Starting phenix.real_space_refine on Sun Aug 24 17:54:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8spw_40688/08_2025/8spw_40688.cif Found real_map, /net/cci-nas-00/data/ceres_data/8spw_40688/08_2025/8spw_40688.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8spw_40688/08_2025/8spw_40688.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8spw_40688/08_2025/8spw_40688.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8spw_40688/08_2025/8spw_40688.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8spw_40688/08_2025/8spw_40688.map" } resolution = 3.5 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= 0.002 sd= 0.026 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: 6 Type Number sf(0) Gaussians P 15 5.49 5 Mg 5 5.21 5 S 67 5.16 5 C 13830 2.51 5 N 3820 2.21 5 O 4223 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21960 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 3636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3636 Classifications: {'peptide': 474} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 451} Chain: "B" Number of atoms: 3644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3644 Classifications: {'peptide': 475} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 452} Chain: "C" Number of atoms: 3650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3650 Classifications: {'peptide': 476} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 453} Chain: "D" Number of atoms: 3623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3623 Classifications: {'peptide': 470} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 446} Chain: "E" Number of atoms: 3623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3623 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 446} Chain: "F" Number of atoms: 3623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3623 Classifications: {'peptide': 470} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 446} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.96, per 1000 atoms: 0.23 Number of scatterers: 21960 At special positions: 0 Unit cell: (112.56, 120.12, 126.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 67 16.00 P 15 15.00 Mg 5 11.99 O 4223 8.00 N 3820 7.00 C 13830 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: 1.83 Conformation dependent library (CDL) restraints added in 930.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5148 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 23 sheets defined 45.5% alpha, 14.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 100 through 104 removed outlier: 3.866A pdb=" N LEU A 103 " --> pdb=" O GLY A 100 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE A 104 " --> pdb=" O GLU A 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 100 through 104' Processing helix chain 'A' and resid 150 through 157 Processing helix chain 'A' and resid 175 through 186 removed outlier: 3.878A pdb=" N ALA A 179 " --> pdb=" O LYS A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 215 removed outlier: 3.602A pdb=" N HIS A 215 " --> pdb=" O THR A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 219 removed outlier: 4.346A pdb=" N ASP A 219 " --> pdb=" O GLY A 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 216 through 219' Processing helix chain 'A' and resid 231 through 253 removed outlier: 3.737A pdb=" N LEU A 235 " --> pdb=" O PRO A 231 " (cutoff:3.500A) Proline residue: A 239 - end of helix removed outlier: 3.989A pdb=" N MET A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY A 246 " --> pdb=" O GLY A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 277 removed outlier: 3.596A pdb=" N LEU A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 299 Processing helix chain 'A' and resid 322 through 325 Processing helix chain 'A' and resid 328 through 338 Processing helix chain 'A' and resid 345 through 351 Processing helix chain 'A' and resid 372 through 397 removed outlier: 4.185A pdb=" N THR A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA A 394 " --> pdb=" O ARG A 390 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N PHE A 395 " --> pdb=" O GLU A 391 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLN A 397 " --> pdb=" O GLU A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 421 removed outlier: 3.570A pdb=" N LEU A 420 " --> pdb=" O THR A 416 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS A 421 " --> pdb=" O VAL A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 442 Processing helix chain 'A' and resid 449 through 451 No H-bonds generated for 'chain 'A' and resid 449 through 451' Processing helix chain 'A' and resid 452 through 467 removed outlier: 3.547A pdb=" N LYS A 458 " --> pdb=" O ARG A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 479 removed outlier: 3.989A pdb=" N LEU A 472 " --> pdb=" O GLY A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 498 removed outlier: 3.748A pdb=" N THR A 497 " --> pdb=" O ALA A 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 157 Processing helix chain 'B' and resid 174 through 186 Processing helix chain 'B' and resid 201 through 214 Processing helix chain 'B' and resid 215 through 220 removed outlier: 5.803A pdb=" N LEU B 218 " --> pdb=" O HIS B 215 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR B 220 " --> pdb=" O ALA B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 253 Proline residue: B 239 - end of helix removed outlier: 3.697A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 277 removed outlier: 4.157A pdb=" N GLN B 266 " --> pdb=" O ASP B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 299 Processing helix chain 'B' and resid 305 through 309 Processing helix chain 'B' and resid 328 through 336 Processing helix chain 'B' and resid 345 through 352 Processing helix chain 'B' and resid 372 through 379 Processing helix chain 'B' and resid 380 through 399 removed outlier: 4.499A pdb=" N LEU B 384 " --> pdb=" O GLY B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 421 removed outlier: 3.623A pdb=" N LYS B 421 " --> pdb=" O VAL B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 442 Processing helix chain 'B' and resid 444 through 448 removed outlier: 4.058A pdb=" N ASP B 447 " --> pdb=" O PHE B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 467 removed outlier: 4.271A pdb=" N ARG B 455 " --> pdb=" O GLU B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 479 removed outlier: 3.527A pdb=" N LEU B 472 " --> pdb=" O GLY B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 498 Processing helix chain 'C' and resid 100 through 104 Processing helix chain 'C' and resid 150 through 156 Processing helix chain 'C' and resid 174 through 186 Processing helix chain 'C' and resid 201 through 215 Processing helix chain 'C' and resid 231 through 252 Proline residue: C 239 - end of helix removed outlier: 3.671A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS C 252 " --> pdb=" O TYR C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 277 Processing helix chain 'C' and resid 289 through 300 removed outlier: 4.013A pdb=" N ARG C 300 " --> pdb=" O ARG C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 325 Processing helix chain 'C' and resid 328 through 336 Processing helix chain 'C' and resid 345 through 352 removed outlier: 3.662A pdb=" N GLY C 352 " --> pdb=" O LEU C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 379 Processing helix chain 'C' and resid 379 through 399 removed outlier: 3.827A pdb=" N ARG C 383 " --> pdb=" O ALA C 379 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LEU C 384 " --> pdb=" O GLY C 380 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA C 394 " --> pdb=" O ARG C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 420 Processing helix chain 'C' and resid 429 through 443 removed outlier: 3.639A pdb=" N GLY C 443 " --> pdb=" O ALA C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 447 removed outlier: 4.141A pdb=" N ASP C 447 " --> pdb=" O PHE C 444 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 444 through 447' Processing helix chain 'C' and resid 449 through 467 removed outlier: 4.243A pdb=" N ARG C 454 " --> pdb=" O VAL C 450 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ARG C 455 " --> pdb=" O GLU C 451 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS C 458 " --> pdb=" O ARG C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 479 removed outlier: 3.944A pdb=" N LEU C 472 " --> pdb=" O GLY C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 498 Processing helix chain 'D' and resid 88 through 92 Processing helix chain 'D' and resid 124 through 128 Processing helix chain 'D' and resid 139 through 146 Processing helix chain 'D' and resid 163 through 179 removed outlier: 3.719A pdb=" N LEU D 167 " --> pdb=" O GLY D 163 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU D 178 " --> pdb=" O ASN D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 206 Processing helix chain 'D' and resid 207 through 209 No H-bonds generated for 'chain 'D' and resid 207 through 209' Processing helix chain 'D' and resid 221 through 242 removed outlier: 3.843A pdb=" N ARG D 225 " --> pdb=" O PRO D 221 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ALA D 229 " --> pdb=" O ARG D 225 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N LEU D 230 " --> pdb=" O MET D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 269 removed outlier: 4.096A pdb=" N THR D 258 " --> pdb=" O ILE D 254 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU D 267 " --> pdb=" O GLU D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 292 removed outlier: 3.687A pdb=" N ILE D 292 " --> pdb=" O LEU D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 323 removed outlier: 3.993A pdb=" N SER D 323 " --> pdb=" O ALA D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 339 Processing helix chain 'D' and resid 355 through 360 Processing helix chain 'D' and resid 360 through 388 removed outlier: 4.289A pdb=" N ASP D 382 " --> pdb=" O LYS D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 410 removed outlier: 3.692A pdb=" N ARG D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU D 410 " --> pdb=" O ILE D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 422 removed outlier: 4.161A pdb=" N PHE D 420 " --> pdb=" O VAL D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 442 Processing helix chain 'D' and resid 450 through 454 Processing helix chain 'D' and resid 458 through 470 Processing helix chain 'E' and resid 88 through 92 removed outlier: 3.584A pdb=" N THR E 91 " --> pdb=" O GLY E 88 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU E 92 " --> pdb=" O GLU E 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 88 through 92' Processing helix chain 'E' and resid 139 through 146 Processing helix chain 'E' and resid 163 through 179 Processing helix chain 'E' and resid 191 through 205 Processing helix chain 'E' and resid 207 through 209 No H-bonds generated for 'chain 'E' and resid 207 through 209' Processing helix chain 'E' and resid 221 through 243 removed outlier: 3.600A pdb=" N ARG E 225 " --> pdb=" O PRO E 221 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ALA E 229 " --> pdb=" O ARG E 225 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LEU E 230 " --> pdb=" O MET E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 269 Processing helix chain 'E' and resid 281 through 291 Processing helix chain 'E' and resid 315 through 323 Processing helix chain 'E' and resid 332 through 338 Processing helix chain 'E' and resid 355 through 360 Processing helix chain 'E' and resid 360 through 388 removed outlier: 4.365A pdb=" N ASP E 382 " --> pdb=" O LYS E 378 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ILE E 383 " --> pdb=" O GLU E 379 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE E 386 " --> pdb=" O ASP E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 393 through 410 removed outlier: 3.758A pdb=" N ARG E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 416 No H-bonds generated for 'chain 'E' and resid 414 through 416' Processing helix chain 'E' and resid 417 through 422 Processing helix chain 'E' and resid 429 through 443 Processing helix chain 'E' and resid 449 through 454 Processing helix chain 'E' and resid 458 through 470 Processing helix chain 'F' and resid 124 through 128 removed outlier: 3.533A pdb=" N LEU F 128 " --> pdb=" O PHE F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 145 Processing helix chain 'F' and resid 163 through 178 Processing helix chain 'F' and resid 193 through 205 removed outlier: 4.000A pdb=" N ASP F 197 " --> pdb=" O ARG F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 210 Processing helix chain 'F' and resid 221 through 242 removed outlier: 5.140A pdb=" N ALA F 229 " --> pdb=" O ARG F 225 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LEU F 230 " --> pdb=" O MET F 226 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA F 236 " --> pdb=" O GLY F 232 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE F 239 " --> pdb=" O MET F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 269 removed outlier: 3.936A pdb=" N THR F 258 " --> pdb=" O ILE F 254 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLU F 263 " --> pdb=" O GLN F 259 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA F 266 " --> pdb=" O SER F 262 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLY F 269 " --> pdb=" O SER F 265 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 290 removed outlier: 3.709A pdb=" N LEU F 288 " --> pdb=" O GLU F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 315 through 325 removed outlier: 3.908A pdb=" N HIS F 324 " --> pdb=" O THR F 320 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU F 325 " --> pdb=" O THR F 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 338 removed outlier: 3.647A pdb=" N MET F 338 " --> pdb=" O LYS F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 360 through 387 removed outlier: 3.554A pdb=" N ILE F 386 " --> pdb=" O ASP F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 410 removed outlier: 3.719A pdb=" N VAL F 399 " --> pdb=" O GLU F 395 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL F 400 " --> pdb=" O ASP F 396 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG F 405 " --> pdb=" O HIS F 401 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU F 410 " --> pdb=" O ILE F 406 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 420 removed outlier: 3.715A pdb=" N GLN F 419 " --> pdb=" O VAL F 416 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 443 removed outlier: 3.942A pdb=" N GLU F 439 " --> pdb=" O ARG F 435 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE F 440 " --> pdb=" O GLY F 436 " (cutoff:3.500A) Processing helix chain 'F' and resid 449 through 453 Processing helix chain 'F' and resid 458 through 469 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 35 removed outlier: 6.230A pdb=" N ARG A 40 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N VAL A 34 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL A 74 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N ALA A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY A 29 " --> pdb=" O VAL A 88 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 99 Processing sheet with id=AA3, first strand: chain 'A' and resid 107 through 108 removed outlier: 3.952A pdb=" N ILE A 222 " --> pdb=" O SER A 193 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ILE A 192 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N VAL A 259 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE A 194 " --> pdb=" O VAL A 259 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TYR A 260 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL A 363 " --> pdb=" O GLN A 341 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 28 through 33 removed outlier: 6.419A pdb=" N ARG B 40 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N VAL B 74 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N ALA B 63 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU B 76 " --> pdb=" O GLY B 61 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N GLY B 61 " --> pdb=" O LEU B 76 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 96 through 99 Processing sheet with id=AA6, first strand: chain 'B' and resid 107 through 108 removed outlier: 6.137A pdb=" N VAL B 108 " --> pdb=" O THR B 225 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 318 through 321 removed outlier: 6.704A pdb=" N ILE B 167 " --> pdb=" O VAL B 319 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N THR B 321 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N GLY B 169 " --> pdb=" O THR B 321 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASP B 170 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 28 through 31 removed outlier: 6.703A pdb=" N VAL C 74 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N ALA C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLU C 51 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N LEU C 52 " --> pdb=" O THR C 91 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 96 through 99 Processing sheet with id=AB1, first strand: chain 'C' and resid 107 through 108 removed outlier: 3.503A pdb=" N TYR C 260 " --> pdb=" O LEU C 316 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 318 through 320 removed outlier: 6.748A pdb=" N ILE C 167 " --> pdb=" O VAL C 319 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 3 through 10 removed outlier: 6.723A pdb=" N ASP D 15 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N VAL D 9 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL D 13 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N THR D 58 " --> pdb=" O HIS D 53 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N HIS D 53 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ARG D 60 " --> pdb=" O ALA D 51 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE D 44 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N GLN D 33 " --> pdb=" O GLU D 75 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLU D 75 " --> pdb=" O GLN D 33 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 84 through 86 Processing sheet with id=AB5, first strand: chain 'D' and resid 95 through 96 removed outlier: 6.822A pdb=" N PHE D 96 " --> pdb=" O PHE D 215 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N SER D 183 " --> pdb=" O ALA D 212 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N VAL D 214 " --> pdb=" O SER D 183 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N PHE D 185 " --> pdb=" O VAL D 214 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N GLY D 216 " --> pdb=" O PHE D 185 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N GLY D 187 " --> pdb=" O GLY D 216 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE D 182 " --> pdb=" O LEU D 248 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N PHE D 250 " --> pdb=" O ILE D 182 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL D 184 " --> pdb=" O PHE D 250 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N ASP D 252 " --> pdb=" O VAL D 184 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ALA D 186 " --> pdb=" O ASP D 252 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N VAL D 247 " --> pdb=" O THR D 301 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N ILE D 303 " --> pdb=" O VAL D 247 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU D 249 " --> pdb=" O ILE D 303 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N ALA D 305 " --> pdb=" O LEU D 249 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N ILE D 251 " --> pdb=" O ALA D 305 " (cutoff:3.500A) removed outlier: 8.777A pdb=" N TYR D 307 " --> pdb=" O ILE D 251 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE D 154 " --> pdb=" O GLN D 304 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ILE D 306 " --> pdb=" O ILE D 154 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU D 156 " --> pdb=" O ILE D 306 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 4 through 10 removed outlier: 5.928A pdb=" N VAL E 6 " --> pdb=" O LYS E 17 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N LYS E 17 " --> pdb=" O VAL E 6 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN E 8 " --> pdb=" O ASP E 15 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N VAL E 13 " --> pdb=" O MET E 10 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N THR E 58 " --> pdb=" O HIS E 53 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N HIS E 53 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ARG E 60 " --> pdb=" O ALA E 51 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N GLN E 33 " --> pdb=" O GLU E 75 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLU E 75 " --> pdb=" O GLN E 33 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 84 through 87 removed outlier: 3.704A pdb=" N ARG E 114 " --> pdb=" O VAL E 87 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 95 through 96 removed outlier: 6.122A pdb=" N PHE E 96 " --> pdb=" O PHE E 215 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N GLN E 217 " --> pdb=" O PHE E 96 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL E 184 " --> pdb=" O PHE E 250 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA E 305 " --> pdb=" O ILE E 251 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE E 154 " --> pdb=" O GLN E 304 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ILE E 306 " --> pdb=" O ILE E 154 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N LEU E 156 " --> pdb=" O ILE E 306 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LYS E 153 " --> pdb=" O ALA E 327 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N THR E 329 " --> pdb=" O LYS E 153 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N GLY E 155 " --> pdb=" O THR E 329 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N LEU E 331 " --> pdb=" O GLY E 155 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N PHE E 157 " --> pdb=" O LEU E 331 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 134 through 135 removed outlier: 4.258A pdb=" N TYR E 148 " --> pdb=" O LEU E 135 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 3 through 5 removed outlier: 5.891A pdb=" N GLU F 75 " --> pdb=" O GLN F 33 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N GLN F 33 " --> pdb=" O GLU F 75 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ARG F 60 " --> pdb=" O ALA F 51 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 84 through 86 Processing sheet with id=AC3, first strand: chain 'F' and resid 134 through 135 removed outlier: 4.591A pdb=" N TYR F 148 " --> pdb=" O LEU F 135 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 304 through 306 Processing sheet with id=AC5, first strand: chain 'F' and resid 183 through 184 985 hydrogen bonds defined for protein. 2841 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: 3.59 Time building geometry restraints manager: 2.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7465 1.34 - 1.46: 2997 1.46 - 1.58: 11713 1.58 - 1.69: 21 1.69 - 1.81: 134 Bond restraints: 22330 Sorted by residual: bond pdb=" O2 PO4 E 501 " pdb=" P PO4 E 501 " ideal model delta sigma weight residual 1.567 1.500 0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" O3 PO4 E 501 " pdb=" P PO4 E 501 " ideal model delta sigma weight residual 1.569 1.505 0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" O4 PO4 E 501 " pdb=" P PO4 E 501 " ideal model delta sigma weight residual 1.568 1.505 0.063 2.00e-02 2.50e+03 9.94e+00 bond pdb=" O1 PO4 E 501 " pdb=" P PO4 E 501 " ideal model delta sigma weight residual 1.565 1.505 0.060 2.00e-02 2.50e+03 9.02e+00 bond pdb=" CA PRO B 280 " pdb=" C PRO B 280 " ideal model delta sigma weight residual 1.517 1.528 -0.011 6.70e-03 2.23e+04 2.54e+00 ... (remaining 22325 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 29234 1.42 - 2.85: 897 2.85 - 4.27: 117 4.27 - 5.69: 30 5.69 - 7.11: 5 Bond angle restraints: 30283 Sorted by residual: angle pdb=" C LYS C 377 " pdb=" N VAL C 378 " pdb=" CA VAL C 378 " ideal model delta sigma weight residual 123.08 119.52 3.56 1.01e+00 9.80e-01 1.24e+01 angle pdb=" N VAL F 132 " pdb=" CA VAL F 132 " pdb=" C VAL F 132 " ideal model delta sigma weight residual 113.71 110.78 2.93 9.50e-01 1.11e+00 9.54e+00 angle pdb=" N ASP A 262 " pdb=" CA ASP A 262 " pdb=" C ASP A 262 " ideal model delta sigma weight residual 107.49 112.85 -5.36 1.74e+00 3.30e-01 9.50e+00 angle pdb=" CA ILE F 7 " pdb=" C ILE F 7 " pdb=" N GLN F 8 " ideal model delta sigma weight residual 116.60 120.76 -4.16 1.45e+00 4.76e-01 8.23e+00 angle pdb=" N GLY D 223 " pdb=" CA GLY D 223 " pdb=" C GLY D 223 " ideal model delta sigma weight residual 112.83 116.19 -3.36 1.22e+00 6.72e-01 7.57e+00 ... (remaining 30278 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.84: 13164 28.84 - 57.68: 409 57.68 - 86.52: 42 86.52 - 115.36: 4 115.36 - 144.20: 1 Dihedral angle restraints: 13620 sinusoidal: 5565 harmonic: 8055 Sorted by residual: dihedral pdb=" O2A ADP E 500 " pdb=" O3A ADP E 500 " pdb=" PA ADP E 500 " pdb=" PB ADP E 500 " ideal model delta sinusoidal sigma weight residual -60.00 84.20 -144.20 1 2.00e+01 2.50e-03 4.35e+01 dihedral pdb=" O1B ADP E 500 " pdb=" O3A ADP E 500 " pdb=" PB ADP E 500 " pdb=" PA ADP E 500 " ideal model delta sinusoidal sigma weight residual -60.00 -167.52 107.51 1 2.00e+01 2.50e-03 3.12e+01 dihedral pdb=" CA PHE F 215 " pdb=" C PHE F 215 " pdb=" N GLY F 216 " pdb=" CA GLY F 216 " ideal model delta harmonic sigma weight residual 180.00 158.15 21.85 0 5.00e+00 4.00e-02 1.91e+01 ... (remaining 13617 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1942 0.029 - 0.058: 968 0.058 - 0.087: 296 0.087 - 0.117: 207 0.117 - 0.146: 67 Chirality restraints: 3480 Sorted by residual: chirality pdb=" CA ILE A 38 " pdb=" N ILE A 38 " pdb=" C ILE A 38 " pdb=" CB ILE A 38 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.31e-01 chirality pdb=" CA PRO D 309 " pdb=" N PRO D 309 " pdb=" C PRO D 309 " pdb=" CB PRO D 309 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.14 2.00e-01 2.50e+01 5.20e-01 chirality pdb=" CA ILE A 342 " pdb=" N ILE A 342 " pdb=" C ILE A 342 " pdb=" CB ILE A 342 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.14e-01 ... (remaining 3477 not shown) Planarity restraints: 3960 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR F 199 " 0.011 2.00e-02 2.50e+03 2.27e-02 5.13e+00 pdb=" C TYR F 199 " -0.039 2.00e-02 2.50e+03 pdb=" O TYR F 199 " 0.015 2.00e-02 2.50e+03 pdb=" N HIS F 200 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS D 173 " 0.009 2.00e-02 2.50e+03 1.80e-02 3.25e+00 pdb=" C HIS D 173 " -0.031 2.00e-02 2.50e+03 pdb=" O HIS D 173 " 0.012 2.00e-02 2.50e+03 pdb=" N ASN D 174 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG D 120 " -0.029 5.00e-02 4.00e+02 4.40e-02 3.09e+00 pdb=" N PRO D 121 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO D 121 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 121 " -0.024 5.00e-02 4.00e+02 ... (remaining 3957 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 72 2.46 - 3.07: 14819 3.07 - 3.68: 32254 3.68 - 4.29: 46978 4.29 - 4.90: 78517 Nonbonded interactions: 172640 Sorted by model distance: nonbonded pdb=" O3 PO4 E 501 " pdb="MG MG E 502 " model vdw 1.846 2.170 nonbonded pdb=" O3B ADP E 500 " pdb="MG MG E 502 " model vdw 1.888 2.170 nonbonded pdb=" O2G ATP B 600 " pdb="MG MG B 601 " model vdw 1.909 2.170 nonbonded pdb=" O2B ATP D 500 " pdb="MG MG D 501 " model vdw 1.926 2.170 nonbonded pdb=" OG1 THR C 176 " pdb="MG MG C 601 " model vdw 2.011 2.170 ... (remaining 172635 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 27 through 601) selection = (chain 'B' and (resid 27 through 499 or resid 600 through 601)) selection = (chain 'C' and (resid 27 through 499 or resid 600 through 601)) } ncs_group { reference = (chain 'D' and resid 2 through 470) selection = (chain 'E' and resid 2 through 470) selection = (chain 'F' and resid 2 through 470) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 19.570 Find NCS groups from input model: 0.770 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:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6530 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 : 0.003 0.067 22330 Z= 0.168 Angle : 0.611 7.113 30283 Z= 0.346 Chirality : 0.045 0.146 3480 Planarity : 0.005 0.044 3960 Dihedral : 13.740 144.202 8472 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.11 % Allowed : 7.72 % Favored : 90.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % 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 aren not related in a simple way. whole: -0.04 (0.15), residues: 2823 helix: 0.68 (0.15), residues: 1110 sheet: 0.17 (0.24), residues: 427 loop : -0.64 (0.17), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 240 TYR 0.015 0.002 TYR F 238 PHE 0.026 0.002 PHE C 494 HIS 0.005 0.001 HIS F 200 Details of bonding type rmsd covalent geometry : bond 0.00341 (22330) covalent geometry : angle 0.61061 (30283) hydrogen bonds : bond 0.15837 ( 985) hydrogen bonds : angle 7.00569 ( 2841) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 572 time to evaluate : 0.711 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: A 444 PHE cc_start: 0.6239 (m-80) cc_final: 0.6002 (m-80) REVERT: A 471 LEU cc_start: 0.7510 (mt) cc_final: 0.7156 (mp) REVERT: B 191 MET cc_start: 0.6369 (mmt) cc_final: 0.5698 (mmt) REVERT: B 236 PHE cc_start: 0.6486 (OUTLIER) cc_final: 0.6246 (p90) REVERT: B 318 PHE cc_start: 0.4423 (m-80) cc_final: 0.4029 (m-80) REVERT: C 95 MET cc_start: 0.5219 (tpp) cc_final: 0.4981 (mmm) REVERT: C 361 LEU cc_start: 0.7258 (tp) cc_final: 0.6993 (mp) REVERT: E 202 MET cc_start: 0.5628 (mmt) cc_final: 0.5411 (ttm) REVERT: E 285 MET cc_start: 0.8383 (tpp) cc_final: 0.7962 (tpp) REVERT: F 49 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7147 (pt0) REVERT: F 256 ARG cc_start: 0.4814 (OUTLIER) cc_final: 0.4293 (mtm-85) REVERT: F 264 VAL cc_start: 0.2961 (t) cc_final: 0.2731 (t) outliers start: 49 outliers final: 12 residues processed: 610 average time/residue: 0.1610 time to fit residues: 144.8497 Evaluate side-chains 338 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 323 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 236 PHE Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 196 ASN Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 256 ARG Chi-restraints excluded: chain F residue 359 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 0.0020 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 7.9990 chunk 111 optimal weight: 4.9990 overall best weight: 3.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 GLN A 345 GLN A 474 HIS ** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 143 HIS C 425 HIS C 474 HIS D 22 HIS ** D 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 330 ASN ** E 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 119 HIS E 169 GLN E 173 HIS E 259 GLN E 289 GLN E 304 GLN F 53 HIS F 253 ASN F 278 GLN ** F 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 324 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.188883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.155315 restraints weight = 27838.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.157824 restraints weight = 20644.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.159200 restraints weight = 14446.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.160398 restraints weight = 11934.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.160541 restraints weight = 10472.155| |-----------------------------------------------------------------------------| r_work (final): 0.4061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 22330 Z= 0.226 Angle : 0.725 8.653 30283 Z= 0.388 Chirality : 0.050 0.268 3480 Planarity : 0.006 0.056 3960 Dihedral : 9.289 124.695 3254 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 4.48 % Allowed : 13.93 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % 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 aren not related in a simple way. whole: -0.48 (0.15), residues: 2823 helix: 0.50 (0.15), residues: 1121 sheet: -0.10 (0.24), residues: 423 loop : -1.09 (0.17), residues: 1279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 476 TYR 0.026 0.002 TYR C 195 PHE 0.046 0.003 PHE E 414 HIS 0.006 0.001 HIS B 474 Details of bonding type rmsd covalent geometry : bond 0.00530 (22330) covalent geometry : angle 0.72545 (30283) hydrogen bonds : bond 0.05981 ( 985) hydrogen bonds : angle 5.71887 ( 2841) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 343 time to evaluate : 0.635 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: A 95 MET cc_start: 0.6037 (ptt) cc_final: 0.5752 (pmm) REVERT: A 444 PHE cc_start: 0.6939 (m-80) cc_final: 0.6723 (m-80) REVERT: B 318 PHE cc_start: 0.4658 (m-80) cc_final: 0.4422 (m-80) REVERT: B 406 THR cc_start: 0.8548 (OUTLIER) cc_final: 0.8271 (t) REVERT: C 137 MET cc_start: 0.5822 (mmm) cc_final: 0.5577 (mmp) REVERT: D 235 MET cc_start: 0.7111 (mtt) cc_final: 0.6570 (mtp) REVERT: D 271 MET cc_start: 0.7281 (mtt) cc_final: 0.6911 (mtt) REVERT: E 213 MET cc_start: 0.6418 (OUTLIER) cc_final: 0.6091 (mtt) REVERT: E 259 GLN cc_start: 0.7420 (OUTLIER) cc_final: 0.6902 (mt0) REVERT: E 268 LEU cc_start: 0.6638 (OUTLIER) cc_final: 0.6136 (mm) REVERT: E 285 MET cc_start: 0.8445 (tpp) cc_final: 0.8066 (tpp) REVERT: F 49 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.6811 (pt0) REVERT: F 201 GLU cc_start: 0.5983 (OUTLIER) cc_final: 0.5446 (mm-30) REVERT: F 235 MET cc_start: 0.6499 (mmt) cc_final: 0.6290 (mmt) REVERT: F 253 ASN cc_start: 0.5056 (OUTLIER) cc_final: 0.4169 (p0) REVERT: F 264 VAL cc_start: 0.4243 (t) cc_final: 0.3951 (t) outliers start: 104 outliers final: 55 residues processed: 422 average time/residue: 0.1307 time to fit residues: 86.1262 Evaluate side-chains 344 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 282 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 200 GLN Chi-restraints excluded: chain C residue 236 PHE Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 34 HIS Chi-restraints excluded: chain D residue 35 LYS Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 322 PHE Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 419 GLN Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 213 MET Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 259 GLN Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 411 SER Chi-restraints excluded: chain F residue 7 ILE Chi-restraints excluded: chain F residue 18 PHE Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 201 GLU Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 251 ILE Chi-restraints excluded: chain F residue 253 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 255 optimal weight: 6.9990 chunk 136 optimal weight: 10.0000 chunk 56 optimal weight: 20.0000 chunk 59 optimal weight: 10.0000 chunk 118 optimal weight: 2.9990 chunk 114 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 160 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 200 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 GLN A 358 ASN B 185 ASN ** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 ASN ** C 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 333 ASN C 474 HIS D 219 ASN D 330 ASN ** E 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 259 GLN E 372 GLN F 169 GLN ** F 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.188193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.151138 restraints weight = 27307.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.155137 restraints weight = 19722.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.156376 restraints weight = 13997.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.157155 restraints weight = 10512.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.157979 restraints weight = 9985.245| |-----------------------------------------------------------------------------| r_work (final): 0.3976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.4060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 22330 Z= 0.299 Angle : 0.789 9.204 30283 Z= 0.425 Chirality : 0.053 0.250 3480 Planarity : 0.007 0.067 3960 Dihedral : 9.344 120.430 3245 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 6.25 % Allowed : 17.68 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % 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 aren not related in a simple way. whole: -1.14 (0.15), residues: 2823 helix: 0.08 (0.15), residues: 1104 sheet: -0.60 (0.24), residues: 437 loop : -1.51 (0.16), residues: 1282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 127 TYR 0.030 0.003 TYR B 240 PHE 0.059 0.003 PHE E 414 HIS 0.007 0.002 HIS A 255 Details of bonding type rmsd covalent geometry : bond 0.00721 (22330) covalent geometry : angle 0.78930 (30283) hydrogen bonds : bond 0.06553 ( 985) hydrogen bonds : angle 5.84173 ( 2841) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 318 time to evaluate : 0.839 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: A 95 MET cc_start: 0.6279 (ptt) cc_final: 0.6022 (pmm) REVERT: A 172 GLN cc_start: 0.8736 (tm-30) cc_final: 0.8443 (tm-30) REVERT: A 184 ILE cc_start: 0.6920 (OUTLIER) cc_final: 0.6714 (mt) REVERT: A 245 MET cc_start: 0.5497 (ptp) cc_final: 0.4727 (mmm) REVERT: A 314 THR cc_start: 0.7263 (OUTLIER) cc_final: 0.7037 (t) REVERT: B 36 ASP cc_start: 0.7680 (p0) cc_final: 0.7465 (p0) REVERT: B 191 MET cc_start: 0.6526 (mmt) cc_final: 0.6194 (mmt) REVERT: B 250 MET cc_start: 0.5732 (tpt) cc_final: 0.5447 (tpt) REVERT: B 406 THR cc_start: 0.8616 (OUTLIER) cc_final: 0.8300 (t) REVERT: C 198 ILE cc_start: 0.5849 (OUTLIER) cc_final: 0.5641 (mt) REVERT: D 368 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7237 (tpp-160) REVERT: E 202 MET cc_start: 0.7395 (OUTLIER) cc_final: 0.7054 (mmp) REVERT: E 213 MET cc_start: 0.6597 (OUTLIER) cc_final: 0.6397 (mtt) REVERT: E 268 LEU cc_start: 0.6738 (OUTLIER) cc_final: 0.6246 (mm) REVERT: E 285 MET cc_start: 0.8442 (tpp) cc_final: 0.8138 (tpp) REVERT: E 469 MET cc_start: 0.5742 (ttm) cc_final: 0.5455 (ttm) REVERT: F 48 LEU cc_start: 0.7056 (OUTLIER) cc_final: 0.6712 (mt) REVERT: F 49 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6991 (tt0) REVERT: F 191 ARG cc_start: 0.5090 (OUTLIER) cc_final: 0.2618 (tpp-160) REVERT: F 201 GLU cc_start: 0.5923 (OUTLIER) cc_final: 0.5441 (mm-30) REVERT: F 235 MET cc_start: 0.6531 (mmt) cc_final: 0.6289 (mmt) outliers start: 145 outliers final: 100 residues processed: 429 average time/residue: 0.1334 time to fit residues: 89.6449 Evaluate side-chains 390 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 278 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 200 GLN Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 236 PHE Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 406 THR Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 34 HIS Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 368 ARG Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 419 GLN Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 197 ASP Chi-restraints excluded: chain E residue 202 MET Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 213 MET Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 259 GLN Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 411 SER Chi-restraints excluded: chain E residue 423 GLN Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 7 ILE Chi-restraints excluded: chain F residue 18 PHE Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 191 ARG Chi-restraints excluded: chain F residue 193 ARG Chi-restraints excluded: chain F residue 201 GLU Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 251 ILE Chi-restraints excluded: chain F residue 253 ASN Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain F residue 321 THR Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 437 PHE Chi-restraints excluded: chain F residue 456 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 261 optimal weight: 0.0870 chunk 242 optimal weight: 2.9990 chunk 220 optimal weight: 7.9990 chunk 232 optimal weight: 5.9990 chunk 123 optimal weight: 0.1980 chunk 212 optimal weight: 0.9990 chunk 271 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 chunk 234 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 overall best weight: 0.8162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 HIS ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 345 GLN D 219 ASN D 330 ASN E 177 GLN E 259 GLN F 253 ASN F 407 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.197283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.160221 restraints weight = 26299.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.164149 restraints weight = 17012.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.165944 restraints weight = 11160.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.166810 restraints weight = 9108.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.167379 restraints weight = 8099.082| |-----------------------------------------------------------------------------| r_work (final): 0.4075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 moved from start: 0.4197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 22330 Z= 0.124 Angle : 0.582 7.733 30283 Z= 0.306 Chirality : 0.045 0.212 3480 Planarity : 0.005 0.057 3960 Dihedral : 8.371 90.579 3244 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 4.14 % Allowed : 20.05 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % 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 aren not related in a simple way. whole: -0.53 (0.15), residues: 2823 helix: 0.66 (0.15), residues: 1116 sheet: -0.35 (0.25), residues: 416 loop : -1.22 (0.17), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 278 TYR 0.015 0.001 TYR B 438 PHE 0.022 0.002 PHE B 349 HIS 0.006 0.001 HIS B 474 Details of bonding type rmsd covalent geometry : bond 0.00260 (22330) covalent geometry : angle 0.58223 (30283) hydrogen bonds : bond 0.04378 ( 985) hydrogen bonds : angle 5.16349 ( 2841) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 306 time to evaluate : 0.819 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: A 198 ILE cc_start: 0.6328 (OUTLIER) cc_final: 0.5419 (pt) REVERT: A 245 MET cc_start: 0.5161 (ptp) cc_final: 0.4621 (tpt) REVERT: A 444 PHE cc_start: 0.7069 (m-80) cc_final: 0.6803 (m-80) REVERT: B 95 MET cc_start: 0.8284 (tpt) cc_final: 0.8029 (tpt) REVERT: C 93 ARG cc_start: 0.7192 (ptt-90) cc_final: 0.6894 (ptt-90) REVERT: C 415 ARG cc_start: 0.8095 (mtt90) cc_final: 0.7761 (mpt-90) REVERT: D 235 MET cc_start: 0.7187 (mtt) cc_final: 0.6675 (mtp) REVERT: D 338 MET cc_start: 0.7163 (mtp) cc_final: 0.6824 (tpt) REVERT: D 368 ARG cc_start: 0.7689 (OUTLIER) cc_final: 0.6846 (tpp-160) REVERT: E 202 MET cc_start: 0.7223 (mmp) cc_final: 0.6846 (mmp) REVERT: E 259 GLN cc_start: 0.7653 (OUTLIER) cc_final: 0.6593 (mp-120) REVERT: E 285 MET cc_start: 0.8254 (tpp) cc_final: 0.7994 (tpp) REVERT: E 290 GLU cc_start: 0.6588 (OUTLIER) cc_final: 0.5977 (mm-30) REVERT: E 337 GLU cc_start: 0.6527 (pt0) cc_final: 0.6218 (mt-10) REVERT: E 469 MET cc_start: 0.5686 (ttm) cc_final: 0.5477 (mtt) REVERT: F 49 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.6957 (tt0) REVERT: F 191 ARG cc_start: 0.4751 (OUTLIER) cc_final: 0.2182 (mmm160) REVERT: F 235 MET cc_start: 0.6523 (mmt) cc_final: 0.6269 (mmt) REVERT: F 253 ASN cc_start: 0.5021 (OUTLIER) cc_final: 0.4016 (p0) REVERT: F 285 MET cc_start: 0.7265 (ttm) cc_final: 0.6772 (tpp) REVERT: F 404 ARG cc_start: 0.8253 (mmm-85) cc_final: 0.7531 (tpp80) outliers start: 96 outliers final: 50 residues processed: 377 average time/residue: 0.1307 time to fit residues: 77.4189 Evaluate side-chains 325 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 268 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 200 GLN Chi-restraints excluded: chain C residue 236 PHE Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 34 HIS Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 368 ARG Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 35 LYS Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 74 MET Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 259 GLN Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 383 ILE Chi-restraints excluded: chain E residue 423 GLN Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 191 ARG Chi-restraints excluded: chain F residue 193 ARG Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 253 ASN Chi-restraints excluded: chain F residue 400 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 231 optimal weight: 7.9990 chunk 82 optimal weight: 10.0000 chunk 4 optimal weight: 8.9990 chunk 177 optimal weight: 7.9990 chunk 220 optimal weight: 0.7980 chunk 145 optimal weight: 7.9990 chunk 172 optimal weight: 4.9990 chunk 126 optimal weight: 9.9990 chunk 60 optimal weight: 8.9990 chunk 250 optimal weight: 9.9990 chunk 193 optimal weight: 9.9990 overall best weight: 5.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 GLN B 294 HIS ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 ASN D 330 ASN E 28 ASN ** E 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 259 GLN E 278 GLN ** F 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.181709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.145117 restraints weight = 27245.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.146967 restraints weight = 19892.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.148826 restraints weight = 14254.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.149636 restraints weight = 11235.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.149995 restraints weight = 10172.112| |-----------------------------------------------------------------------------| r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.4756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.091 22330 Z= 0.296 Angle : 0.771 8.733 30283 Z= 0.411 Chirality : 0.052 0.332 3480 Planarity : 0.006 0.056 3960 Dihedral : 8.888 88.815 3244 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 6.55 % Allowed : 19.32 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % 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 aren not related in a simple way. whole: -1.17 (0.15), residues: 2823 helix: 0.13 (0.15), residues: 1107 sheet: -0.84 (0.25), residues: 412 loop : -1.52 (0.16), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 127 TYR 0.026 0.003 TYR B 240 PHE 0.033 0.003 PHE C 460 HIS 0.007 0.001 HIS A 255 Details of bonding type rmsd covalent geometry : bond 0.00723 (22330) covalent geometry : angle 0.77133 (30283) hydrogen bonds : bond 0.06197 ( 985) hydrogen bonds : angle 5.66193 ( 2841) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 286 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 MET cc_start: 0.5416 (ptp) cc_final: 0.4575 (tpt) REVERT: A 444 PHE cc_start: 0.7205 (m-80) cc_final: 0.6889 (m-80) REVERT: B 95 MET cc_start: 0.8380 (tpt) cc_final: 0.8000 (tpt) REVERT: C 415 ARG cc_start: 0.8290 (mtt90) cc_final: 0.7917 (mpt-90) REVERT: D 218 MET cc_start: 0.8198 (ptt) cc_final: 0.7954 (ptt) REVERT: D 235 MET cc_start: 0.7183 (mtt) cc_final: 0.6588 (mtp) REVERT: D 338 MET cc_start: 0.7397 (mtp) cc_final: 0.6947 (tpt) REVERT: D 368 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7346 (tpp-160) REVERT: E 202 MET cc_start: 0.7645 (OUTLIER) cc_final: 0.6835 (mmt) REVERT: E 259 GLN cc_start: 0.7992 (OUTLIER) cc_final: 0.6952 (mp-120) REVERT: E 268 LEU cc_start: 0.6709 (OUTLIER) cc_final: 0.6217 (mm) REVERT: E 285 MET cc_start: 0.8400 (tpp) cc_final: 0.8044 (tpp) REVERT: E 288 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7443 (tp) REVERT: E 369 LYS cc_start: 0.7336 (pttm) cc_final: 0.6600 (tptt) REVERT: E 469 MET cc_start: 0.5843 (ttm) cc_final: 0.5546 (ttm) REVERT: F 48 LEU cc_start: 0.7258 (OUTLIER) cc_final: 0.6935 (mt) REVERT: F 49 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.6973 (tt0) REVERT: F 191 ARG cc_start: 0.5037 (OUTLIER) cc_final: 0.2751 (tpp-160) REVERT: F 235 MET cc_start: 0.6621 (mmt) cc_final: 0.6383 (mmt) REVERT: F 288 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8505 (tp) REVERT: F 402 ARG cc_start: 0.8252 (ttp-170) cc_final: 0.7776 (ttt180) outliers start: 152 outliers final: 106 residues processed: 404 average time/residue: 0.1238 time to fit residues: 80.0004 Evaluate side-chains 379 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 264 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 260 TYR Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 200 GLN Chi-restraints excluded: chain C residue 236 PHE Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 406 THR Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 34 HIS Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 368 ARG Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain D residue 419 GLN Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 74 MET Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 197 ASP Chi-restraints excluded: chain E residue 202 MET Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 259 GLN Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 278 GLN Chi-restraints excluded: chain E residue 288 LEU Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 411 SER Chi-restraints excluded: chain E residue 423 GLN Chi-restraints excluded: chain E residue 447 HIS Chi-restraints excluded: chain F residue 18 PHE Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 191 ARG Chi-restraints excluded: chain F residue 193 ARG Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 251 ILE Chi-restraints excluded: chain F residue 288 LEU Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 304 GLN Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain F residue 321 THR Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 437 PHE Chi-restraints excluded: chain F residue 456 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 194 optimal weight: 2.9990 chunk 138 optimal weight: 20.0000 chunk 28 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 265 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 193 optimal weight: 3.9990 chunk 39 optimal weight: 8.9990 chunk 258 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 GLN C 147 GLN ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 HIS D 219 ASN E 174 ASN E 259 GLN E 365 GLN E 412 GLN ** F 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 304 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 = 0.4352 r_free = 0.4352 target = 0.190645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.153556 restraints weight = 26778.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.156836 restraints weight = 19345.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.158672 restraints weight = 12963.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.159474 restraints weight = 9702.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.159723 restraints weight = 9257.818| |-----------------------------------------------------------------------------| r_work (final): 0.3995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.4869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 22330 Z= 0.160 Angle : 0.633 9.798 30283 Z= 0.334 Chirality : 0.046 0.199 3480 Planarity : 0.005 0.060 3960 Dihedral : 8.495 88.711 3244 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 4.36 % Allowed : 22.34 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % 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 aren not related in a simple way. whole: -0.91 (0.15), residues: 2823 helix: 0.45 (0.15), residues: 1104 sheet: -0.77 (0.25), residues: 404 loop : -1.45 (0.16), residues: 1315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 278 TYR 0.018 0.002 TYR B 461 PHE 0.026 0.002 PHE F 255 HIS 0.004 0.001 HIS F 179 Details of bonding type rmsd covalent geometry : bond 0.00378 (22330) covalent geometry : angle 0.63299 (30283) hydrogen bonds : bond 0.04973 ( 985) hydrogen bonds : angle 5.31217 ( 2841) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 289 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 GLN cc_start: 0.8720 (tm-30) cc_final: 0.7985 (tm-30) REVERT: A 245 MET cc_start: 0.5189 (ptp) cc_final: 0.4344 (tpt) REVERT: A 444 PHE cc_start: 0.7168 (m-80) cc_final: 0.6808 (m-80) REVERT: B 176 THR cc_start: 0.7890 (m) cc_final: 0.7541 (p) REVERT: C 93 ARG cc_start: 0.7394 (ptt-90) cc_final: 0.6973 (ptt-90) REVERT: C 361 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7630 (tp) REVERT: C 415 ARG cc_start: 0.8246 (mtt90) cc_final: 0.7900 (mpt-90) REVERT: D 218 MET cc_start: 0.8165 (ptt) cc_final: 0.7879 (ptt) REVERT: D 235 MET cc_start: 0.7230 (mtt) cc_final: 0.6669 (mtp) REVERT: D 288 LEU cc_start: 0.7677 (tp) cc_final: 0.7221 (tp) REVERT: D 338 MET cc_start: 0.7464 (mtp) cc_final: 0.6901 (tpt) REVERT: D 368 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.7002 (tpp-160) REVERT: E 202 MET cc_start: 0.7609 (mmp) cc_final: 0.7283 (mmt) REVERT: E 285 MET cc_start: 0.8277 (tpp) cc_final: 0.7888 (tpp) REVERT: E 337 GLU cc_start: 0.6565 (pt0) cc_final: 0.6142 (mt-10) REVERT: E 453 PHE cc_start: 0.7643 (m-80) cc_final: 0.7280 (m-80) REVERT: E 469 MET cc_start: 0.5849 (ttm) cc_final: 0.5550 (ttm) REVERT: F 49 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.6863 (tt0) REVERT: F 191 ARG cc_start: 0.4724 (OUTLIER) cc_final: 0.2758 (tpp-160) REVERT: F 255 PHE cc_start: 0.2079 (t80) cc_final: 0.1749 (t80) REVERT: F 288 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8472 (tp) REVERT: F 402 ARG cc_start: 0.8243 (ttp-170) cc_final: 0.7749 (ttt180) REVERT: F 404 ARG cc_start: 0.8296 (mmm-85) cc_final: 0.8013 (mmm-85) outliers start: 101 outliers final: 75 residues processed: 362 average time/residue: 0.1258 time to fit residues: 72.4001 Evaluate side-chains 353 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 273 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 200 GLN Chi-restraints excluded: chain C residue 236 PHE Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 34 HIS Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 368 ARG Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 35 LYS Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 74 MET Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 174 ASN Chi-restraints excluded: chain E residue 197 ASP Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 423 GLN Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 18 PHE Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 191 ARG Chi-restraints excluded: chain F residue 193 ARG Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 253 ASN Chi-restraints excluded: chain F residue 288 LEU Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 304 GLN Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 437 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 106 optimal weight: 5.9990 chunk 221 optimal weight: 9.9990 chunk 53 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 120 optimal weight: 6.9990 chunk 264 optimal weight: 3.9990 chunk 168 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 21 optimal weight: 8.9990 chunk 13 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 HIS ** B 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 GLN ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 ASN E 174 ASN E 278 GLN ** F 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.183075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.146914 restraints weight = 27169.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.149586 restraints weight = 20010.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.151491 restraints weight = 14327.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.151979 restraints weight = 10568.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.152348 restraints weight = 9500.832| |-----------------------------------------------------------------------------| r_work (final): 0.3965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.5101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 22330 Z= 0.217 Angle : 0.688 10.350 30283 Z= 0.363 Chirality : 0.048 0.189 3480 Planarity : 0.006 0.059 3960 Dihedral : 8.578 88.356 3244 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 5.61 % Allowed : 21.56 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % 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 aren not related in a simple way. whole: -1.09 (0.15), residues: 2823 helix: 0.34 (0.15), residues: 1104 sheet: -0.93 (0.25), residues: 398 loop : -1.57 (0.16), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 404 TYR 0.018 0.002 TYR A 461 PHE 0.031 0.002 PHE C 460 HIS 0.005 0.001 HIS A 255 Details of bonding type rmsd covalent geometry : bond 0.00527 (22330) covalent geometry : angle 0.68850 (30283) hydrogen bonds : bond 0.05398 ( 985) hydrogen bonds : angle 5.43045 ( 2841) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 282 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 GLN cc_start: 0.8714 (tm-30) cc_final: 0.8374 (tm-30) REVERT: A 245 MET cc_start: 0.5385 (ptp) cc_final: 0.4581 (tpt) REVERT: A 294 HIS cc_start: 0.7740 (OUTLIER) cc_final: 0.7180 (m-70) REVERT: A 444 PHE cc_start: 0.7130 (m-80) cc_final: 0.6805 (m-80) REVERT: B 176 THR cc_start: 0.8028 (m) cc_final: 0.7676 (p) REVERT: C 93 ARG cc_start: 0.7424 (ptt-90) cc_final: 0.7027 (ptt-90) REVERT: C 137 MET cc_start: 0.5563 (mmm) cc_final: 0.5013 (mmm) REVERT: C 198 ILE cc_start: 0.5810 (OUTLIER) cc_final: 0.5506 (mt) REVERT: C 361 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7587 (tp) REVERT: C 415 ARG cc_start: 0.8257 (mtt90) cc_final: 0.7914 (mpt-90) REVERT: D 64 MET cc_start: 0.6508 (mmm) cc_final: 0.6068 (mmp) REVERT: D 127 GLU cc_start: 0.6972 (OUTLIER) cc_final: 0.6102 (mt-10) REVERT: D 218 MET cc_start: 0.8324 (ptt) cc_final: 0.8032 (ptt) REVERT: D 235 MET cc_start: 0.7150 (mtt) cc_final: 0.6593 (mtp) REVERT: D 288 LEU cc_start: 0.7857 (tp) cc_final: 0.7421 (tp) REVERT: D 338 MET cc_start: 0.7344 (mtp) cc_final: 0.6895 (tpt) REVERT: D 368 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7290 (tpp-160) REVERT: E 174 ASN cc_start: 0.5648 (OUTLIER) cc_final: 0.5322 (m-40) REVERT: E 202 MET cc_start: 0.7583 (OUTLIER) cc_final: 0.7144 (mmt) REVERT: E 285 MET cc_start: 0.8315 (tpp) cc_final: 0.7963 (tpp) REVERT: E 337 GLU cc_start: 0.6624 (pt0) cc_final: 0.6298 (mt-10) REVERT: E 369 LYS cc_start: 0.7249 (pttm) cc_final: 0.6507 (tptm) REVERT: E 453 PHE cc_start: 0.7728 (m-80) cc_final: 0.7411 (m-80) REVERT: E 469 MET cc_start: 0.5815 (ttm) cc_final: 0.5548 (ttm) REVERT: F 49 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.6951 (tt0) REVERT: F 191 ARG cc_start: 0.4914 (OUTLIER) cc_final: 0.2768 (mmp80) REVERT: F 288 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8490 (tp) REVERT: F 404 ARG cc_start: 0.8311 (mmm-85) cc_final: 0.8027 (mmm-85) outliers start: 130 outliers final: 98 residues processed: 383 average time/residue: 0.1319 time to fit residues: 80.1903 Evaluate side-chains 379 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 271 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 294 HIS Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 260 TYR Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 200 GLN Chi-restraints excluded: chain C residue 236 PHE Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 34 HIS Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 368 ARG Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 419 GLN Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 74 MET Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 174 ASN Chi-restraints excluded: chain E residue 197 ASP Chi-restraints excluded: chain E residue 202 MET Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 278 GLN Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 423 GLN Chi-restraints excluded: chain F residue 18 PHE Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 191 ARG Chi-restraints excluded: chain F residue 193 ARG Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 262 SER Chi-restraints excluded: chain F residue 288 LEU Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 304 GLN Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 437 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 155 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 chunk 140 optimal weight: 5.9990 chunk 93 optimal weight: 6.9990 chunk 130 optimal weight: 20.0000 chunk 54 optimal weight: 0.9990 chunk 228 optimal weight: 10.0000 chunk 185 optimal weight: 9.9990 chunk 83 optimal weight: 8.9990 chunk 169 optimal weight: 4.9990 chunk 219 optimal weight: 0.6980 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN A 294 HIS A 474 HIS ** B 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 GLN ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 ASN E 174 ASN F 253 ASN ** F 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.190661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.154876 restraints weight = 26500.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.158403 restraints weight = 18153.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.159792 restraints weight = 12367.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.160474 restraints weight = 10149.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.160771 restraints weight = 9073.697| |-----------------------------------------------------------------------------| r_work (final): 0.4003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.5169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 22330 Z= 0.158 Angle : 0.636 9.825 30283 Z= 0.333 Chirality : 0.047 0.322 3480 Planarity : 0.005 0.062 3960 Dihedral : 8.362 87.751 3244 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 4.87 % Allowed : 22.77 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % 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 aren not related in a simple way. whole: -0.96 (0.15), residues: 2823 helix: 0.50 (0.15), residues: 1106 sheet: -0.99 (0.24), residues: 414 loop : -1.49 (0.16), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 278 TYR 0.016 0.002 TYR A 461 PHE 0.019 0.002 PHE F 255 HIS 0.011 0.001 HIS A 294 Details of bonding type rmsd covalent geometry : bond 0.00373 (22330) covalent geometry : angle 0.63650 (30283) hydrogen bonds : bond 0.04826 ( 985) hydrogen bonds : angle 5.27710 ( 2841) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 279 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 GLN cc_start: 0.8683 (tm-30) cc_final: 0.7910 (tm-30) REVERT: A 245 MET cc_start: 0.5295 (ptp) cc_final: 0.4409 (tpt) REVERT: A 444 PHE cc_start: 0.7108 (m-80) cc_final: 0.6766 (m-80) REVERT: B 176 THR cc_start: 0.7948 (m) cc_final: 0.7633 (p) REVERT: C 93 ARG cc_start: 0.7357 (ptt-90) cc_final: 0.7033 (ptt-90) REVERT: C 137 MET cc_start: 0.5612 (mmm) cc_final: 0.5045 (mmm) REVERT: C 361 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7534 (tp) REVERT: C 415 ARG cc_start: 0.8216 (mtt90) cc_final: 0.7892 (mpt-90) REVERT: D 64 MET cc_start: 0.6456 (mmm) cc_final: 0.6126 (mmp) REVERT: D 127 GLU cc_start: 0.6848 (OUTLIER) cc_final: 0.5987 (mt-10) REVERT: D 218 MET cc_start: 0.8279 (ptt) cc_final: 0.7990 (ptt) REVERT: D 235 MET cc_start: 0.7259 (mtt) cc_final: 0.6711 (mtp) REVERT: D 338 MET cc_start: 0.7423 (mtp) cc_final: 0.6902 (tpt) REVERT: D 368 ARG cc_start: 0.8004 (OUTLIER) cc_final: 0.7092 (tpp-160) REVERT: E 202 MET cc_start: 0.7595 (OUTLIER) cc_final: 0.7001 (mmt) REVERT: E 268 LEU cc_start: 0.6605 (OUTLIER) cc_final: 0.6235 (mm) REVERT: E 285 MET cc_start: 0.8267 (tpp) cc_final: 0.7844 (tpp) REVERT: E 337 GLU cc_start: 0.6576 (pt0) cc_final: 0.6228 (mt-10) REVERT: E 369 LYS cc_start: 0.7226 (pttm) cc_final: 0.6441 (tttp) REVERT: E 453 PHE cc_start: 0.7697 (m-80) cc_final: 0.7386 (m-80) REVERT: E 469 MET cc_start: 0.5833 (ttm) cc_final: 0.5575 (ttm) REVERT: F 48 LEU cc_start: 0.7261 (OUTLIER) cc_final: 0.6977 (mt) REVERT: F 49 GLU cc_start: 0.7119 (OUTLIER) cc_final: 0.6788 (tt0) REVERT: F 191 ARG cc_start: 0.4794 (OUTLIER) cc_final: 0.2744 (tpp-160) REVERT: F 288 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8516 (tp) REVERT: F 404 ARG cc_start: 0.8330 (mmm-85) cc_final: 0.8029 (mmm-85) outliers start: 113 outliers final: 90 residues processed: 364 average time/residue: 0.1189 time to fit residues: 69.1280 Evaluate side-chains 365 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 266 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 260 TYR Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 200 GLN Chi-restraints excluded: chain C residue 236 PHE Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 34 HIS Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 368 ARG Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 74 MET Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 197 ASP Chi-restraints excluded: chain E residue 202 MET Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 18 PHE Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 191 ARG Chi-restraints excluded: chain F residue 193 ARG Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 253 ASN Chi-restraints excluded: chain F residue 288 LEU Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 304 GLN Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 411 SER Chi-restraints excluded: chain F residue 437 PHE Chi-restraints excluded: chain F residue 456 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 197 optimal weight: 5.9990 chunk 170 optimal weight: 8.9990 chunk 112 optimal weight: 2.9990 chunk 160 optimal weight: 8.9990 chunk 222 optimal weight: 0.0870 chunk 102 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 150 optimal weight: 8.9990 chunk 229 optimal weight: 2.9990 overall best weight: 1.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 345 GLN D 365 GLN F 253 ASN ** F 304 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 = 0.4368 r_free = 0.4368 target = 0.192283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.154720 restraints weight = 26563.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.159706 restraints weight = 17073.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.161524 restraints weight = 9957.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.162534 restraints weight = 8382.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.162898 restraints weight = 7616.147| |-----------------------------------------------------------------------------| r_work (final): 0.4031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.5225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22330 Z= 0.134 Angle : 0.618 11.651 30283 Z= 0.321 Chirality : 0.046 0.320 3480 Planarity : 0.005 0.064 3960 Dihedral : 8.186 87.355 3244 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 4.27 % Allowed : 23.33 % Favored : 72.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % 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 aren not related in a simple way. whole: -0.84 (0.15), residues: 2823 helix: 0.59 (0.15), residues: 1112 sheet: -0.85 (0.25), residues: 408 loop : -1.45 (0.16), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 278 TYR 0.021 0.001 TYR B 461 PHE 0.029 0.002 PHE C 460 HIS 0.005 0.001 HIS E 173 Details of bonding type rmsd covalent geometry : bond 0.00308 (22330) covalent geometry : angle 0.61838 (30283) hydrogen bonds : bond 0.04504 ( 985) hydrogen bonds : angle 5.15541 ( 2841) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 271 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 GLN cc_start: 0.8668 (tm-30) cc_final: 0.7906 (tm-30) REVERT: A 245 MET cc_start: 0.5102 (ptp) cc_final: 0.4295 (tpt) REVERT: A 444 PHE cc_start: 0.7160 (m-80) cc_final: 0.6694 (m-80) REVERT: A 480 ASP cc_start: 0.7777 (t70) cc_final: 0.7064 (p0) REVERT: B 95 MET cc_start: 0.8324 (tpt) cc_final: 0.8012 (tpt) REVERT: B 176 THR cc_start: 0.7899 (m) cc_final: 0.7608 (p) REVERT: B 390 ARG cc_start: 0.6618 (OUTLIER) cc_final: 0.6188 (mpt180) REVERT: C 93 ARG cc_start: 0.7390 (ptt-90) cc_final: 0.7100 (ptt-90) REVERT: C 137 MET cc_start: 0.5784 (mmm) cc_final: 0.5274 (mmm) REVERT: C 415 ARG cc_start: 0.8215 (mtt90) cc_final: 0.7898 (mpt-90) REVERT: D 127 GLU cc_start: 0.6816 (OUTLIER) cc_final: 0.6028 (mt-10) REVERT: D 218 MET cc_start: 0.8256 (ptt) cc_final: 0.7959 (ptt) REVERT: D 235 MET cc_start: 0.7279 (mtt) cc_final: 0.6706 (mtp) REVERT: D 270 ARG cc_start: 0.7222 (OUTLIER) cc_final: 0.6581 (mtm-85) REVERT: D 338 MET cc_start: 0.7364 (mtp) cc_final: 0.6890 (tpt) REVERT: D 368 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.7018 (tpp-160) REVERT: E 202 MET cc_start: 0.7527 (OUTLIER) cc_final: 0.6976 (mmt) REVERT: E 268 LEU cc_start: 0.6558 (OUTLIER) cc_final: 0.6204 (mm) REVERT: E 337 GLU cc_start: 0.6516 (pt0) cc_final: 0.6148 (mt-10) REVERT: E 369 LYS cc_start: 0.7207 (pttm) cc_final: 0.6432 (tttp) REVERT: E 453 PHE cc_start: 0.7670 (m-80) cc_final: 0.7414 (m-80) REVERT: E 469 MET cc_start: 0.5793 (ttm) cc_final: 0.5541 (ttm) REVERT: F 48 LEU cc_start: 0.7263 (OUTLIER) cc_final: 0.6940 (mt) REVERT: F 49 GLU cc_start: 0.7067 (OUTLIER) cc_final: 0.6756 (tt0) REVERT: F 191 ARG cc_start: 0.4682 (OUTLIER) cc_final: 0.2661 (tpp-160) REVERT: F 255 PHE cc_start: 0.2054 (t80) cc_final: 0.1812 (t80) REVERT: F 288 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8523 (tp) REVERT: F 404 ARG cc_start: 0.8348 (mmm-85) cc_final: 0.8045 (mmm-85) outliers start: 99 outliers final: 79 residues processed: 347 average time/residue: 0.1286 time to fit residues: 70.7447 Evaluate side-chains 350 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 261 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 260 TYR Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 390 ARG Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 200 GLN Chi-restraints excluded: chain C residue 236 PHE Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 34 HIS Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 270 ARG Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 368 ARG Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 419 GLN Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 74 MET Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 197 ASP Chi-restraints excluded: chain E residue 202 MET Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 462 VAL Chi-restraints excluded: chain F residue 15 ASP Chi-restraints excluded: chain F residue 18 PHE Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 191 ARG Chi-restraints excluded: chain F residue 193 ARG Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 253 ASN Chi-restraints excluded: chain F residue 288 LEU Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 304 GLN Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 411 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 198 optimal weight: 0.9990 chunk 65 optimal weight: 10.0000 chunk 185 optimal weight: 4.9990 chunk 195 optimal weight: 0.9980 chunk 224 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 122 optimal weight: 10.0000 chunk 138 optimal weight: 10.0000 chunk 186 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 173 optimal weight: 10.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 466 GLN ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.189634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.152667 restraints weight = 26704.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.157025 restraints weight = 17547.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.158744 restraints weight = 11031.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.159153 restraints weight = 8885.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.159541 restraints weight = 8197.130| |-----------------------------------------------------------------------------| r_work (final): 0.3986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.5319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 22330 Z= 0.167 Angle : 0.650 12.766 30283 Z= 0.338 Chirality : 0.047 0.303 3480 Planarity : 0.005 0.061 3960 Dihedral : 8.189 86.824 3244 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 4.57 % Allowed : 23.37 % Favored : 72.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % 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 aren not related in a simple way. whole: -0.91 (0.15), residues: 2823 helix: 0.51 (0.15), residues: 1109 sheet: -0.88 (0.25), residues: 393 loop : -1.48 (0.16), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 278 TYR 0.028 0.002 TYR B 461 PHE 0.025 0.002 PHE F 255 HIS 0.007 0.001 HIS F 179 Details of bonding type rmsd covalent geometry : bond 0.00399 (22330) covalent geometry : angle 0.64983 (30283) hydrogen bonds : bond 0.04739 ( 985) hydrogen bonds : angle 5.22109 ( 2841) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 267 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 ILE cc_start: 0.7730 (OUTLIER) cc_final: 0.6997 (pt) REVERT: A 172 GLN cc_start: 0.8667 (tm-30) cc_final: 0.7893 (tm-30) REVERT: A 245 MET cc_start: 0.5193 (ptp) cc_final: 0.4319 (tpt) REVERT: A 444 PHE cc_start: 0.7269 (m-80) cc_final: 0.6699 (m-80) REVERT: A 480 ASP cc_start: 0.7796 (t70) cc_final: 0.7046 (p0) REVERT: B 176 THR cc_start: 0.7860 (m) cc_final: 0.7553 (p) REVERT: B 390 ARG cc_start: 0.6472 (OUTLIER) cc_final: 0.6038 (mpt180) REVERT: C 93 ARG cc_start: 0.7456 (ptt-90) cc_final: 0.7162 (ptt-90) REVERT: C 137 MET cc_start: 0.5772 (mmm) cc_final: 0.5233 (mmm) REVERT: C 415 ARG cc_start: 0.8175 (mtt90) cc_final: 0.7852 (mpt-90) REVERT: C 476 ARG cc_start: 0.7469 (mtt90) cc_final: 0.7213 (mmt90) REVERT: D 64 MET cc_start: 0.6429 (mmm) cc_final: 0.6076 (mmp) REVERT: D 127 GLU cc_start: 0.6762 (OUTLIER) cc_final: 0.5897 (mt-10) REVERT: D 235 MET cc_start: 0.7325 (mtt) cc_final: 0.6740 (mtp) REVERT: D 270 ARG cc_start: 0.7279 (OUTLIER) cc_final: 0.6628 (mtm-85) REVERT: D 338 MET cc_start: 0.7483 (mtp) cc_final: 0.6942 (tpt) REVERT: D 368 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.6968 (tpp-160) REVERT: E 202 MET cc_start: 0.7593 (OUTLIER) cc_final: 0.7002 (mmt) REVERT: E 268 LEU cc_start: 0.6657 (OUTLIER) cc_final: 0.6282 (mm) REVERT: E 337 GLU cc_start: 0.6537 (pt0) cc_final: 0.6157 (mt-10) REVERT: E 369 LYS cc_start: 0.7213 (pttm) cc_final: 0.6426 (tttp) REVERT: E 453 PHE cc_start: 0.7694 (m-80) cc_final: 0.7407 (m-80) REVERT: E 469 MET cc_start: 0.5779 (ttm) cc_final: 0.5535 (ttm) REVERT: F 48 LEU cc_start: 0.7270 (OUTLIER) cc_final: 0.6913 (mt) REVERT: F 49 GLU cc_start: 0.7043 (OUTLIER) cc_final: 0.6725 (tt0) REVERT: F 191 ARG cc_start: 0.4617 (OUTLIER) cc_final: 0.2437 (mmp80) REVERT: F 226 MET cc_start: 0.5308 (ttp) cc_final: 0.5089 (ttp) REVERT: F 255 PHE cc_start: 0.1829 (t80) cc_final: 0.1501 (t80) REVERT: F 288 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8487 (tp) REVERT: F 402 ARG cc_start: 0.8067 (ttm-80) cc_final: 0.7704 (ttt-90) REVERT: F 404 ARG cc_start: 0.8380 (mmm-85) cc_final: 0.8065 (mmm-85) outliers start: 106 outliers final: 82 residues processed: 347 average time/residue: 0.1288 time to fit residues: 70.7266 Evaluate side-chains 354 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 261 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 260 TYR Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 390 ARG Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 200 GLN Chi-restraints excluded: chain C residue 236 PHE Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 270 ARG Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 368 ARG Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 419 GLN Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 197 ASP Chi-restraints excluded: chain E residue 202 MET Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 447 HIS Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 462 VAL Chi-restraints excluded: chain F residue 15 ASP Chi-restraints excluded: chain F residue 18 PHE Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 191 ARG Chi-restraints excluded: chain F residue 193 ARG Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 288 LEU Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 304 GLN Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 411 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 55 optimal weight: 10.0000 chunk 169 optimal weight: 10.0000 chunk 132 optimal weight: 20.0000 chunk 88 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 249 optimal weight: 4.9990 chunk 221 optimal weight: 9.9990 chunk 166 optimal weight: 6.9990 chunk 113 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 470 HIS B 466 GLN B 474 HIS ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 ASN ** F 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.185474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.149540 restraints weight = 27089.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.151209 restraints weight = 19113.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.152915 restraints weight = 14534.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.154803 restraints weight = 11483.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.155201 restraints weight = 9862.300| |-----------------------------------------------------------------------------| r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.5569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 22330 Z= 0.240 Angle : 0.734 13.011 30283 Z= 0.386 Chirality : 0.050 0.281 3480 Planarity : 0.006 0.080 3960 Dihedral : 8.566 85.821 3243 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 5.26 % Allowed : 22.81 % Favored : 71.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % 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 aren not related in a simple way. whole: -1.27 (0.15), residues: 2823 helix: 0.25 (0.15), residues: 1102 sheet: -1.14 (0.24), residues: 428 loop : -1.68 (0.16), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 127 TYR 0.029 0.002 TYR B 461 PHE 0.041 0.002 PHE C 460 HIS 0.009 0.001 HIS E 173 Details of bonding type rmsd covalent geometry : bond 0.00586 (22330) covalent geometry : angle 0.73368 (30283) hydrogen bonds : bond 0.05635 ( 985) hydrogen bonds : angle 5.49394 ( 2841) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2989.30 seconds wall clock time: 52 minutes 26.27 seconds (3146.27 seconds total)