER) cc_final: 0.7090 (pt) REVERT: U 325 MET cc_start: 0.9302 (mtp) cc_final: 0.8914 (tpp) REVERT: U 332 GLU cc_start: 0.8551 (tt0) cc_final: 0.8162 (tp30) REVERT: U 675 MET cc_start: 0.9576 (OUTLIER) cc_final: 0.9230 (ttp) REVERT: U 885 MET cc_start: 0.8283 (mpp) cc_final: 0.7576 (mpp) REVERT: V 66 GLU cc_start: 0.9379 (mm-30) cc_final: 0.8996 (mm-30) REVERT: V 150 ARG cc_start: 0.8402 (ttm170) cc_final: 0.8121 (ttm170) REVERT: V 175 MET cc_start: 0.8315 (ppp) cc_final: 0.8086 (ppp) REVERT: V 176 MET cc_start: 0.9036 (ttp) cc_final: 0.8719 (tmm) REVERT: V 211 TYR cc_start: 0.8366 (m-80) cc_final: 0.8017 (m-80) REVERT: V 409 MET cc_start: 0.8806 (tmm) cc_final: 0.8419 (ppp) REVERT: V 471 GLU cc_start: 0.9016 (tp30) cc_final: 0.8703 (tp30) REVERT: V 494 MET cc_start: 0.8680 (mmm) cc_final: 0.8054 (mmm) REVERT: W 212 LYS cc_start: 0.9434 (tppt) cc_final: 0.9012 (tptt) REVERT: X 328 ASP cc_start: 0.9581 (m-30) cc_final: 0.9200 (t70) REVERT: X 332 GLU cc_start: 0.9064 (tm-30) cc_final: 0.8751 (pp20) REVERT: X 380 GLN cc_start: 0.9045 (OUTLIER) cc_final: 0.8455 (tt0) REVERT: X 382 GLU cc_start: 0.8866 (pm20) cc_final: 0.8563 (pm20) REVERT: X 394 ASP cc_start: 0.7659 (t0) cc_final: 0.7291 (t0) REVERT: X 405 GLN cc_start: 0.8606 (tm-30) cc_final: 0.8117 (tm-30) REVERT: Y 83 ARG cc_start: 0.9602 (mtt180) cc_final: 0.9304 (tpm170) REVERT: Y 374 ASP cc_start: 0.8848 (m-30) cc_final: 0.8578 (m-30) REVERT: Z 79 TYR cc_start: 0.8771 (t80) cc_final: 0.8515 (t80) REVERT: Z 138 TYR cc_start: 0.9366 (m-10) cc_final: 0.9053 (m-10) REVERT: a 23 HIS cc_start: 0.9333 (OUTLIER) cc_final: 0.8917 (m170) REVERT: a 78 GLU cc_start: 0.9232 (mt-10) cc_final: 0.9030 (mt-10) REVERT: b 7 MET cc_start: 0.8493 (tpp) cc_final: 0.8168 (tpt) REVERT: b 67 ASP cc_start: 0.8969 (t0) cc_final: 0.8481 (t70) REVERT: b 181 ASP cc_start: 0.9634 (m-30) cc_final: 0.9123 (p0) REVERT: c 64 ASP cc_start: 0.9323 (m-30) cc_final: 0.8653 (t0) REVERT: c 107 MET cc_start: 0.8851 (ptm) cc_final: 0.8616 (ptm) REVERT: c 158 ASP cc_start: 0.8609 (t0) cc_final: 0.8176 (t0) REVERT: c 279 ASP cc_start: 0.9174 (t0) cc_final: 0.8502 (p0) REVERT: c 282 ARG cc_start: 0.8712 (ttp80) cc_final: 0.8374 (tmm160) REVERT: c 303 MET cc_start: 0.9221 (mmm) cc_final: 0.8657 (mpp) REVERT: d 153 GLN cc_start: 0.8363 (mm110) cc_final: 0.7791 (mp10) REVERT: d 160 ASP cc_start: 0.8501 (t0) cc_final: 0.8226 (t0) REVERT: d 207 GLU cc_start: 0.8570 (mp0) cc_final: 0.8262 (mp0) REVERT: e 45 ASP cc_start: 0.5932 (OUTLIER) cc_final: 0.4287 (t70) REVERT: g 127 MET cc_start: 0.9000 (mmp) cc_final: 0.8542 (mmp) REVERT: g 204 MET cc_start: 0.8512 (ptm) cc_final: 0.8246 (ptm) REVERT: g 225 ILE cc_start: 0.8739 (pt) cc_final: 0.8463 (pt) REVERT: g 230 ILE cc_start: 0.7926 (OUTLIER) cc_final: 0.7687 (tp) outliers start: 79 outliers final: 53 residues processed: 480 average time/residue: 0.2663 time to fit residues: 211.4378 Evaluate side-chains 472 residues out of total 4573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 413 time to evaluate : 1.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 112 CYS Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 345 PHE Chi-restraints excluded: chain E residue 19 HIS Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 406 ILE Chi-restraints excluded: chain U residue 69 TYR Chi-restraints excluded: chain U residue 333 MET Chi-restraints excluded: chain U residue 505 ASP Chi-restraints excluded: chain U residue 555 VAL Chi-restraints excluded: chain U residue 675 MET Chi-restraints excluded: chain V residue 157 THR Chi-restraints excluded: chain V residue 229 SER Chi-restraints excluded: chain V residue 251 LEU Chi-restraints excluded: chain W residue 178 GLU Chi-restraints excluded: chain W residue 213 PHE Chi-restraints excluded: chain W residue 236 HIS Chi-restraints excluded: chain X residue 380 GLN Chi-restraints excluded: chain X residue 419 LYS Chi-restraints excluded: chain Y residue 47 ASP Chi-restraints excluded: chain Y residue 174 TRP Chi-restraints excluded: chain Y residue 277 VAL Chi-restraints excluded: chain Z residue 18 SER Chi-restraints excluded: chain Z residue 70 LEU Chi-restraints excluded: chain Z residue 120 VAL Chi-restraints excluded: chain Z residue 160 SER Chi-restraints excluded: chain Z residue 180 LYS Chi-restraints excluded: chain a residue 23 HIS Chi-restraints excluded: chain a residue 269 LEU Chi-restraints excluded: chain a residue 277 LEU Chi-restraints excluded: chain c residue 60 GLU Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain c residue 98 MET Chi-restraints excluded: chain c residue 156 VAL Chi-restraints excluded: chain c residue 176 GLN Chi-restraints excluded: chain c residue 248 MET Chi-restraints excluded: chain d residue 87 VAL Chi-restraints excluded: chain d residue 205 VAL Chi-restraints excluded: chain d residue 277 LYS Chi-restraints excluded: chain d residue 309 VAL Chi-restraints excluded: chain e residue 45 ASP Chi-restraints excluded: chain e residue 65 TYR Chi-restraints excluded: chain g residue 118 ASP Chi-restraints excluded: chain g residue 230 ILE Chi-restraints excluded: chain g residue 231 VAL Chi-restraints excluded: chain g residue 246 ILE Chi-restraints excluded: chain g residue 266 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 476 optimal weight: 0.9980 chunk 301 optimal weight: 0.7980 chunk 440 optimal weight: 3.9990 chunk 504 optimal weight: 0.4980 chunk 71 optimal weight: 6.9990 chunk 186 optimal weight: 2.9990 chunk 429 optimal weight: 3.9990 chunk 323 optimal weight: 0.0770 chunk 221 optimal weight: 6.9990 chunk 362 optimal weight: 2.9990 chunk 217 optimal weight: 5.9990 overall best weight: 1.0740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 315 ASN F 417 HIS ** U 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 214 HIS W 288 HIS ** Z 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 35 HIS a 52 GLN c 283 HIS ** d 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 189 HIS ** g 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.088955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.062333 restraints weight = 157816.733| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 4.03 r_work: 0.3073 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3089 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3089 r_free = 0.3089 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 40 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3089 r_free = 0.3089 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 40 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3089 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.4207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 42318 Z= 0.120 Angle : 0.590 12.748 57155 Z= 0.294 Chirality : 0.041 0.200 6495 Planarity : 0.003 0.046 7357 Dihedral : 6.969 143.578 5762 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.78 % Favored : 96.20 % Rotamer: Outliers : 1.68 % Allowed : 14.48 % Favored : 83.84 % 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: 0.63 (0.12), residues: 5162 helix: 1.32 (0.10), residues: 2983 sheet: -0.70 (0.26), residues: 404 loop : -0.79 (0.15), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG W 289 TYR 0.032 0.001 TYR W 226 PHE 0.024 0.001 PHE F 284 TRP 0.020 0.001 TRP a 356 HIS 0.009 0.001 HIS D 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (42315) covalent geometry : angle 0.59019 / 0.29 (57155) hydrogen bonds : bond 0.03492 / 2.34 ( 2214) hydrogen bonds : angle 4.09019 / 2.81 ( 6489) metal coordination : bond 0.00738 / 0.38 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10324 Ramachandran restraints generated. 5162 Oldfield, 0 Emsley, 5162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10324 Ramachandran restraints generated. 5162 Oldfield, 0 Emsley, 5162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 4573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 432 time to evaluate : 1.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 213 ARG cc_start: 0.8831 (pmt-80) cc_final: 0.8557 (pmt-80) REVERT: C 223 PHE cc_start: 0.8474 (m-80) cc_final: 0.8209 (m-80) REVERT: C 230 MET cc_start: 0.7271 (tpp) cc_final: 0.7049 (tmm) REVERT: D 64 GLU cc_start: 0.9318 (tp30) cc_final: 0.9020 (tt0) REVERT: D 120 ASP cc_start: 0.9015 (m-30) cc_final: 0.8189 (p0) REVERT: D 141 ASP cc_start: 0.8853 (t0) cc_final: 0.8644 (t0) REVERT: D 214 MET cc_start: 0.8844 (ptm) cc_final: 0.8474 (ptm) REVERT: D 317 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8978 (tt) REVERT: D 351 LYS cc_start: 0.9356 (pttm) cc_final: 0.8957 (tptp) REVERT: E 66 GLU cc_start: 0.8810 (tp30) cc_final: 0.8477 (tp30) REVERT: E 120 TYR cc_start: 0.8528 (t80) cc_final: 0.8256 (t80) REVERT: E 132 TYR cc_start: 0.7838 (t80) cc_final: 0.7496 (m-80) REVERT: E 151 LEU cc_start: 0.8914 (tp) cc_final: 0.8621 (tp) REVERT: E 155 ASN cc_start: 0.8519 (t0) cc_final: 0.8021 (t0) REVERT: E 220 ASN cc_start: 0.9298 (m-40) cc_final: 0.9033 (m110) REVERT: E 275 MET cc_start: 0.8809 (mmm) cc_final: 0.8337 (mpp) REVERT: F 55 MET cc_start: 0.7989 (ptm) cc_final: 0.7299 (ppp) REVERT: F 386 ARG cc_start: 0.9474 (tpm170) cc_final: 0.9051 (ttp80) REVERT: U 332 GLU cc_start: 0.8575 (tt0) cc_final: 0.8192 (tp30) REVERT: U 361 ARG cc_start: 0.8680 (mmm160) cc_final: 0.8445 (mmm160) REVERT: U 505 ASP cc_start: 0.8752 (OUTLIER) cc_final: 0.8542 (t0) REVERT: U 675 MET cc_start: 0.9581 (OUTLIER) cc_final: 0.9292 (ttp) REVERT: U 885 MET cc_start: 0.8294 (mpp) cc_final: 0.7571 (mpp) REVERT: V 66 GLU cc_start: 0.9376 (mm-30) cc_final: 0.8995 (mm-30) REVERT: V 150 ARG cc_start: 0.8397 (ttm170) cc_final: 0.8134 (ttm170) REVERT: V 175 MET cc_start: 0.8395 (ppp) cc_final: 0.8171 (ppp) REVERT: V 176 MET cc_start: 0.9179 (ttp) cc_final: 0.8753 (tmm) REVERT: V 180 ARG cc_start: 0.8650 (mmp80) cc_final: 0.8053 (mmp80) REVERT: V 211 TYR cc_start: 0.8362 (m-80) cc_final: 0.8026 (m-80) REVERT: V 212 TYR cc_start: 0.7145 (OUTLIER) cc_final: 0.6775 (m-80) REVERT: V 409 MET cc_start: 0.8780 (tmm) cc_final: 0.8405 (ppp) REVERT: V 471 GLU cc_start: 0.9053 (tp30) cc_final: 0.8724 (tp30) REVERT: V 494 MET cc_start: 0.8668 (mmm) cc_final: 0.8325 (mmt) REVERT: W 177 MET cc_start: 0.6552 (ptm) cc_final: 0.6180 (ptm) REVERT: W 212 LYS cc_start: 0.9434 (tppt) cc_final: 0.9013 (tptt) REVERT: X 322 HIS cc_start: 0.9300 (m90) cc_final: 0.8928 (m90) REVERT: X 328 ASP cc_start: 0.9581 (m-30) cc_final: 0.9267 (t70) REVERT: X 380 GLN cc_start: 0.8971 (OUTLIER) cc_final: 0.8442 (tt0) REVERT: X 382 GLU cc_start: 0.8969 (pm20) cc_final: 0.8690 (pm20) REVERT: X 394 ASP cc_start: 0.7659 (t0) cc_final: 0.7274 (t0) REVERT: X 405 GLN cc_start: 0.8673 (tm-30) cc_final: 0.8206 (tm-30) REVERT: X 419 LYS cc_start: 0.9483 (OUTLIER) cc_final: 0.9253 (mtmm) REVERT: Y 83 ARG cc_start: 0.9648 (mtt180) cc_final: 0.9377 (tpm170) REVERT: Y 374 ASP cc_start: 0.8882 (m-30) cc_final: 0.8594 (m-30) REVERT: Z 79 TYR cc_start: 0.8842 (t80) cc_final: 0.8545 (t80) REVERT: Z 90 ARG cc_start: 0.8685 (mtm-85) cc_final: 0.8448 (mtm110) REVERT: Z 138 TYR cc_start: 0.9375 (m-10) cc_final: 0.9087 (m-10) REVERT: Z 244 GLU cc_start: 0.8808 (mp0) cc_final: 0.8438 (tp30) REVERT: b 1 MET cc_start: 0.4532 (mmp) cc_final: 0.2724 (tpp) REVERT: b 7 MET cc_start: 0.8329 (tpp) cc_final: 0.8092 (tpt) REVERT: b 67 ASP cc_start: 0.8961 (t0) cc_final: 0.8463 (t70) REVERT: b 181 ASP cc_start: 0.9655 (m-30) cc_final: 0.9144 (p0) REVERT: c 54 MET cc_start: 0.8905 (tpp) cc_final: 0.8613 (tmm) REVERT: c 64 ASP cc_start: 0.9339 (m-30) cc_final: 0.8633 (t0) REVERT: c 107 MET cc_start: 0.8866 (ptm) cc_final: 0.8594 (ptm) REVERT: c 158 ASP cc_start: 0.8597 (t0) cc_final: 0.8077 (t0) REVERT: c 167 MET cc_start: 0.8984 (mmm) cc_final: 0.8286 (mmm) REVERT: c 279 ASP cc_start: 0.9191 (t0) cc_final: 0.8604 (p0) REVERT: c 303 MET cc_start: 0.9233 (mmm) cc_final: 0.8618 (mpp) REVERT: d 153 GLN cc_start: 0.8359 (mm110) cc_final: 0.7785 (mp10) REVERT: d 160 ASP cc_start: 0.8574 (t0) cc_final: 0.8282 (t0) REVERT: d 207 GLU cc_start: 0.8365 (mp0) cc_final: 0.8101 (mp0) REVERT: g 127 MET cc_start: 0.8996 (mmp) cc_final: 0.8544 (mmp) REVERT: g 204 MET cc_start: 0.8580 (ptm) cc_final: 0.8312 (ptm) REVERT: g 225 ILE cc_start: 0.8785 (pt) cc_final: 0.8511 (pt) REVERT: g 230 ILE cc_start: 0.7932 (OUTLIER) cc_final: 0.7698 (tp) outliers start: 77 outliers final: 49 residues processed: 480 average time/residue: 0.2632 time to fit residues: 209.1992 Evaluate side-chains 471 residues out of total 4573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 415 time to evaluate : 1.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 112 CYS Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain E residue 19 HIS Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain U residue 69 TYR Chi-restraints excluded: chain U residue 333 MET Chi-restraints excluded: chain U residue 505 ASP Chi-restraints excluded: chain U residue 555 VAL Chi-restraints excluded: chain U residue 675 MET Chi-restraints excluded: chain V residue 157 THR Chi-restraints excluded: chain V residue 212 TYR Chi-restraints excluded: chain V residue 229 SER Chi-restraints excluded: chain V residue 251 LEU Chi-restraints excluded: chain W residue 178 GLU Chi-restraints excluded: chain W residue 213 PHE Chi-restraints excluded: chain W residue 236 HIS Chi-restraints excluded: chain X residue 380 GLN Chi-restraints excluded: chain X residue 419 LYS Chi-restraints excluded: chain Y residue 47 ASP Chi-restraints excluded: chain Y residue 157 ILE Chi-restraints excluded: chain Y residue 174 TRP Chi-restraints excluded: chain Y residue 277 VAL Chi-restraints excluded: chain Y residue 302 HIS Chi-restraints excluded: chain Z residue 70 LEU Chi-restraints excluded: chain Z residue 120 VAL Chi-restraints excluded: chain Z residue 180 LYS Chi-restraints excluded: chain a residue 277 LEU Chi-restraints excluded: chain c residue 60 GLU Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain c residue 156 VAL Chi-restraints excluded: chain c residue 176 GLN Chi-restraints excluded: chain c residue 248 MET Chi-restraints excluded: chain c residue 288 VAL Chi-restraints excluded: chain d residue 87 VAL Chi-restraints excluded: chain d residue 205 VAL Chi-restraints excluded: chain d residue 277 LYS Chi-restraints excluded: chain d residue 309 VAL Chi-restraints excluded: chain e residue 52 PHE Chi-restraints excluded: chain e residue 54 ASN Chi-restraints excluded: chain e residue 65 TYR Chi-restraints excluded: chain g residue 118 ASP Chi-restraints excluded: chain g residue 220 LEU Chi-restraints excluded: chain g residue 230 ILE Chi-restraints excluded: chain g residue 231 VAL Chi-restraints excluded: chain g residue 236 VAL Chi-restraints excluded: chain g residue 246 ILE Chi-restraints excluded: chain g residue 266 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 112 optimal weight: 0.9980 chunk 428 optimal weight: 0.9990 chunk 115 optimal weight: 5.9990 chunk 495 optimal weight: 2.9990 chunk 377 optimal weight: 0.9990 chunk 434 optimal weight: 4.9990 chunk 193 optimal weight: 4.9990 chunk 443 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 152 optimal weight: 5.9990 chunk 230 optimal weight: 7.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 HIS ** E 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 GLN F 380 ASN U 373 ASN U 377 HIS ** U 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 246 HIS W 361 HIS ** Z 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 48 ASN c 283 HIS ** d 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 189 HIS ** g 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.087999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.061093 restraints weight = 159909.354| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 4.06 r_work: 0.3080 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3081 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 40 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 40 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3081 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.4404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 42318 Z= 0.130 Angle : 0.605 12.518 57155 Z= 0.301 Chirality : 0.041 0.242 6495 Planarity : 0.003 0.046 7357 Dihedral : 6.942 144.195 5762 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.84 % Favored : 96.14 % Rotamer: Outliers : 1.73 % Allowed : 14.80 % Favored : 83.47 % 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: 0.69 (0.12), residues: 5162 helix: 1.37 (0.10), residues: 2984 sheet: -0.79 (0.26), residues: 412 loop : -0.74 (0.15), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 229 TYR 0.031 0.001 TYR W 226 PHE 0.022 0.001 PHE F 284 TRP 0.020 0.001 TRP a 356 HIS 0.008 0.001 HIS W 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (42315) covalent geometry : angle 0.60501 / 0.30 (57155) hydrogen bonds : bond 0.03504 / 2.35 ( 2214) hydrogen bonds : angle 4.08071 / 2.81 ( 6489) metal coordination : bond 0.00865 / 0.44 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10324 Ramachandran restraints generated. 5162 Oldfield, 0 Emsley, 5162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10324 Ramachandran restraints generated. 5162 Oldfield, 0 Emsley, 5162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 4573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 425 time to evaluate : 1.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 213 ARG cc_start: 0.8875 (pmt-80) cc_final: 0.8649 (pmt-80) REVERT: C 223 PHE cc_start: 0.8507 (m-80) cc_final: 0.8239 (m-80) REVERT: D 64 GLU cc_start: 0.9285 (tp30) cc_final: 0.9004 (tt0) REVERT: D 120 ASP cc_start: 0.9028 (m-30) cc_final: 0.8219 (p0) REVERT: D 141 ASP cc_start: 0.8857 (t0) cc_final: 0.8643 (t0) REVERT: D 163 MET cc_start: 0.9542 (mmm) cc_final: 0.9265 (mmm) REVERT: D 214 MET cc_start: 0.8870 (ptm) cc_final: 0.8476 (ptm) REVERT: D 317 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.9020 (tt) REVERT: D 351 LYS cc_start: 0.9369 (pttm) cc_final: 0.8938 (tptp) REVERT: E 66 GLU cc_start: 0.8833 (tp30) cc_final: 0.8520 (tp30) REVERT: E 132 TYR cc_start: 0.7803 (t80) cc_final: 0.7527 (m-80) REVERT: E 151 LEU cc_start: 0.8914 (tp) cc_final: 0.8686 (tp) REVERT: E 155 ASN cc_start: 0.8653 (t0) cc_final: 0.8318 (t0) REVERT: E 220 ASN cc_start: 0.9317 (m-40) cc_final: 0.9067 (m110) REVERT: E 221 TYR cc_start: 0.9189 (t80) cc_final: 0.8972 (t80) REVERT: E 275 MET cc_start: 0.8925 (mmm) cc_final: 0.8448 (mpp) REVERT: F 55 MET cc_start: 0.7962 (ptm) cc_final: 0.7288 (ppp) REVERT: F 379 VAL cc_start: -0.0363 (OUTLIER) cc_final: -0.0895 (m) REVERT: F 386 ARG cc_start: 0.9487 (tpm170) cc_final: 0.9099 (ttp80) REVERT: U 332 GLU cc_start: 0.8521 (tt0) cc_final: 0.8188 (tp30) REVERT: U 361 ARG cc_start: 0.8746 (mmm160) cc_final: 0.8535 (mmm160) REVERT: U 675 MET cc_start: 0.9552 (OUTLIER) cc_final: 0.9320 (ttp) REVERT: U 885 MET cc_start: 0.8440 (mpp) cc_final: 0.7782 (mpp) REVERT: V 66 GLU cc_start: 0.9409 (mm-30) cc_final: 0.9021 (mm-30) REVERT: V 150 ARG cc_start: 0.8420 (ttm170) cc_final: 0.8162 (ttm170) REVERT: V 175 MET cc_start: 0.8339 (ppp) cc_final: 0.8124 (ppp) REVERT: V 176 MET cc_start: 0.9196 (ttp) cc_final: 0.8698 (tmm) REVERT: V 180 ARG cc_start: 0.8624 (mmp80) cc_final: 0.7726 (mpt180) REVERT: V 212 TYR cc_start: 0.7141 (OUTLIER) cc_final: 0.6566 (m-80) REVERT: V 409 MET cc_start: 0.8817 (tmm) cc_final: 0.8426 (ppp) REVERT: V 494 MET cc_start: 0.8682 (mmm) cc_final: 0.8290 (mmt) REVERT: W 212 LYS cc_start: 0.9446 (tppt) cc_final: 0.9025 (tptt) REVERT: X 322 HIS cc_start: 0.9278 (m90) cc_final: 0.8893 (m90) REVERT: X 328 ASP cc_start: 0.9587 (m-30) cc_final: 0.9199 (t70) REVERT: X 332 GLU cc_start: 0.9180 (tm-30) cc_final: 0.8838 (pp20) REVERT: X 380 GLN cc_start: 0.9017 (OUTLIER) cc_final: 0.8483 (tt0) REVERT: X 382 GLU cc_start: 0.9003 (pm20) cc_final: 0.8778 (pm20) REVERT: X 394 ASP cc_start: 0.7877 (t0) cc_final: 0.7498 (t0) REVERT: X 405 GLN cc_start: 0.8708 (tm-30) cc_final: 0.8250 (tm-30) REVERT: X 419 LYS cc_start: 0.9478 (OUTLIER) cc_final: 0.9258 (mtmm) REVERT: Y 83 ARG cc_start: 0.9592 (mtt180) cc_final: 0.9349 (tpm170) REVERT: Y 374 ASP cc_start: 0.8873 (m-30) cc_final: 0.8579 (m-30) REVERT: Z 79 TYR cc_start: 0.8894 (t80) cc_final: 0.8595 (t80) REVERT: Z 138 TYR cc_start: 0.9381 (m-10) cc_final: 0.9119 (m-10) REVERT: Z 180 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8538 (tmtt) REVERT: Z 244 GLU cc_start: 0.8788 (mp0) cc_final: 0.8377 (tp30) REVERT: b 1 MET cc_start: 0.4327 (mmp) cc_final: 0.2517 (tpp) REVERT: b 67 ASP cc_start: 0.8985 (t0) cc_final: 0.8528 (t70) REVERT: b 181 ASP cc_start: 0.9642 (m-30) cc_final: 0.9135 (p0) REVERT: c 64 ASP cc_start: 0.9346 (m-30) cc_final: 0.8665 (t0) REVERT: c 107 MET cc_start: 0.8974 (ptm) cc_final: 0.8688 (ptm) REVERT: c 158 ASP cc_start: 0.8588 (t0) cc_final: 0.8114 (t0) REVERT: c 168 MET cc_start: 0.8016 (pmm) cc_final: 0.7793 (pmm) REVERT: c 279 ASP cc_start: 0.9164 (t0) cc_final: 0.8586 (p0) REVERT: c 303 MET cc_start: 0.9236 (mmm) cc_final: 0.8648 (mpp) REVERT: d 153 GLN cc_start: 0.8375 (mm110) cc_final: 0.7874 (mp10) REVERT: d 160 ASP cc_start: 0.8577 (t0) cc_final: 0.7630 (p0) REVERT: d 211 GLU cc_start: 0.9126 (mm-30) cc_final: 0.8818 (tp30) REVERT: d 299 MET cc_start: 0.8432 (mtp) cc_final: 0.8156 (mtp) REVERT: g 127 MET cc_start: 0.9007 (mmp) cc_final: 0.8593 (mmp) REVERT: g 204 MET cc_start: 0.8658 (ptm) cc_final: 0.8399 (ptm) REVERT: g 225 ILE cc_start: 0.8806 (pt) cc_final: 0.8540 (pt) REVERT: g 230 ILE cc_start: 0.7978 (OUTLIER) cc_final: 0.7751 (tp) outliers start: 79 outliers final: 52 residues processed: 480 average time/residue: 0.2635 time to fit residues: 208.3293 Evaluate side-chains 469 residues out of total 4573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 409 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 345 PHE Chi-restraints excluded: chain E residue 19 HIS Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain U residue 69 TYR Chi-restraints excluded: chain U residue 333 MET Chi-restraints excluded: chain U residue 555 VAL Chi-restraints excluded: chain U residue 675 MET Chi-restraints excluded: chain V residue 157 THR Chi-restraints excluded: chain V residue 212 TYR Chi-restraints excluded: chain V residue 229 SER Chi-restraints excluded: chain W residue 178 GLU Chi-restraints excluded: chain W residue 213 PHE Chi-restraints excluded: chain W residue 236 HIS Chi-restraints excluded: chain X residue 380 GLN Chi-restraints excluded: chain X residue 419 LYS Chi-restraints excluded: chain Y residue 157 ILE Chi-restraints excluded: chain Y residue 174 TRP Chi-restraints excluded: chain Y residue 277 VAL Chi-restraints excluded: chain Y residue 347 ILE Chi-restraints excluded: chain Z residue 70 LEU Chi-restraints excluded: chain Z residue 120 VAL Chi-restraints excluded: chain Z residue 160 SER Chi-restraints excluded: chain Z residue 180 LYS Chi-restraints excluded: chain a residue 39 LEU Chi-restraints excluded: chain a residue 84 VAL Chi-restraints excluded: chain a residue 218 MET Chi-restraints excluded: chain a residue 269 LEU Chi-restraints excluded: chain a residue 277 LEU Chi-restraints excluded: chain c residue 60 GLU Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain c residue 145 VAL Chi-restraints excluded: chain c residue 156 VAL Chi-restraints excluded: chain c residue 176 GLN Chi-restraints excluded: chain c residue 248 MET Chi-restraints excluded: chain c residue 283 HIS Chi-restraints excluded: chain d residue 87 VAL Chi-restraints excluded: chain d residue 205 VAL Chi-restraints excluded: chain d residue 277 LYS Chi-restraints excluded: chain d residue 309 VAL Chi-restraints excluded: chain e residue 52 PHE Chi-restraints excluded: chain e residue 65 TYR Chi-restraints excluded: chain g residue 118 ASP Chi-restraints excluded: chain g residue 220 LEU Chi-restraints excluded: chain g residue 230 ILE Chi-restraints excluded: chain g residue 231 VAL Chi-restraints excluded: chain g residue 236 VAL Chi-restraints excluded: chain g residue 246 ILE Chi-restraints excluded: chain g residue 266 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 83 optimal weight: 7.9990 chunk 149 optimal weight: 10.0000 chunk 55 optimal weight: 7.9990 chunk 269 optimal weight: 7.9990 chunk 208 optimal weight: 0.8980 chunk 13 optimal weight: 6.9990 chunk 148 optimal weight: 6.9990 chunk 49 optimal weight: 0.0870 chunk 78 optimal weight: 6.9990 chunk 500 optimal weight: 7.9990 chunk 391 optimal weight: 10.0000 overall best weight: 4.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 332 HIS D 98 GLN ** E 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 215 ASN U 373 ASN ** U 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 707 ASN V 260 HIS W 288 HIS Y 77 ASN ** Z 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 13 ASN a 18 GLN a 86 GLN a 129 GLN a 264 ASN c 183 HIS ** d 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 189 HIS ** g 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 289 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.085068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.057454 restraints weight = 160237.365| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 4.02 r_work: 0.2968 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2957 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2957 r_free = 0.2957 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 40 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2957 r_free = 0.2957 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 40 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2957 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.5005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.155 42318 Z= 0.297 Angle : 0.751 20.433 57155 Z= 0.377 Chirality : 0.045 0.349 6495 Planarity : 0.004 0.099 7357 Dihedral : 7.211 147.402 5762 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.42 % Favored : 95.56 % Rotamer: Outliers : 1.49 % Allowed : 15.24 % Favored : 83.27 % 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: 0.45 (0.12), residues: 5162 helix: 1.12 (0.09), residues: 2994 sheet: -0.94 (0.26), residues: 409 loop : -0.71 (0.16), residues: 1759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 229 TYR 0.051 0.002 TYR W 226 PHE 0.020 0.002 PHE U 74 TRP 0.037 0.003 TRP d 102 HIS 0.008 0.001 HIS U 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00664 / 0.30 (42315) covalent geometry : angle 0.75145 / 0.38 (57155) hydrogen bonds : bond 0.04260 / 2.84 ( 2214) hydrogen bonds : angle 4.40362 / 3.03 ( 6489) metal coordination : bond 0.09078 / 4.54 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10324 Ramachandran restraints generated. 5162 Oldfield, 0 Emsley, 5162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10324 Ramachandran restraints generated. 5162 Oldfield, 0 Emsley, 5162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 4573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 401 time to evaluate : 1.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 230 MET cc_start: 0.7282 (tpp) cc_final: 0.7021 (tmm) REVERT: C 293 MET cc_start: 0.7442 (tpt) cc_final: 0.6969 (tpt) REVERT: D 64 GLU cc_start: 0.9337 (tp30) cc_final: 0.8900 (tt0) REVERT: D 141 ASP cc_start: 0.9006 (t0) cc_final: 0.8694 (t0) REVERT: D 163 MET cc_start: 0.9597 (mmm) cc_final: 0.9353 (mmm) REVERT: D 214 MET cc_start: 0.8947 (ptm) cc_final: 0.8564 (ptm) REVERT: D 317 LEU cc_start: 0.9391 (OUTLIER) cc_final: 0.9151 (tt) REVERT: E 66 GLU cc_start: 0.8893 (tp30) cc_final: 0.8609 (tp30) REVERT: E 120 TYR cc_start: 0.8669 (t80) cc_final: 0.8418 (t80) REVERT: E 151 LEU cc_start: 0.8908 (tp) cc_final: 0.8671 (tp) REVERT: E 155 ASN cc_start: 0.8706 (t0) cc_final: 0.8325 (t0) REVERT: E 275 MET cc_start: 0.9116 (mmm) cc_final: 0.8665 (mpp) REVERT: F 55 MET cc_start: 0.7998 (ptm) cc_final: 0.7409 (ppp) REVERT: F 379 VAL cc_start: -0.0606 (OUTLIER) cc_final: -0.1165 (m) REVERT: F 386 ARG cc_start: 0.9468 (tpm170) cc_final: 0.9074 (ttp80) REVERT: U 176 MET cc_start: 0.9080 (tpp) cc_final: 0.8875 (tpt) REVERT: U 505 ASP cc_start: 0.8896 (t0) cc_final: 0.8652 (t0) REVERT: U 797 MET cc_start: 0.8978 (mtp) cc_final: 0.8751 (mtp) REVERT: U 885 MET cc_start: 0.8448 (mpp) cc_final: 0.8012 (mtp) REVERT: V 66 GLU cc_start: 0.9516 (mm-30) cc_final: 0.9195 (mm-30) REVERT: V 175 MET cc_start: 0.8183 (ppp) cc_final: 0.7891 (ppp) REVERT: V 176 MET cc_start: 0.9219 (ttp) cc_final: 0.8769 (tmm) REVERT: V 212 TYR cc_start: 0.7545 (OUTLIER) cc_final: 0.6812 (m-80) REVERT: V 409 MET cc_start: 0.8884 (tmm) cc_final: 0.8557 (ppp) REVERT: V 494 MET cc_start: 0.8988 (mmm) cc_final: 0.8781 (mmt) REVERT: W 289 ARG cc_start: 0.8523 (mtm110) cc_final: 0.8135 (mtm110) REVERT: X 322 HIS cc_start: 0.9319 (m90) cc_final: 0.8947 (m90) REVERT: X 328 ASP cc_start: 0.9601 (m-30) cc_final: 0.9200 (t70) REVERT: X 332 GLU cc_start: 0.9107 (tm-30) cc_final: 0.8836 (pp20) REVERT: X 389 ASP cc_start: 0.8826 (t0) cc_final: 0.8617 (t0) REVERT: X 394 ASP cc_start: 0.8558 (t0) cc_final: 0.8149 (t0) REVERT: X 405 GLN cc_start: 0.8859 (tm-30) cc_final: 0.8453 (tm-30) REVERT: X 419 LYS cc_start: 0.9476 (OUTLIER) cc_final: 0.9168 (mtmm) REVERT: Y 83 ARG cc_start: 0.9665 (mtt180) cc_final: 0.9391 (tpm170) REVERT: Y 214 MET cc_start: 0.6426 (ppp) cc_final: 0.5906 (ptt) REVERT: Z 225 GLN cc_start: 0.9487 (tp-100) cc_final: 0.8798 (tp-100) REVERT: Z 244 GLU cc_start: 0.8884 (mp0) cc_final: 0.8575 (tp30) REVERT: b 1 MET cc_start: 0.4488 (mmp) cc_final: 0.2812 (tpp) REVERT: b 67 ASP cc_start: 0.8963 (t0) cc_final: 0.8494 (t70) REVERT: c 64 ASP cc_start: 0.9436 (m-30) cc_final: 0.8787 (t0) REVERT: c 107 MET cc_start: 0.9152 (ptm) cc_final: 0.8916 (ptm) REVERT: c 158 ASP cc_start: 0.8685 (t0) cc_final: 0.8156 (t0) REVERT: c 279 ASP cc_start: 0.9224 (t0) cc_final: 0.8594 (p0) REVERT: c 303 MET cc_start: 0.9307 (mmm) cc_final: 0.8793 (mpp) REVERT: c 310 LYS cc_start: 0.7830 (mmmt) cc_final: 0.6643 (pttp) REVERT: d 102 TRP cc_start: 0.7884 (t-100) cc_final: 0.7007 (m-90) REVERT: d 153 GLN cc_start: 0.8621 (mm110) cc_final: 0.8213 (mp10) REVERT: d 160 ASP cc_start: 0.8766 (t0) cc_final: 0.8427 (t0) REVERT: d 167 TYR cc_start: 0.8906 (m-80) cc_final: 0.8635 (m-80) REVERT: d 211 GLU cc_start: 0.9129 (mm-30) cc_final: 0.8875 (tp30) REVERT: d 299 MET cc_start: 0.8371 (mtp) cc_final: 0.8047 (mtp) REVERT: g 127 MET cc_start: 0.9075 (mmp) cc_final: 0.8720 (mmp) REVERT: g 164 GLN cc_start: 0.7960 (mm110) cc_final: 0.7616 (mm110) REVERT: g 202 ARG cc_start: 0.8530 (ptt-90) cc_final: 0.8185 (ptt-90) REVERT: g 204 MET cc_start: 0.8818 (ptm) cc_final: 0.8563 (ptm) REVERT: g 225 ILE cc_start: 0.8926 (pt) cc_final: 0.8666 (pt) REVERT: g 230 ILE cc_start: 0.8123 (OUTLIER) cc_final: 0.7900 (tp) outliers start: 68 outliers final: 47 residues processed: 443 average time/residue: 0.2357 time to fit residues: 172.4412 Evaluate side-chains 431 residues out of total 4573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 379 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain E residue 19 HIS Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain U residue 69 TYR Chi-restraints excluded: chain U residue 333 MET Chi-restraints excluded: chain U residue 555 VAL Chi-restraints excluded: chain U residue 732 LEU Chi-restraints excluded: chain V residue 157 THR Chi-restraints excluded: chain V residue 212 TYR Chi-restraints excluded: chain V residue 229 SER Chi-restraints excluded: chain V residue 367 VAL Chi-restraints excluded: chain W residue 213 PHE Chi-restraints excluded: chain X residue 380 GLN Chi-restraints excluded: chain X residue 419 LYS Chi-restraints excluded: chain Y residue 157 ILE Chi-restraints excluded: chain Y residue 174 TRP Chi-restraints excluded: chain Y residue 277 VAL Chi-restraints excluded: chain Y residue 302 HIS Chi-restraints excluded: chain Y residue 347 ILE Chi-restraints excluded: chain Z residue 70 LEU Chi-restraints excluded: chain Z residue 120 VAL Chi-restraints excluded: chain Z residue 160 SER Chi-restraints excluded: chain Z residue 180 LYS Chi-restraints excluded: chain a residue 13 ASN Chi-restraints excluded: chain a residue 84 VAL Chi-restraints excluded: chain a residue 218 MET Chi-restraints excluded: chain a residue 269 LEU Chi-restraints excluded: chain a residue 277 LEU Chi-restraints excluded: chain c residue 60 GLU Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain c residue 176 GLN Chi-restraints excluded: chain c residue 248 MET Chi-restraints excluded: chain d residue 205 VAL Chi-restraints excluded: chain d residue 277 LYS Chi-restraints excluded: chain d residue 309 VAL Chi-restraints excluded: chain e residue 54 ASN Chi-restraints excluded: chain e residue 65 TYR Chi-restraints excluded: chain g residue 118 ASP Chi-restraints excluded: chain g residue 220 LEU Chi-restraints excluded: chain g residue 230 ILE Chi-restraints excluded: chain g residue 231 VAL Chi-restraints excluded: chain g residue 236 VAL Chi-restraints excluded: chain g residue 246 ILE Chi-restraints excluded: chain g residue 266 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 216 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 319 optimal weight: 6.9990 chunk 243 optimal weight: 0.9990 chunk 176 optimal weight: 2.9990 chunk 440 optimal weight: 0.0670 chunk 101 optimal weight: 6.9990 chunk 404 optimal weight: 0.9980 chunk 428 optimal weight: 0.9990 chunk 311 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 overall best weight: 0.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 707 ASN ** Z 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 231 GLN ** a 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 283 HIS ** c 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.087770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.060599 restraints weight = 156608.649| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 4.03 r_work: 0.3019 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3034 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 40 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 41 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3034 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.4955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 42318 Z= 0.124 Angle : 0.648 14.175 57155 Z= 0.322 Chirality : 0.042 0.419 6495 Planarity : 0.004 0.047 7357 Dihedral : 7.084 147.577 5762 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.89 % Favored : 96.09 % Rotamer: Outliers : 1.12 % Allowed : 15.66 % Favored : 83.23 % 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: 0.66 (0.12), residues: 5162 helix: 1.34 (0.10), residues: 2979 sheet: -0.80 (0.26), residues: 406 loop : -0.73 (0.15), residues: 1777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 232 TYR 0.023 0.001 TYR E 12 PHE 0.020 0.001 PHE F 284 TRP 0.022 0.002 TRP a 356 HIS 0.008 0.001 HIS U 756 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (42315) covalent geometry : angle 0.64844 / 0.32 (57155) hydrogen bonds : bond 0.03649 / 2.45 ( 2214) hydrogen bonds : angle 4.17362 / 2.87 ( 6489) metal coordination : bond 0.00303 / 0.16 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10324 Ramachandran restraints generated. 5162 Oldfield, 0 Emsley, 5162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10324 Ramachandran restraints generated. 5162 Oldfield, 0 Emsley, 5162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 4573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 414 time to evaluate : 1.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 230 MET cc_start: 0.7221 (tpp) cc_final: 0.6939 (tmm) REVERT: C 293 MET cc_start: 0.7309 (tpt) cc_final: 0.6858 (tpt) REVERT: D 64 GLU cc_start: 0.9319 (tp30) cc_final: 0.9093 (tt0) REVERT: D 120 ASP cc_start: 0.9062 (m-30) cc_final: 0.8177 (p0) REVERT: D 141 ASP cc_start: 0.8876 (t0) cc_final: 0.8625 (t0) REVERT: D 163 MET cc_start: 0.9597 (mmm) cc_final: 0.9374 (mmm) REVERT: D 214 MET cc_start: 0.8969 (ptm) cc_final: 0.8580 (ptm) REVERT: D 317 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.9117 (tt) REVERT: E 66 GLU cc_start: 0.8884 (tp30) cc_final: 0.8583 (tp30) REVERT: E 120 TYR cc_start: 0.8647 (t80) cc_final: 0.8364 (t80) REVERT: E 151 LEU cc_start: 0.8862 (tp) cc_final: 0.8632 (tp) REVERT: E 155 ASN cc_start: 0.8684 (t0) cc_final: 0.8309 (t0) REVERT: E 220 ASN cc_start: 0.9321 (m-40) cc_final: 0.9072 (m110) REVERT: E 275 MET cc_start: 0.8988 (mmm) cc_final: 0.8497 (mpp) REVERT: F 55 MET cc_start: 0.7931 (ptm) cc_final: 0.7338 (ppp) REVERT: F 379 VAL cc_start: -0.0620 (OUTLIER) cc_final: -0.1018 (m) REVERT: F 386 ARG cc_start: 0.9454 (tpm170) cc_final: 0.9062 (ttp80) REVERT: U 505 ASP cc_start: 0.8842 (t0) cc_final: 0.8573 (t0) REVERT: U 885 MET cc_start: 0.8313 (mpp) cc_final: 0.7678 (mtp) REVERT: V 62 HIS cc_start: 0.8761 (m170) cc_final: 0.8036 (m170) REVERT: V 66 GLU cc_start: 0.9445 (mm-30) cc_final: 0.9047 (mm-30) REVERT: V 175 MET cc_start: 0.8151 (ppp) cc_final: 0.7875 (ppp) REVERT: V 176 MET cc_start: 0.9180 (ttp) cc_final: 0.8668 (tmm) REVERT: V 180 ARG cc_start: 0.8602 (mmp80) cc_final: 0.7874 (mmp80) REVERT: V 212 TYR cc_start: 0.7253 (OUTLIER) cc_final: 0.6551 (m-80) REVERT: V 245 ASP cc_start: 0.8874 (t70) cc_final: 0.8593 (p0) REVERT: V 409 MET cc_start: 0.8835 (tmm) cc_final: 0.8511 (ppp) REVERT: V 494 MET cc_start: 0.8832 (mmm) cc_final: 0.8514 (mmt) REVERT: W 212 LYS cc_start: 0.9479 (tppt) cc_final: 0.9153 (tptp) REVERT: X 322 HIS cc_start: 0.9309 (m90) cc_final: 0.8936 (m90) REVERT: X 328 ASP cc_start: 0.9585 (m-30) cc_final: 0.9175 (t70) REVERT: X 332 GLU cc_start: 0.9162 (tm-30) cc_final: 0.8852 (pp20) REVERT: X 380 GLN cc_start: 0.9045 (OUTLIER) cc_final: 0.8439 (tt0) REVERT: X 394 ASP cc_start: 0.8312 (t0) cc_final: 0.7786 (t0) REVERT: X 405 GLN cc_start: 0.8727 (tm-30) cc_final: 0.8056 (tm-30) REVERT: X 408 SER cc_start: 0.9153 (m) cc_final: 0.8885 (p) REVERT: X 419 LYS cc_start: 0.9486 (OUTLIER) cc_final: 0.9268 (mtmm) REVERT: Y 83 ARG cc_start: 0.9655 (mtt180) cc_final: 0.9390 (tpm170) REVERT: Y 214 MET cc_start: 0.6161 (ppp) cc_final: 0.5658 (ptt) REVERT: Y 374 ASP cc_start: 0.8929 (m-30) cc_final: 0.8456 (m-30) REVERT: Z 90 ARG cc_start: 0.8997 (mtm-85) cc_final: 0.8732 (mtm110) REVERT: Z 138 TYR cc_start: 0.9363 (m-10) cc_final: 0.9148 (m-10) REVERT: Z 225 GLN cc_start: 0.9419 (tp-100) cc_final: 0.9168 (tp40) REVERT: b 1 MET cc_start: 0.4378 (mmp) cc_final: 0.2630 (tpp) REVERT: b 7 MET cc_start: 0.8416 (tpp) cc_final: 0.8159 (tpt) REVERT: b 67 ASP cc_start: 0.8987 (t0) cc_final: 0.8531 (t70) REVERT: b 181 ASP cc_start: 0.9614 (m-30) cc_final: 0.9002 (p0) REVERT: c 64 ASP cc_start: 0.9399 (m-30) cc_final: 0.8714 (t0) REVERT: c 158 ASP cc_start: 0.8625 (t0) cc_final: 0.8044 (t0) REVERT: c 279 ASP cc_start: 0.9169 (t0) cc_final: 0.8513 (p0) REVERT: c 303 MET cc_start: 0.9315 (mmm) cc_final: 0.8578 (mpp) REVERT: d 102 TRP cc_start: 0.7668 (t-100) cc_final: 0.6952 (m-90) REVERT: d 153 GLN cc_start: 0.8525 (mm110) cc_final: 0.8168 (mp10) REVERT: d 160 ASP cc_start: 0.8711 (t0) cc_final: 0.7739 (p0) REVERT: d 167 TYR cc_start: 0.8895 (m-80) cc_final: 0.8688 (m-80) REVERT: d 211 GLU cc_start: 0.9142 (mm-30) cc_final: 0.8811 (tp30) REVERT: d 299 MET cc_start: 0.8478 (mtp) cc_final: 0.8245 (mtp) REVERT: g 127 MET cc_start: 0.9047 (mmp) cc_final: 0.8669 (mmp) REVERT: g 202 ARG cc_start: 0.8393 (ptt-90) cc_final: 0.8024 (ptt-90) REVERT: g 204 MET cc_start: 0.8692 (ptm) cc_final: 0.8415 (ptm) REVERT: g 210 GLU cc_start: 0.8823 (mt-10) cc_final: 0.8596 (mt-10) REVERT: g 225 ILE cc_start: 0.8857 (pt) cc_final: 0.8589 (pt) REVERT: g 230 ILE cc_start: 0.8046 (OUTLIER) cc_final: 0.7821 (tp) outliers start: 51 outliers final: 37 residues processed: 451 average time/residue: 0.2551 time to fit residues: 189.8944 Evaluate side-chains 443 residues out of total 4573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 400 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 345 PHE Chi-restraints excluded: chain E residue 19 HIS Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain U residue 69 TYR Chi-restraints excluded: chain U residue 333 MET Chi-restraints excluded: chain V residue 157 THR Chi-restraints excluded: chain V residue 212 TYR Chi-restraints excluded: chain W residue 213 PHE Chi-restraints excluded: chain X residue 380 GLN Chi-restraints excluded: chain X residue 419 LYS Chi-restraints excluded: chain Y residue 157 ILE Chi-restraints excluded: chain Y residue 174 TRP Chi-restraints excluded: chain Z residue 70 LEU Chi-restraints excluded: chain Z residue 120 VAL Chi-restraints excluded: chain Z residue 160 SER Chi-restraints excluded: chain Z residue 180 LYS Chi-restraints excluded: chain a residue 13 ASN Chi-restraints excluded: chain a residue 84 VAL Chi-restraints excluded: chain a residue 218 MET Chi-restraints excluded: chain a residue 269 LEU Chi-restraints excluded: chain a residue 277 LEU Chi-restraints excluded: chain c residue 60 GLU Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain c residue 176 GLN Chi-restraints excluded: chain c residue 248 MET Chi-restraints excluded: chain d residue 132 THR Chi-restraints excluded: chain d residue 309 VAL Chi-restraints excluded: chain e residue 65 TYR Chi-restraints excluded: chain g residue 118 ASP Chi-restraints excluded: chain g residue 220 LEU Chi-restraints excluded: chain g residue 230 ILE Chi-restraints excluded: chain g residue 231 VAL Chi-restraints excluded: chain g residue 236 VAL Chi-restraints excluded: chain g residue 266 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 8 optimal weight: 3.9990 chunk 406 optimal weight: 2.9990 chunk 180 optimal weight: 0.9990 chunk 491 optimal weight: 2.9990 chunk 341 optimal weight: 5.9990 chunk 220 optimal weight: 0.5980 chunk 427 optimal weight: 0.0370 chunk 183 optimal weight: 0.6980 chunk 345 optimal weight: 0.6980 chunk 6 optimal weight: 6.9990 chunk 396 optimal weight: 0.9980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 421 GLN U 685 GLN V 62 HIS V 279 GLN ** Z 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 35 HIS c 283 HIS ** c 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.088454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.061261 restraints weight = 157615.972| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 4.09 r_work: 0.3037 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3053 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3053 r_free = 0.3053 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 41 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3053 r_free = 0.3053 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 41 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3053 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.4996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 42318 Z= 0.119 Angle : 0.640 12.496 57155 Z= 0.319 Chirality : 0.042 0.395 6495 Planarity : 0.004 0.051 7357 Dihedral : 6.989 145.738 5762 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.01 % Favored : 95.97 % Rotamer: Outliers : 1.20 % Allowed : 15.90 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.12), residues: 5162 helix: 1.38 (0.10), residues: 2985 sheet: -0.75 (0.26), residues: 402 loop : -0.69 (0.15), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 229 TYR 0.039 0.001 TYR Z 261 PHE 0.020 0.001 PHE V 147 TRP 0.026 0.002 TRP e 43 HIS 0.007 0.001 HIS W 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (42315) covalent geometry : angle 0.64029 / 0.32 (57155) hydrogen bonds : bond 0.03526 / 2.37 ( 2214) hydrogen bonds : angle 4.10262 / 2.83 ( 6489) metal coordination : bond 0.00167 / 0.08 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16037.25 seconds wall clock time: 273 minutes 31.14 seconds (16411.14 seconds total)