Starting phenix.real_space_refine on Wed May 21 18:30:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8spw_40688/05_2025/8spw_40688.cif Found real_map, /net/cci-nas-00/data/ceres_data/8spw_40688/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8spw_40688/05_2025/8spw_40688.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8spw_40688/05_2025/8spw_40688.map" model { file = "/net/cci-nas-00/data/ceres_data/8spw_40688/05_2025/8spw_40688.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8spw_40688/05_2025/8spw_40688.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 13.36, per 1000 atoms: 0.61 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: 5.91 Conformation dependent library (CDL) restraints added in 3.0 seconds 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: 2.83 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: 7.44 Time building geometry restraints manager: 6.85 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 499 or resid 600 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: 1.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.810 Check model and map are aligned: 0.170 Set scattering table: 0.200 Process input model: 50.280 Find NCS groups from input model: 1.390 Set up NCS constraints: 0.090 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: 0.020 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.190 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.005 0.001 HIS F 200 PHE 0.026 0.002 PHE C 494 TYR 0.015 0.002 TYR F 238 ARG 0.003 0.000 ARG F 240 Details of bonding type rmsd hydrogen bonds : bond 0.15837 ( 985) hydrogen bonds : angle 7.00569 ( 2841) covalent geometry : bond 0.00341 (22330) covalent geometry : angle 0.61061 (30283) *********************** 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 : 2.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 444 PHE cc_start: 0.6239 (m-80) cc_final: 0.6007 (m-80) REVERT: A 471 LEU cc_start: 0.7510 (mt) cc_final: 0.7198 (mp) REVERT: B 191 MET cc_start: 0.6369 (mmt) cc_final: 0.5695 (mmt) REVERT: B 236 PHE cc_start: 0.6486 (OUTLIER) cc_final: 0.6244 (p90) REVERT: B 318 PHE cc_start: 0.4423 (m-80) cc_final: 0.4030 (m-80) REVERT: C 95 MET cc_start: 0.5219 (tpp) cc_final: 0.4984 (mmm) REVERT: C 361 LEU cc_start: 0.7258 (tp) cc_final: 0.6991 (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: 0.7959 (tpp) REVERT: F 49 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7150 (pt0) REVERT: F 256 ARG cc_start: 0.4814 (OUTLIER) cc_final: 0.4292 (mtm-85) REVERT: F 264 VAL cc_start: 0.2961 (t) cc_final: 0.2732 (t) outliers start: 49 outliers final: 12 residues processed: 610 average time/residue: 0.3801 time to fit residues: 340.9293 Evaluate side-chains 340 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 325 time to evaluate : 2.257 ------------------------------------------------------------------------------- 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 238 optimal weight: 0.6980 chunk 213 optimal weight: 0.9990 chunk 118 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 144 optimal weight: 8.9990 chunk 114 optimal weight: 0.0050 chunk 221 optimal weight: 9.9990 chunk 85 optimal weight: 30.0000 chunk 134 optimal weight: 10.0000 chunk 164 optimal weight: 7.9990 chunk 256 optimal weight: 1.9990 overall best weight: 1.3400 ------------------------------------------------------------------------------- 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 185 ASN A 186 GLN A 345 GLN A 474 HIS ** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 143 HIS C 474 HIS D 330 ASN E 119 HIS E 169 GLN E 289 GLN E 304 GLN F 53 HIS F 253 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.196267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.162506 restraints weight = 27005.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.165660 restraints weight = 17068.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.167679 restraints weight = 12767.019| |-----------------------------------------------------------------------------| r_work (final): 0.4133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6764 moved from start: 0.2429 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= 0.143 Angle : 0.615 7.522 30283 Z= 0.327 Chirality : 0.046 0.287 3480 Planarity : 0.005 0.048 3960 Dihedral : 9.014 119.528 3254 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.02 % Allowed : 14.32 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.15), residues: 2823 helix: 0.94 (0.15), residues: 1122 sheet: 0.10 (0.25), residues: 412 loop : -0.75 (0.17), residues: 1289 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 474 PHE 0.037 0.002 PHE E 414 TYR 0.020 0.001 TYR C 195 ARG 0.008 0.001 ARG D 5 Details of bonding type rmsd hydrogen bonds : bond 0.05164 ( 985) hydrogen bonds : angle 5.53008 ( 2841) covalent geometry : bond 0.00311 (22330) covalent geometry : angle 0.61454 (30283) *********************** 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 426 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 356 time to evaluate : 2.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 MET cc_start: 0.6488 (OUTLIER) cc_final: 0.6071 (ttm) REVERT: A 444 PHE cc_start: 0.6960 (m-80) cc_final: 0.6672 (m-80) REVERT: B 236 PHE cc_start: 0.6739 (OUTLIER) cc_final: 0.6513 (p90) REVERT: B 406 THR cc_start: 0.8596 (OUTLIER) cc_final: 0.8340 (t) REVERT: B 438 TYR cc_start: 0.8129 (t80) cc_final: 0.7738 (t80) REVERT: D 235 MET cc_start: 0.7096 (mtt) cc_final: 0.6576 (mtp) REVERT: D 271 MET cc_start: 0.7332 (mtt) cc_final: 0.6876 (mtt) REVERT: D 338 MET cc_start: 0.7452 (OUTLIER) cc_final: 0.6914 (tpt) REVERT: E 126 GLU cc_start: 0.6264 (pm20) cc_final: 0.5941 (pm20) REVERT: E 202 MET cc_start: 0.5639 (mmt) cc_final: 0.3658 (mtp) REVERT: F 235 MET cc_start: 0.6269 (mmt) cc_final: 0.6002 (mmt) REVERT: F 253 ASN cc_start: 0.4857 (OUTLIER) cc_final: 0.4476 (p0) REVERT: F 256 ARG cc_start: 0.4543 (OUTLIER) cc_final: 0.4185 (mtm-85) REVERT: F 264 VAL cc_start: 0.4178 (t) cc_final: 0.3545 (t) REVERT: F 404 ARG cc_start: 0.8368 (mmm-85) cc_final: 0.7713 (tpp80) outliers start: 70 outliers final: 38 residues processed: 411 average time/residue: 0.3299 time to fit residues: 209.1671 Evaluate side-chains 343 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 299 time to evaluate : 2.584 ------------------------------------------------------------------------------- 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 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 375 MET Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 166 LEU 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 111 LEU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 188 ASP 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 435 LEU Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 338 MET Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain D residue 419 GLN Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 411 SER Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 162 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 Chi-restraints excluded: chain F residue 256 ARG Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 397 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 268 optimal weight: 0.5980 chunk 112 optimal weight: 0.0370 chunk 267 optimal weight: 0.6980 chunk 99 optimal weight: 7.9990 chunk 47 optimal weight: 0.1980 chunk 257 optimal weight: 0.9990 chunk 214 optimal weight: 10.0000 chunk 255 optimal weight: 8.9990 chunk 223 optimal weight: 0.8980 chunk 232 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN A 185 ASN A 358 ASN A 474 HIS ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 345 GLN C 143 HIS C 333 ASN D 365 GLN E 179 HIS E 196 ASN E 259 GLN F 324 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.207058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.169445 restraints weight = 25551.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.173702 restraints weight = 16513.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.176221 restraints weight = 10681.034| |-----------------------------------------------------------------------------| r_work (final): 0.4166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6689 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 22330 Z= 0.113 Angle : 0.548 8.918 30283 Z= 0.289 Chirality : 0.044 0.236 3480 Planarity : 0.004 0.054 3960 Dihedral : 8.425 101.431 3246 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.36 % Allowed : 15.65 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.16), residues: 2823 helix: 1.03 (0.16), residues: 1131 sheet: 0.26 (0.25), residues: 417 loop : -0.69 (0.17), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 474 PHE 0.043 0.002 PHE E 414 TYR 0.011 0.001 TYR F 445 ARG 0.004 0.000 ARG C 415 Details of bonding type rmsd hydrogen bonds : bond 0.04293 ( 985) hydrogen bonds : angle 5.09155 ( 2841) covalent geometry : bond 0.00232 (22330) covalent geometry : angle 0.54795 (30283) *********************** 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 412 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 334 time to evaluate : 2.414 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: 0.8543 (tm-30) cc_final: 0.8311 (tm-30) REVERT: A 245 MET cc_start: 0.5705 (ptp) cc_final: 0.5084 (mmm) REVERT: A 320 GLU cc_start: 0.4205 (tt0) cc_final: 0.3913 (tt0) REVERT: B 156 LEU cc_start: 0.7650 (mt) cc_final: 0.7422 (mp) REVERT: B 236 PHE cc_start: 0.6640 (OUTLIER) cc_final: 0.6385 (p90) REVERT: B 317 PRO cc_start: 0.7766 (Cg_endo) cc_final: 0.7528 (Cg_exo) REVERT: C 93 ARG cc_start: 0.7159 (ptt-90) cc_final: 0.6854 (ptt-90) REVERT: D 198 LEU cc_start: 0.8588 (tp) cc_final: 0.8380 (tp) REVERT: D 235 MET cc_start: 0.7059 (mtt) cc_final: 0.6513 (mtp) REVERT: D 271 MET cc_start: 0.7430 (mtt) cc_final: 0.6993 (mtt) REVERT: D 338 MET cc_start: 0.7506 (OUTLIER) cc_final: 0.7051 (tpt) REVERT: E 126 GLU cc_start: 0.6296 (pm20) cc_final: 0.6075 (pm20) REVERT: E 202 MET cc_start: 0.5319 (mmt) cc_final: 0.4888 (ttm) REVERT: E 290 GLU cc_start: 0.6317 (OUTLIER) cc_final: 0.5823 (mm-30) REVERT: E 369 LYS cc_start: 0.7430 (ptpp) cc_final: 0.6757 (tptm) REVERT: F 235 MET cc_start: 0.6233 (mmt) cc_final: 0.5941 (mmt) REVERT: F 253 ASN cc_start: 0.5466 (OUTLIER) cc_final: 0.5058 (p0) REVERT: F 256 ARG cc_start: 0.4269 (OUTLIER) cc_final: 0.3181 (mmp80) outliers start: 78 outliers final: 32 residues processed: 398 average time/residue: 0.3116 time to fit residues: 196.1966 Evaluate side-chains 327 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 290 time to evaluate : 2.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL 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 336 SER Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 366 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 290 ILE Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain D residue 9 VAL 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 247 VAL Chi-restraints excluded: chain D residue 338 MET 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 85 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 423 GLN Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 130 THR 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 256 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 125 optimal weight: 0.6980 chunk 183 optimal weight: 20.0000 chunk 119 optimal weight: 1.9990 chunk 106 optimal weight: 8.9990 chunk 257 optimal weight: 4.9990 chunk 203 optimal weight: 3.9990 chunk 145 optimal weight: 7.9990 chunk 10 optimal weight: 10.0000 chunk 109 optimal weight: 5.9990 chunk 55 optimal weight: 0.4980 chunk 115 optimal weight: 0.8980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 HIS ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 345 GLN ** D 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4461 r_free = 0.4461 target = 0.202706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.165707 restraints weight = 26273.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.170251 restraints weight = 16214.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.172709 restraints weight = 10248.737| |-----------------------------------------------------------------------------| r_work (final): 0.4131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6772 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 22330 Z= 0.130 Angle : 0.563 9.244 30283 Z= 0.294 Chirality : 0.045 0.294 3480 Planarity : 0.005 0.058 3960 Dihedral : 7.955 84.569 3240 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.05 % Allowed : 16.65 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.16), residues: 2823 helix: 1.01 (0.16), residues: 1118 sheet: 0.13 (0.24), residues: 434 loop : -0.73 (0.17), residues: 1271 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS B 474 PHE 0.028 0.002 PHE A 494 TYR 0.025 0.001 TYR B 438 ARG 0.019 0.000 ARG C 127 Details of bonding type rmsd hydrogen bonds : bond 0.04305 ( 985) hydrogen bonds : angle 4.94900 ( 2841) covalent geometry : bond 0.00293 (22330) covalent geometry : angle 0.56266 (30283) *********************** 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 411 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 317 time to evaluate : 2.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 MET cc_start: 0.5831 (ptp) cc_final: 0.5085 (mmm) REVERT: A 471 LEU cc_start: 0.7588 (mt) cc_final: 0.6848 (mp) REVERT: B 32 ILE cc_start: 0.8056 (OUTLIER) cc_final: 0.7846 (mm) REVERT: B 236 PHE cc_start: 0.6723 (OUTLIER) cc_final: 0.6520 (p90) REVERT: B 250 MET cc_start: 0.5011 (tpt) cc_final: 0.4732 (tpt) REVERT: D 64 MET cc_start: 0.6349 (mmm) cc_final: 0.5935 (mmp) REVERT: D 271 MET cc_start: 0.7400 (mtt) cc_final: 0.7040 (mtt) REVERT: D 368 ARG cc_start: 0.7371 (OUTLIER) cc_final: 0.6527 (tpp-160) REVERT: E 64 MET cc_start: 0.5146 (mmp) cc_final: 0.4778 (mmm) REVERT: E 202 MET cc_start: 0.5534 (mmt) cc_final: 0.3262 (mtp) REVERT: E 259 GLN cc_start: 0.7304 (OUTLIER) cc_final: 0.6176 (mp-120) REVERT: E 268 LEU cc_start: 0.6629 (OUTLIER) cc_final: 0.6234 (mm) REVERT: E 351 SER cc_start: 0.8325 (t) cc_final: 0.8062 (t) REVERT: E 469 MET cc_start: 0.5695 (ttm) cc_final: 0.5412 (ttm) REVERT: F 105 LEU cc_start: 0.6348 (OUTLIER) cc_final: 0.6127 (mt) REVERT: F 154 ILE cc_start: 0.7786 (OUTLIER) cc_final: 0.7391 (mt) REVERT: F 235 MET cc_start: 0.6272 (mmt) cc_final: 0.6008 (mmt) REVERT: F 404 ARG cc_start: 0.8275 (mmm-85) cc_final: 0.7565 (tpp80) outliers start: 94 outliers final: 55 residues processed: 391 average time/residue: 0.3044 time to fit residues: 188.5749 Evaluate side-chains 348 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 286 time to evaluate : 2.434 ------------------------------------------------------------------------------- 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 182 THR 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 406 THR Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain B residue 32 ILE 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 366 VAL Chi-restraints excluded: chain B residue 436 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 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 67 THR Chi-restraints excluded: chain D residue 74 MET 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 247 VAL Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 368 ARG Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain D residue 419 GLN 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 85 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 197 ASP Chi-restraints excluded: chain E residue 231 THR 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 423 GLN Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 154 ILE 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 406 ILE Chi-restraints excluded: chain F residue 437 PHE Chi-restraints excluded: chain F residue 456 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 72 optimal weight: 10.0000 chunk 154 optimal weight: 10.0000 chunk 226 optimal weight: 0.0050 chunk 219 optimal weight: 9.9990 chunk 187 optimal weight: 8.9990 chunk 19 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 173 optimal weight: 8.9990 chunk 5 optimal weight: 0.0170 chunk 276 optimal weight: 3.9990 chunk 27 optimal weight: 9.9990 overall best weight: 2.0036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN A 474 HIS B 185 ASN ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 HIS ** D 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 330 ASN ** E 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 173 HIS ** E 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 169 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 = 0.4441 r_free = 0.4441 target = 0.200514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.163462 restraints weight = 26122.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.168678 restraints weight = 16425.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.170649 restraints weight = 10282.932| |-----------------------------------------------------------------------------| r_work (final): 0.4106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6825 moved from start: 0.3715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22330 Z= 0.137 Angle : 0.570 9.955 30283 Z= 0.297 Chirality : 0.045 0.296 3480 Planarity : 0.005 0.059 3960 Dihedral : 7.708 83.155 3236 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 4.14 % Allowed : 17.59 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.16), residues: 2823 helix: 0.99 (0.16), residues: 1117 sheet: 0.02 (0.25), residues: 428 loop : -0.83 (0.17), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 173 PHE 0.036 0.002 PHE C 460 TYR 0.020 0.001 TYR B 438 ARG 0.006 0.000 ARG A 278 Details of bonding type rmsd hydrogen bonds : bond 0.04309 ( 985) hydrogen bonds : angle 4.89847 ( 2841) covalent geometry : bond 0.00315 (22330) covalent geometry : angle 0.56953 (30283) *********************** 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 408 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 312 time to evaluate : 2.332 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 172 GLN cc_start: 0.8680 (tm-30) cc_final: 0.7962 (tm-30) REVERT: A 245 MET cc_start: 0.5465 (ptp) cc_final: 0.4831 (mmm) REVERT: B 32 ILE cc_start: 0.8011 (OUTLIER) cc_final: 0.7792 (mm) REVERT: B 236 PHE cc_start: 0.6783 (OUTLIER) cc_final: 0.6577 (p90) REVERT: C 93 ARG cc_start: 0.7292 (ptt-90) cc_final: 0.6844 (ptt-90) REVERT: C 333 ASN cc_start: 0.7231 (OUTLIER) cc_final: 0.6888 (t0) REVERT: C 415 ARG cc_start: 0.8081 (mtt90) cc_final: 0.7733 (mpt-90) REVERT: D 235 MET cc_start: 0.7074 (mtt) cc_final: 0.6563 (mtp) REVERT: D 271 MET cc_start: 0.7416 (mtt) cc_final: 0.7070 (mtt) REVERT: D 368 ARG cc_start: 0.7514 (OUTLIER) cc_final: 0.6569 (tpp-160) REVERT: E 64 MET cc_start: 0.5366 (mmp) cc_final: 0.5031 (mmm) REVERT: E 202 MET cc_start: 0.5568 (mmt) cc_final: 0.3783 (mtp) REVERT: E 259 GLN cc_start: 0.7370 (OUTLIER) cc_final: 0.6218 (mp-120) REVERT: E 268 LEU cc_start: 0.6619 (OUTLIER) cc_final: 0.6220 (mm) REVERT: E 351 SER cc_start: 0.8402 (t) cc_final: 0.8073 (t) REVERT: E 369 LYS cc_start: 0.7257 (pttm) cc_final: 0.6423 (tttp) REVERT: E 469 MET cc_start: 0.5676 (ttm) cc_final: 0.5410 (ttm) REVERT: F 105 LEU cc_start: 0.6366 (OUTLIER) cc_final: 0.6148 (mt) REVERT: F 191 ARG cc_start: 0.4622 (OUTLIER) cc_final: 0.2012 (mmm160) REVERT: F 235 MET cc_start: 0.6389 (mmt) cc_final: 0.6120 (mmt) REVERT: F 285 MET cc_start: 0.7493 (OUTLIER) cc_final: 0.6748 (ttm) REVERT: F 404 ARG cc_start: 0.8274 (mmm-85) cc_final: 0.7596 (tpp80) outliers start: 96 outliers final: 62 residues processed: 382 average time/residue: 0.3255 time to fit residues: 196.1515 Evaluate side-chains 355 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 284 time to evaluate : 2.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 59 VAL 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 182 THR Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 62 MET 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 366 VAL 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 276 LEU Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 333 ASN 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 52 LEU Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 74 MET 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 247 VAL Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 322 PHE Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 368 ARG Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 419 GLN 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 85 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 197 ASP 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 456 VAL Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 105 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 247 VAL Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 251 ILE Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 285 MET Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 406 ILE 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 57 optimal weight: 9.9990 chunk 42 optimal weight: 7.9990 chunk 172 optimal weight: 0.4980 chunk 178 optimal weight: 1.9990 chunk 243 optimal weight: 2.9990 chunk 218 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 127 optimal weight: 10.0000 chunk 16 optimal weight: 0.9980 chunk 99 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 294 HIS C 474 HIS ** D 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 330 ASN ** E 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 407 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.200591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.162812 restraints weight = 25983.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.166630 restraints weight = 15602.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.169542 restraints weight = 11231.091| |-----------------------------------------------------------------------------| r_work (final): 0.4090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6842 moved from start: 0.4032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22330 Z= 0.122 Angle : 0.557 10.736 30283 Z= 0.288 Chirality : 0.044 0.237 3480 Planarity : 0.005 0.061 3960 Dihedral : 7.478 83.078 3236 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 4.10 % Allowed : 18.93 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.16), residues: 2823 helix: 1.06 (0.16), residues: 1114 sheet: -0.02 (0.25), residues: 440 loop : -0.82 (0.17), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 324 PHE 0.033 0.002 PHE A 494 TYR 0.018 0.001 TYR A 461 ARG 0.011 0.000 ARG C 127 Details of bonding type rmsd hydrogen bonds : bond 0.04020 ( 985) hydrogen bonds : angle 4.81017 ( 2841) covalent geometry : bond 0.00277 (22330) covalent geometry : angle 0.55717 (30283) *********************** 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 387 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 292 time to evaluate : 2.429 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: 0.8596 (tm-30) cc_final: 0.7908 (tm-30) REVERT: A 184 ILE cc_start: 0.6629 (OUTLIER) cc_final: 0.6328 (mp) REVERT: A 245 MET cc_start: 0.5419 (ptp) cc_final: 0.4829 (mmm) REVERT: A 418 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7383 (tm-30) REVERT: B 32 ILE cc_start: 0.8039 (OUTLIER) cc_final: 0.7792 (mm) REVERT: B 236 PHE cc_start: 0.6820 (OUTLIER) cc_final: 0.6538 (p90) REVERT: C 93 ARG cc_start: 0.7260 (ptt-90) cc_final: 0.6929 (ptt-90) REVERT: C 333 ASN cc_start: 0.7231 (OUTLIER) cc_final: 0.6857 (t0) REVERT: C 415 ARG cc_start: 0.8124 (mtt90) cc_final: 0.7788 (mpt-90) REVERT: D 235 MET cc_start: 0.7136 (mtt) cc_final: 0.6640 (mtp) REVERT: D 271 MET cc_start: 0.7404 (mtt) cc_final: 0.7098 (mtt) REVERT: D 368 ARG cc_start: 0.7428 (OUTLIER) cc_final: 0.6461 (tpp-160) REVERT: E 202 MET cc_start: 0.5892 (mmt) cc_final: 0.3948 (mtp) REVERT: E 259 GLN cc_start: 0.7342 (OUTLIER) cc_final: 0.6177 (mp-120) REVERT: E 268 LEU cc_start: 0.6681 (OUTLIER) cc_final: 0.6319 (mm) REVERT: E 351 SER cc_start: 0.8565 (t) cc_final: 0.8199 (t) REVERT: E 369 LYS cc_start: 0.7476 (pttm) cc_final: 0.7241 (pttm) REVERT: E 469 MET cc_start: 0.5405 (ttm) cc_final: 0.5158 (ttm) REVERT: F 105 LEU cc_start: 0.6202 (OUTLIER) cc_final: 0.5984 (mt) REVERT: F 154 ILE cc_start: 0.7694 (OUTLIER) cc_final: 0.7350 (mt) REVERT: F 191 ARG cc_start: 0.4609 (OUTLIER) cc_final: 0.2182 (mmm160) REVERT: F 225 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.7787 (ttp-170) REVERT: F 235 MET cc_start: 0.6442 (mmt) cc_final: 0.6197 (mmt) REVERT: F 256 ARG cc_start: 0.4180 (OUTLIER) cc_final: 0.2887 (mmp80) REVERT: F 285 MET cc_start: 0.7406 (OUTLIER) cc_final: 0.6608 (ttm) REVERT: F 404 ARG cc_start: 0.8419 (mmm-85) cc_final: 0.7497 (tpp-160) outliers start: 95 outliers final: 63 residues processed: 373 average time/residue: 0.3087 time to fit residues: 182.8304 Evaluate side-chains 349 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 272 time to evaluate : 2.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 59 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 168 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 260 TYR Chi-restraints excluded: chain B residue 366 VAL 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 294 HIS Chi-restraints excluded: chain C residue 333 ASN Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 475 ILE Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 46 LEU 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 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 293 THR Chi-restraints excluded: chain D residue 322 PHE Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 368 ARG Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain D residue 419 GLN Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 42 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 132 VAL Chi-restraints excluded: chain E residue 197 ASP Chi-restraints excluded: chain E residue 231 THR 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 462 VAL Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain F residue 191 ARG Chi-restraints excluded: chain F residue 225 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 251 ILE Chi-restraints excluded: chain F residue 256 ARG Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 285 MET Chi-restraints excluded: chain F residue 406 ILE Chi-restraints excluded: chain F residue 437 PHE Chi-restraints excluded: chain F residue 456 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 170 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 174 optimal weight: 4.9990 chunk 279 optimal weight: 9.9990 chunk 241 optimal weight: 0.0970 chunk 208 optimal weight: 0.9990 chunk 193 optimal weight: 9.9990 chunk 104 optimal weight: 2.9990 chunk 75 optimal weight: 9.9990 chunk 183 optimal weight: 0.0770 chunk 249 optimal weight: 7.9990 overall best weight: 1.0140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 HIS A 474 HIS ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 330 ASN E 196 ASN E 200 HIS ** 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 = 0.4453 r_free = 0.4453 target = 0.201834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.164474 restraints weight = 25937.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.167650 restraints weight = 17065.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.170401 restraints weight = 11447.742| |-----------------------------------------------------------------------------| r_work (final): 0.4102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6826 moved from start: 0.4172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 22330 Z= 0.111 Angle : 0.557 12.175 30283 Z= 0.283 Chirality : 0.044 0.272 3480 Planarity : 0.004 0.061 3960 Dihedral : 7.343 82.706 3236 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.05 % Allowed : 19.53 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.16), residues: 2823 helix: 1.16 (0.16), residues: 1108 sheet: 0.04 (0.25), residues: 440 loop : -0.78 (0.17), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.030 0.001 HIS C 294 PHE 0.050 0.001 PHE A 494 TYR 0.016 0.001 TYR A 461 ARG 0.006 0.000 ARG A 278 Details of bonding type rmsd hydrogen bonds : bond 0.03826 ( 985) hydrogen bonds : angle 4.76660 ( 2841) covalent geometry : bond 0.00245 (22330) covalent geometry : angle 0.55659 (30283) *********************** 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 382 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 288 time to evaluate : 2.316 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: 0.8540 (tm-30) cc_final: 0.7840 (tm-30) REVERT: A 184 ILE cc_start: 0.6678 (OUTLIER) cc_final: 0.6403 (mp) REVERT: A 245 MET cc_start: 0.5280 (ptp) cc_final: 0.4754 (mmm) REVERT: A 418 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7449 (tm-30) REVERT: B 32 ILE cc_start: 0.8038 (OUTLIER) cc_final: 0.7780 (mm) REVERT: B 236 PHE cc_start: 0.6806 (OUTLIER) cc_final: 0.6553 (p90) REVERT: C 93 ARG cc_start: 0.7295 (ptt-90) cc_final: 0.6974 (ptt-90) REVERT: C 325 ASP cc_start: 0.6506 (p0) cc_final: 0.6277 (p0) REVERT: C 333 ASN cc_start: 0.7258 (OUTLIER) cc_final: 0.6880 (t0) REVERT: C 415 ARG cc_start: 0.8096 (mtt90) cc_final: 0.7779 (mpt-90) REVERT: D 64 MET cc_start: 0.6409 (OUTLIER) cc_final: 0.6192 (mmt) REVERT: D 235 MET cc_start: 0.7064 (mtt) cc_final: 0.6582 (mtp) REVERT: D 338 MET cc_start: 0.7247 (mtp) cc_final: 0.6890 (tpt) REVERT: E 3 ARG cc_start: 0.7440 (mmt90) cc_final: 0.7181 (mmt180) REVERT: E 64 MET cc_start: 0.5167 (mmp) cc_final: 0.4638 (mmm) REVERT: E 202 MET cc_start: 0.5865 (mmt) cc_final: 0.4107 (mtp) REVERT: E 268 LEU cc_start: 0.6644 (OUTLIER) cc_final: 0.6290 (mm) REVERT: E 290 GLU cc_start: 0.6557 (OUTLIER) cc_final: 0.5914 (mm-30) REVERT: E 351 SER cc_start: 0.8536 (t) cc_final: 0.8174 (t) REVERT: E 369 LYS cc_start: 0.7448 (pttm) cc_final: 0.7197 (pttm) REVERT: E 469 MET cc_start: 0.5606 (ttm) cc_final: 0.5348 (ttm) REVERT: F 154 ILE cc_start: 0.7763 (OUTLIER) cc_final: 0.7375 (mt) REVERT: F 191 ARG cc_start: 0.4525 (OUTLIER) cc_final: 0.2157 (mmm160) REVERT: F 225 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7742 (ttp-170) REVERT: F 235 MET cc_start: 0.6424 (mmt) cc_final: 0.6170 (mmt) REVERT: F 256 ARG cc_start: 0.4088 (OUTLIER) cc_final: 0.2862 (mmp80) REVERT: F 404 ARG cc_start: 0.8342 (mmm-85) cc_final: 0.7525 (tpp-160) outliers start: 94 outliers final: 63 residues processed: 368 average time/residue: 0.3147 time to fit residues: 184.6874 Evaluate side-chains 344 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 269 time to evaluate : 2.343 ------------------------------------------------------------------------------- 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 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 198 ILE Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 260 TYR Chi-restraints excluded: chain B residue 366 VAL 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 276 LEU Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 333 ASN 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 52 LEU Chi-restraints excluded: chain D residue 64 MET 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 247 VAL Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 421 THR 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 85 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 197 ASP 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 392 LEU Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 462 VAL Chi-restraints excluded: chain F residue 58 THR 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 154 ILE Chi-restraints excluded: chain F residue 191 ARG Chi-restraints excluded: chain F residue 225 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 251 ILE Chi-restraints excluded: chain F residue 256 ARG Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain F residue 406 ILE Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 437 PHE Chi-restraints excluded: chain F residue 456 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 69 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 chunk 90 optimal weight: 20.0000 chunk 225 optimal weight: 4.9990 chunk 277 optimal weight: 0.0870 chunk 192 optimal weight: 10.0000 chunk 215 optimal weight: 0.6980 chunk 243 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 122 optimal weight: 9.9990 overall best weight: 2.7564 ------------------------------------------------------------------------------- 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 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.195982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.157662 restraints weight = 26282.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.161468 restraints weight = 16678.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.164262 restraints weight = 10987.524| |-----------------------------------------------------------------------------| r_work (final): 0.4038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 moved from start: 0.4482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 22330 Z= 0.164 Angle : 0.622 12.242 30283 Z= 0.322 Chirality : 0.046 0.167 3480 Planarity : 0.005 0.057 3960 Dihedral : 7.572 85.035 3236 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 4.18 % Allowed : 19.40 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.16), residues: 2823 helix: 0.91 (0.15), residues: 1111 sheet: -0.21 (0.24), residues: 445 loop : -0.95 (0.17), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 179 PHE 0.023 0.002 PHE A 494 TYR 0.026 0.002 TYR D 148 ARG 0.010 0.001 ARG A 278 Details of bonding type rmsd hydrogen bonds : bond 0.04638 ( 985) hydrogen bonds : angle 4.97347 ( 2841) covalent geometry : bond 0.00389 (22330) covalent geometry : angle 0.62200 (30283) *********************** 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 403 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 306 time to evaluate : 2.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 ARG cc_start: 0.7264 (ptt180) cc_final: 0.7018 (ptm160) REVERT: A 172 GLN cc_start: 0.8594 (tm-30) cc_final: 0.7853 (tm-30) REVERT: A 184 ILE cc_start: 0.6553 (OUTLIER) cc_final: 0.6276 (mp) REVERT: A 245 MET cc_start: 0.5248 (ptp) cc_final: 0.4640 (mmm) REVERT: A 418 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7387 (tm-30) REVERT: B 32 ILE cc_start: 0.7931 (OUTLIER) cc_final: 0.7550 (mm) REVERT: B 36 ASP cc_start: 0.7597 (p0) cc_final: 0.7334 (p0) REVERT: C 415 ARG cc_start: 0.8165 (mtt90) cc_final: 0.7825 (mpt-90) REVERT: D 235 MET cc_start: 0.7091 (mtt) cc_final: 0.6546 (mtp) REVERT: D 271 MET cc_start: 0.7580 (mtt) cc_final: 0.7342 (mtt) REVERT: D 338 MET cc_start: 0.7489 (mtp) cc_final: 0.7019 (tpt) REVERT: E 64 MET cc_start: 0.5409 (mmp) cc_final: 0.4696 (mmm) REVERT: E 201 GLU cc_start: 0.6985 (tm-30) cc_final: 0.6770 (tm-30) REVERT: E 202 MET cc_start: 0.6427 (mmt) cc_final: 0.4239 (mtp) REVERT: E 268 LEU cc_start: 0.6632 (OUTLIER) cc_final: 0.6154 (mm) REVERT: E 337 GLU cc_start: 0.6494 (pt0) cc_final: 0.6104 (mt-10) REVERT: E 369 LYS cc_start: 0.7507 (pttm) cc_final: 0.7208 (pttm) REVERT: E 469 MET cc_start: 0.5587 (ttm) cc_final: 0.5329 (ttm) REVERT: F 105 LEU cc_start: 0.6274 (OUTLIER) cc_final: 0.6008 (mt) REVERT: F 154 ILE cc_start: 0.7869 (OUTLIER) cc_final: 0.7490 (mt) REVERT: F 191 ARG cc_start: 0.4747 (OUTLIER) cc_final: 0.2255 (mmm160) REVERT: F 235 MET cc_start: 0.6518 (mmt) cc_final: 0.6208 (mmt) REVERT: F 285 MET cc_start: 0.7413 (OUTLIER) cc_final: 0.6763 (ttm) REVERT: F 404 ARG cc_start: 0.8362 (mmm-85) cc_final: 0.7512 (tpp-160) outliers start: 97 outliers final: 72 residues processed: 380 average time/residue: 0.3100 time to fit residues: 188.7328 Evaluate side-chains 360 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 280 time to evaluate : 2.504 ------------------------------------------------------------------------------- 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 153 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 183 ILE 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 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 276 LEU Chi-restraints excluded: chain C residue 290 ILE 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 52 LEU 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 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 293 THR Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 419 GLN Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 42 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 132 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 197 ASP Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 231 THR 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 392 LEU Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 462 VAL Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 105 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 144 LEU Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain F residue 191 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 251 ILE Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 285 MET Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 400 VAL 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 249 optimal weight: 0.0670 chunk 30 optimal weight: 4.9990 chunk 179 optimal weight: 6.9990 chunk 171 optimal weight: 0.0030 chunk 24 optimal weight: 6.9990 chunk 248 optimal weight: 6.9990 chunk 231 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 132 optimal weight: 10.0000 chunk 102 optimal weight: 0.7980 chunk 188 optimal weight: 8.9990 overall best weight: 1.5732 ------------------------------------------------------------------------------- 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 ** C 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 330 ASN E 365 GLN ** 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 = 0.4423 r_free = 0.4423 target = 0.198291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.161757 restraints weight = 26160.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.163940 restraints weight = 17211.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.167137 restraints weight = 11918.860| |-----------------------------------------------------------------------------| r_work (final): 0.4072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.4632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22330 Z= 0.125 Angle : 0.583 13.850 30283 Z= 0.297 Chirality : 0.044 0.276 3480 Planarity : 0.005 0.060 3960 Dihedral : 7.385 85.228 3236 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 4.01 % Allowed : 20.57 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.16), residues: 2823 helix: 1.01 (0.15), residues: 1114 sheet: -0.13 (0.25), residues: 415 loop : -0.95 (0.17), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 179 PHE 0.036 0.001 PHE C 460 TYR 0.024 0.001 TYR E 148 ARG 0.008 0.000 ARG A 278 Details of bonding type rmsd hydrogen bonds : bond 0.04007 ( 985) hydrogen bonds : angle 4.85720 ( 2841) covalent geometry : bond 0.00289 (22330) covalent geometry : angle 0.58303 (30283) *********************** 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 381 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 288 time to evaluate : 2.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 GLN cc_start: 0.8549 (tm-30) cc_final: 0.7891 (tm-30) REVERT: A 184 ILE cc_start: 0.6752 (OUTLIER) cc_final: 0.6488 (mp) REVERT: A 245 MET cc_start: 0.5280 (ptp) cc_final: 0.4764 (mmm) REVERT: A 418 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7472 (tm-30) REVERT: B 32 ILE cc_start: 0.7946 (OUTLIER) cc_final: 0.7599 (mm) REVERT: B 176 THR cc_start: 0.7910 (m) cc_final: 0.7645 (p) REVERT: C 361 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7554 (tp) REVERT: C 415 ARG cc_start: 0.8160 (mtt90) cc_final: 0.7849 (mpt-90) REVERT: D 64 MET cc_start: 0.6579 (OUTLIER) cc_final: 0.5836 (mmm) REVERT: D 235 MET cc_start: 0.6983 (mtt) cc_final: 0.6516 (mtp) REVERT: D 338 MET cc_start: 0.7262 (mtp) cc_final: 0.6957 (tpt) REVERT: E 19 GLU cc_start: 0.7135 (mm-30) cc_final: 0.6446 (tm-30) REVERT: E 64 MET cc_start: 0.5375 (mmp) cc_final: 0.4712 (mmm) REVERT: E 202 MET cc_start: 0.6572 (mmt) cc_final: 0.4462 (mtp) REVERT: E 268 LEU cc_start: 0.6610 (OUTLIER) cc_final: 0.6271 (mm) REVERT: E 469 MET cc_start: 0.5730 (ttm) cc_final: 0.5446 (ttm) REVERT: F 105 LEU cc_start: 0.6239 (OUTLIER) cc_final: 0.6004 (mt) REVERT: F 154 ILE cc_start: 0.7874 (OUTLIER) cc_final: 0.7492 (mt) REVERT: F 191 ARG cc_start: 0.4824 (OUTLIER) cc_final: 0.2397 (mmm160) REVERT: F 235 MET cc_start: 0.6490 (mmt) cc_final: 0.6286 (mmt) REVERT: F 285 MET cc_start: 0.7458 (OUTLIER) cc_final: 0.7084 (tpp) REVERT: F 306 ILE cc_start: 0.5594 (OUTLIER) cc_final: 0.5321 (tt) REVERT: F 404 ARG cc_start: 0.8344 (mmm-85) cc_final: 0.7714 (tpp-160) outliers start: 93 outliers final: 72 residues processed: 362 average time/residue: 0.2996 time to fit residues: 174.8701 Evaluate side-chains 360 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 277 time to evaluate : 2.339 ------------------------------------------------------------------------------- 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 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 198 ILE Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 260 TYR 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 276 LEU 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 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 46 LEU Chi-restraints excluded: chain D residue 64 MET 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 247 VAL Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 380 LEU 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 42 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 132 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 197 ASP Chi-restraints excluded: chain E residue 231 THR 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 392 LEU Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 462 VAL Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 105 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 143 ASP Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain F residue 191 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 251 ILE Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 285 MET Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 406 ILE Chi-restraints excluded: chain F residue 437 PHE Chi-restraints excluded: chain F residue 456 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 57 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 258 optimal weight: 10.0000 chunk 142 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 188 optimal weight: 0.0370 chunk 250 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 141 optimal weight: 5.9990 chunk 38 optimal weight: 9.9990 chunk 198 optimal weight: 7.9990 overall best weight: 2.9864 ------------------------------------------------------------------------------- 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** ** C 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 330 ASN ** E 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 304 GLN ** 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 = 0.4392 r_free = 0.4392 target = 0.194692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.157530 restraints weight = 26531.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.160299 restraints weight = 17345.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.162575 restraints weight = 11545.743| |-----------------------------------------------------------------------------| r_work (final): 0.4029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 moved from start: 0.4842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 22330 Z= 0.173 Angle : 0.644 13.170 30283 Z= 0.330 Chirality : 0.046 0.174 3480 Planarity : 0.005 0.057 3960 Dihedral : 7.589 86.817 3236 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 4.05 % Allowed : 20.74 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.15), residues: 2823 helix: 0.86 (0.15), residues: 1110 sheet: -0.22 (0.25), residues: 422 loop : -1.08 (0.17), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 179 PHE 0.028 0.002 PHE E 414 TYR 0.027 0.002 TYR D 148 ARG 0.006 0.000 ARG A 278 Details of bonding type rmsd hydrogen bonds : bond 0.04603 ( 985) hydrogen bonds : angle 5.00910 ( 2841) covalent geometry : bond 0.00413 (22330) covalent geometry : angle 0.64351 (30283) ********************** 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 378 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 284 time to evaluate : 2.552 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: 0.8617 (tm-30) cc_final: 0.7860 (tm-30) REVERT: A 184 ILE cc_start: 0.6625 (OUTLIER) cc_final: 0.6388 (mp) REVERT: A 245 MET cc_start: 0.5302 (ptp) cc_final: 0.4694 (mmm) REVERT: A 418 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7447 (tm-30) REVERT: B 32 ILE cc_start: 0.7836 (OUTLIER) cc_final: 0.7508 (mm) REVERT: B 36 ASP cc_start: 0.7595 (p0) cc_final: 0.7344 (p0) REVERT: B 176 THR cc_start: 0.7871 (m) cc_final: 0.7585 (p) REVERT: C 361 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7643 (tp) REVERT: C 415 ARG cc_start: 0.8222 (mtt90) cc_final: 0.7885 (mpt-90) REVERT: D 235 MET cc_start: 0.7210 (mtt) cc_final: 0.6678 (mtp) REVERT: D 338 MET cc_start: 0.7465 (mtp) cc_final: 0.6803 (tpt) REVERT: E 64 MET cc_start: 0.5548 (mmp) cc_final: 0.4925 (mmm) REVERT: E 268 LEU cc_start: 0.6649 (OUTLIER) cc_final: 0.6242 (mm) REVERT: E 369 LYS cc_start: 0.7506 (pttm) cc_final: 0.7201 (pttm) REVERT: E 469 MET cc_start: 0.5678 (ttm) cc_final: 0.5456 (ttm) REVERT: F 105 LEU cc_start: 0.6348 (OUTLIER) cc_final: 0.6102 (mt) REVERT: F 154 ILE cc_start: 0.7909 (OUTLIER) cc_final: 0.7569 (mt) REVERT: F 191 ARG cc_start: 0.4757 (OUTLIER) cc_final: 0.2598 (tpp-160) REVERT: F 285 MET cc_start: 0.7333 (OUTLIER) cc_final: 0.6850 (tpp) REVERT: F 404 ARG cc_start: 0.8356 (mmm-85) cc_final: 0.7576 (tpp80) outliers start: 94 outliers final: 74 residues processed: 358 average time/residue: 0.2997 time to fit residues: 172.9778 Evaluate side-chains 357 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 274 time to evaluate : 2.221 ------------------------------------------------------------------------------- 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 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 198 ILE Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 260 TYR Chi-restraints excluded: chain B residue 319 VAL 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 274 SER Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 361 LEU 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 46 LEU Chi-restraints excluded: chain D residue 52 LEU 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 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 293 THR Chi-restraints excluded: chain D residue 347 LEU 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 42 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 132 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 197 ASP Chi-restraints excluded: chain E residue 231 THR 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 392 LEU Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 462 VAL Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain F residue 191 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 258 THR Chi-restraints excluded: chain F residue 285 MET Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 406 ILE Chi-restraints excluded: chain F residue 437 PHE Chi-restraints excluded: chain F residue 456 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 104 optimal weight: 10.0000 chunk 114 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 246 optimal weight: 8.9990 chunk 126 optimal weight: 20.0000 chunk 16 optimal weight: 6.9990 chunk 27 optimal weight: 9.9990 chunk 125 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 3 optimal weight: 9.9990 chunk 242 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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** ** C 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 HIS ** F 304 GLN ** 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 = 0.4367 r_free = 0.4367 target = 0.192388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.155780 restraints weight = 26389.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.157603 restraints weight = 17817.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.159475 restraints weight = 12430.482| |-----------------------------------------------------------------------------| r_work (final): 0.3984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.5057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 22330 Z= 0.187 Angle : 0.663 13.865 30283 Z= 0.342 Chirality : 0.047 0.177 3480 Planarity : 0.005 0.057 3960 Dihedral : 7.773 88.727 3236 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.92 % Allowed : 21.26 % Favored : 74.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.15), residues: 2823 helix: 0.72 (0.15), residues: 1109 sheet: -0.43 (0.25), residues: 403 loop : -1.25 (0.16), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS A 294 PHE 0.036 0.002 PHE C 460 TYR 0.027 0.002 TYR D 148 ARG 0.007 0.001 ARG D 270 Details of bonding type rmsd hydrogen bonds : bond 0.04799 ( 985) hydrogen bonds : angle 5.13731 ( 2841) covalent geometry : bond 0.00455 (22330) covalent geometry : angle 0.66282 (30283) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6735.26 seconds wall clock time: 118 minutes 30.08 seconds (7110.08 seconds total)