Starting phenix.real_space_refine on Wed Jun 18 22:55:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8spw_40688/06_2025/8spw_40688.cif Found real_map, /net/cci-nas-00/data/ceres_data/8spw_40688/06_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_40688/06_2025/8spw_40688.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8spw_40688/06_2025/8spw_40688.map" model { file = "/net/cci-nas-00/data/ceres_data/8spw_40688/06_2025/8spw_40688.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8spw_40688/06_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-5710/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: 14.02, per 1000 atoms: 0.64 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: 5.89 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: 2.62 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: 8.61 Time building geometry restraints manager: 6.95 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: 1.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.000 Check model and map are aligned: 0.200 Set scattering table: 0.210 Process input model: 53.440 Find NCS groups from input model: 1.490 Set up NCS constraints: 0.120 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:3.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.300 ------------------------------------------------------------------------------- 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 : 2.558 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: 0.4004 time to fit residues: 357.7328 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 : 2.571 ------------------------------------------------------------------------------- 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 = 27005.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.165662 restraints weight = 17067.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.167709 restraints weight = 12764.633| |-----------------------------------------------------------------------------| r_work (final): 0.4134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6763 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 : 2.421 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: 0.6959 (m-80) cc_final: 0.6670 (m-80) REVERT: B 236 PHE cc_start: 0.6740 (OUTLIER) cc_final: 0.6514 (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: 0.7739 (t80) REVERT: D 235 MET cc_start: 0.7095 (mtt) cc_final: 0.6574 (mtp) REVERT: D 271 MET cc_start: 0.7334 (mtt) cc_final: 0.6878 (mtt) REVERT: D 338 MET cc_start: 0.7452 (OUTLIER) cc_final: 0.6915 (tpt) REVERT: E 126 GLU cc_start: 0.6264 (pm20) cc_final: 0.5942 (pm20) REVERT: E 202 MET cc_start: 0.5639 (mmt) cc_final: 0.3661 (mtp) REVERT: F 235 MET cc_start: 0.6270 (mmt) cc_final: 0.6003 (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: 0.4186 (mtm-85) REVERT: F 264 VAL cc_start: 0.4173 (t) cc_final: 0.3540 (t) REVERT: F 404 ARG cc_start: 0.8367 (mmm-85) cc_final: 0.7712 (tpp80) outliers start: 70 outliers final: 38 residues processed: 411 average time/residue: 0.3336 time to fit residues: 210.3581 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 : 2.376 ------------------------------------------------------------------------------- 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: 0.0970 chunk 267 optimal weight: 0.6980 chunk 99 optimal weight: 7.9990 chunk 47 optimal weight: 0.9980 chunk 257 optimal weight: 4.9990 chunk 214 optimal weight: 9.9990 chunk 255 optimal weight: 5.9990 chunk 223 optimal weight: 9.9990 chunk 232 optimal weight: 7.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4493 r_free = 0.4493 target = 0.206173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.168730 restraints weight = 25585.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.172618 restraints weight = 16239.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.175466 restraints weight = 11036.591| |-----------------------------------------------------------------------------| r_work (final): 0.4155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6710 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 22330 Z= 0.116 Angle : 0.553 8.979 30283 Z= 0.292 Chirality : 0.044 0.244 3480 Planarity : 0.005 0.053 3960 Dihedral : 8.485 103.622 3246 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.28 % Allowed : 15.78 % Favored : 80.94 % 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: 1.02 (0.15), residues: 1130 sheet: 0.22 (0.25), residues: 414 loop : -0.71 (0.17), residues: 1279 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 474 PHE 0.046 0.002 PHE E 414 TYR 0.012 0.001 TYR C 195 ARG 0.004 0.000 ARG B 455 Details of bonding type rmsd hydrogen bonds : bond 0.04410 ( 985) hydrogen bonds : angle 5.12901 ( 2841) covalent geometry : bond 0.00241 (22330) covalent geometry : angle 0.55279 (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 403 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 327 time to evaluate : 2.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 GLN cc_start: 0.8559 (tm-30) cc_final: 0.8330 (tm-30) REVERT: A 245 MET cc_start: 0.5728 (ptp) cc_final: 0.5115 (mmm) REVERT: A 320 GLU cc_start: 0.4238 (tt0) cc_final: 0.3977 (tt0) REVERT: A 444 PHE cc_start: 0.7121 (m-80) cc_final: 0.6912 (m-80) REVERT: B 156 LEU cc_start: 0.7660 (mt) cc_final: 0.7423 (mp) REVERT: B 236 PHE cc_start: 0.6651 (OUTLIER) cc_final: 0.6433 (p90) REVERT: B 317 PRO cc_start: 0.7761 (Cg_endo) cc_final: 0.7520 (Cg_exo) REVERT: C 93 ARG cc_start: 0.7180 (ptt-90) cc_final: 0.6860 (ptt-90) REVERT: C 270 TYR cc_start: 0.7608 (t80) cc_final: 0.7403 (t80) REVERT: D 198 LEU cc_start: 0.8573 (tp) cc_final: 0.8364 (tp) REVERT: D 235 MET cc_start: 0.7083 (mtt) cc_final: 0.6533 (mtp) REVERT: D 271 MET cc_start: 0.7496 (mtt) cc_final: 0.7062 (mtt) REVERT: D 338 MET cc_start: 0.7531 (OUTLIER) cc_final: 0.7086 (tpt) REVERT: E 126 GLU cc_start: 0.6321 (pm20) cc_final: 0.6095 (pm20) REVERT: E 202 MET cc_start: 0.5415 (mmt) cc_final: 0.3744 (mtp) REVERT: F 235 MET cc_start: 0.6232 (mmt) cc_final: 0.5960 (mmt) REVERT: F 253 ASN cc_start: 0.5369 (OUTLIER) cc_final: 0.5064 (p0) REVERT: F 256 ARG cc_start: 0.4302 (OUTLIER) cc_final: 0.3168 (mmp80) REVERT: F 404 ARG cc_start: 0.8337 (mmm-85) cc_final: 0.7552 (tpp-160) outliers start: 76 outliers final: 39 residues processed: 390 average time/residue: 0.3100 time to fit residues: 190.5390 Evaluate side-chains 332 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 289 time to evaluate : 2.342 ------------------------------------------------------------------------------- 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 182 THR Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 410 LEU 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 268 LEU 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 411 SER Chi-restraints excluded: chain E residue 423 GLN Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 58 THR 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 253 ASN Chi-restraints excluded: chain F residue 256 ARG Chi-restraints excluded: chain F residue 397 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 125 optimal weight: 10.0000 chunk 183 optimal weight: 8.9990 chunk 119 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 chunk 257 optimal weight: 3.9990 chunk 203 optimal weight: 5.9990 chunk 145 optimal weight: 8.9990 chunk 10 optimal weight: 10.0000 chunk 109 optimal weight: 3.9990 chunk 55 optimal weight: 8.9990 chunk 115 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN A 266 GLN A 474 HIS B 185 ASN B 345 GLN C 185 ASN C 294 HIS C 425 HIS D 22 HIS ** 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 253 ASN ** F 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.191234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.152875 restraints weight = 27105.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.156214 restraints weight = 17748.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.158255 restraints weight = 11944.502| |-----------------------------------------------------------------------------| r_work (final): 0.3975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.3942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 22330 Z= 0.255 Angle : 0.752 9.457 30283 Z= 0.400 Chirality : 0.051 0.241 3480 Planarity : 0.006 0.061 3960 Dihedral : 8.660 92.642 3243 Min Nonbonded Distance : 1.704 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 5.74 % Allowed : 16.39 % Favored : 77.88 % 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: -0.67 (0.15), residues: 2823 helix: 0.38 (0.15), residues: 1111 sheet: -0.28 (0.24), residues: 436 loop : -1.19 (0.17), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS E 200 PHE 0.029 0.003 PHE A 494 TYR 0.029 0.003 TYR A 329 ARG 0.007 0.001 ARG D 256 Details of bonding type rmsd hydrogen bonds : bond 0.06077 ( 985) hydrogen bonds : angle 5.51562 ( 2841) covalent geometry : bond 0.00610 (22330) covalent geometry : angle 0.75171 (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 460 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 327 time to evaluate : 2.623 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 93 ARG cc_start: 0.7381 (ptt180) cc_final: 0.7148 (ptm160) REVERT: A 245 MET cc_start: 0.5812 (ptp) cc_final: 0.4929 (mmm) REVERT: A 444 PHE cc_start: 0.7345 (m-80) cc_final: 0.6785 (m-80) REVERT: B 32 ILE cc_start: 0.7954 (OUTLIER) cc_final: 0.7598 (mm) REVERT: B 250 MET cc_start: 0.5509 (tpt) cc_final: 0.5138 (tpt) REVERT: B 406 THR cc_start: 0.8610 (OUTLIER) cc_final: 0.8282 (t) REVERT: C 137 MET cc_start: 0.5811 (mmm) cc_final: 0.5426 (mtp) REVERT: D 271 MET cc_start: 0.7597 (mtt) cc_final: 0.7372 (mtt) REVERT: D 368 ARG cc_start: 0.7815 (OUTLIER) cc_final: 0.6827 (tpp-160) REVERT: E 64 MET cc_start: 0.5483 (mmp) cc_final: 0.4865 (mmm) REVERT: E 148 TYR cc_start: 0.7571 (m-10) cc_final: 0.7259 (m-80) REVERT: E 259 GLN cc_start: 0.7543 (OUTLIER) cc_final: 0.6222 (mp-120) REVERT: E 268 LEU cc_start: 0.6723 (OUTLIER) cc_final: 0.6206 (mm) REVERT: E 351 SER cc_start: 0.8705 (t) cc_final: 0.8366 (t) REVERT: E 369 LYS cc_start: 0.7355 (pttm) cc_final: 0.7109 (pttm) REVERT: E 469 MET cc_start: 0.5603 (ttm) cc_final: 0.5337 (ttm) REVERT: F 154 ILE cc_start: 0.7817 (OUTLIER) cc_final: 0.7435 (mt) REVERT: F 191 ARG cc_start: 0.4734 (OUTLIER) cc_final: 0.2215 (mmm160) REVERT: F 226 MET cc_start: 0.5488 (ttp) cc_final: 0.5282 (ttp) REVERT: F 404 ARG cc_start: 0.8370 (mmm-85) cc_final: 0.8136 (mmm-85) outliers start: 133 outliers final: 82 residues processed: 428 average time/residue: 0.3228 time to fit residues: 215.8928 Evaluate side-chains 376 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 287 time to evaluate : 2.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 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 326 ILE 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 410 LEU Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain A residue 480 ASP 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 207 THR 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 B residue 406 THR Chi-restraints excluded: chain B residue 466 GLN Chi-restraints excluded: chain C residue 48 MET 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 225 THR Chi-restraints excluded: chain C residue 236 PHE Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 294 HIS 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 145 LEU Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 368 ARG 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 103 ILE 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 237 GLU Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 259 GLN Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 411 SER Chi-restraints excluded: chain E residue 423 GLN Chi-restraints excluded: chain F residue 18 PHE 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 162 VAL 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 253 ASN Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain F residue 321 THR Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 437 PHE Chi-restraints excluded: chain F residue 456 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 72 optimal weight: 0.1980 chunk 154 optimal weight: 6.9990 chunk 226 optimal weight: 20.0000 chunk 219 optimal weight: 0.9980 chunk 187 optimal weight: 6.9990 chunk 19 optimal weight: 8.9990 chunk 30 optimal weight: 0.0670 chunk 173 optimal weight: 0.9990 chunk 5 optimal weight: 6.9990 chunk 276 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.0522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 HIS ** D 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 330 ASN E 196 ASN E 200 HIS F 253 ASN ** F 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 407 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.197830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.160627 restraints weight = 26256.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.164217 restraints weight = 17504.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.166119 restraints weight = 11553.158| |-----------------------------------------------------------------------------| r_work (final): 0.4058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.4093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 22330 Z= 0.121 Angle : 0.571 9.017 30283 Z= 0.300 Chirality : 0.044 0.201 3480 Planarity : 0.005 0.058 3960 Dihedral : 7.982 85.982 3239 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.75 % Allowed : 19.32 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.27 (0.16), residues: 2823 helix: 0.84 (0.16), residues: 1113 sheet: -0.18 (0.25), residues: 422 loop : -1.05 (0.17), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.031 0.001 HIS C 294 PHE 0.035 0.002 PHE C 460 TYR 0.020 0.001 TYR A 461 ARG 0.006 0.000 ARG F 193 Details of bonding type rmsd hydrogen bonds : bond 0.04396 ( 985) hydrogen bonds : angle 5.04667 ( 2841) covalent geometry : bond 0.00264 (22330) covalent geometry : angle 0.57106 (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 391 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 304 time to evaluate : 2.680 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 245 MET cc_start: 0.5325 (ptp) cc_final: 0.4758 (mmm) REVERT: A 444 PHE cc_start: 0.7054 (m-80) cc_final: 0.6615 (m-80) REVERT: B 32 ILE cc_start: 0.7962 (OUTLIER) cc_final: 0.7712 (mm) REVERT: C 93 ARG cc_start: 0.7224 (ptt-90) cc_final: 0.6924 (ptt-90) REVERT: C 333 ASN cc_start: 0.7218 (OUTLIER) cc_final: 0.6973 (t0) REVERT: C 415 ARG cc_start: 0.8158 (mtt90) cc_final: 0.7768 (mpt-90) REVERT: D 235 MET cc_start: 0.7097 (mtt) cc_final: 0.6611 (mtp) REVERT: D 271 MET cc_start: 0.7486 (mtt) cc_final: 0.7094 (mtt) REVERT: D 338 MET cc_start: 0.7329 (OUTLIER) cc_final: 0.7106 (tpt) REVERT: E 268 LEU cc_start: 0.6683 (OUTLIER) cc_final: 0.6293 (mm) REVERT: E 337 GLU cc_start: 0.6535 (pt0) cc_final: 0.6171 (mt-10) REVERT: E 469 MET cc_start: 0.5621 (ttm) cc_final: 0.5407 (mtt) REVERT: F 191 ARG cc_start: 0.4904 (OUTLIER) cc_final: 0.2066 (mmm160) REVERT: F 285 MET cc_start: 0.7334 (ttm) cc_final: 0.6764 (tpp) REVERT: F 402 ARG cc_start: 0.7984 (mtm180) cc_final: 0.7636 (ttm170) REVERT: F 404 ARG cc_start: 0.8334 (mmm-85) cc_final: 0.7507 (tpp-160) outliers start: 87 outliers final: 58 residues processed: 373 average time/residue: 0.3266 time to fit residues: 190.8843 Evaluate side-chains 333 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 270 time to evaluate : 2.302 ------------------------------------------------------------------------------- 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 372 ILE Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain C residue 48 MET 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 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 453 VAL Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 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 268 LEU Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 338 MET Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 74 MET Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 197 ASP Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 411 SER Chi-restraints excluded: chain E residue 423 GLN Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 191 ARG Chi-restraints excluded: chain F residue 193 ARG Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 406 ILE 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: 1.9990 chunk 42 optimal weight: 20.0000 chunk 172 optimal weight: 4.9990 chunk 178 optimal weight: 3.9990 chunk 243 optimal weight: 1.9990 chunk 218 optimal weight: 0.9980 chunk 104 optimal weight: 0.0030 chunk 127 optimal weight: 2.9990 chunk 16 optimal weight: 7.9990 chunk 99 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 overall best weight: 1.5996 ------------------------------------------------------------------------------- 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** ** C 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 330 ASN ** F 253 ASN ** 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 = 0.4413 r_free = 0.4413 target = 0.197267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.160602 restraints weight = 26090.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.164171 restraints weight = 17114.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.165740 restraints weight = 11272.254| |-----------------------------------------------------------------------------| r_work (final): 0.4058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 moved from start: 0.4289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 22330 Z= 0.129 Angle : 0.587 10.894 30283 Z= 0.302 Chirality : 0.044 0.174 3480 Planarity : 0.005 0.066 3960 Dihedral : 7.780 85.643 3238 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 4.14 % Allowed : 19.66 % Favored : 76.20 % 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: -0.24 (0.16), residues: 2823 helix: 0.91 (0.15), residues: 1107 sheet: -0.26 (0.24), residues: 434 loop : -1.03 (0.17), residues: 1282 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS F 179 PHE 0.035 0.002 PHE E 414 TYR 0.021 0.001 TYR B 438 ARG 0.011 0.000 ARG C 127 Details of bonding type rmsd hydrogen bonds : bond 0.04283 ( 985) hydrogen bonds : angle 4.96083 ( 2841) covalent geometry : bond 0.00296 (22330) covalent geometry : angle 0.58732 (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 386 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 290 time to evaluate : 2.405 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: 0.8691 (tm-30) cc_final: 0.7944 (tm-30) REVERT: A 245 MET cc_start: 0.5206 (ptp) cc_final: 0.4744 (mmm) REVERT: A 444 PHE cc_start: 0.6989 (m-80) cc_final: 0.6697 (m-80) REVERT: B 32 ILE cc_start: 0.7998 (OUTLIER) cc_final: 0.7685 (mm) REVERT: B 176 THR cc_start: 0.7903 (m) cc_final: 0.7581 (p) REVERT: B 191 MET cc_start: 0.6447 (mmm) cc_final: 0.6242 (mmm) REVERT: B 349 PHE cc_start: 0.4354 (t80) cc_final: 0.4073 (t80) REVERT: C 93 ARG cc_start: 0.7264 (ptt-90) cc_final: 0.6944 (ptt-90) REVERT: C 333 ASN cc_start: 0.7256 (OUTLIER) cc_final: 0.6984 (t0) REVERT: C 415 ARG cc_start: 0.8136 (mtt90) cc_final: 0.7805 (mpt-90) REVERT: D 235 MET cc_start: 0.7121 (mtt) cc_final: 0.6635 (mtp) REVERT: D 271 MET cc_start: 0.7457 (mtt) cc_final: 0.7062 (mtt) REVERT: D 368 ARG cc_start: 0.7723 (OUTLIER) cc_final: 0.7418 (mmt180) REVERT: E 64 MET cc_start: 0.5196 (mmp) cc_final: 0.4520 (mmm) REVERT: E 268 LEU cc_start: 0.6702 (OUTLIER) cc_final: 0.6334 (mm) REVERT: E 337 GLU cc_start: 0.6453 (pt0) cc_final: 0.6087 (mt-10) REVERT: E 369 LYS cc_start: 0.7249 (pttm) cc_final: 0.6399 (tptm) REVERT: E 469 MET cc_start: 0.5745 (ttm) cc_final: 0.5527 (mtt) REVERT: F 154 ILE cc_start: 0.7822 (OUTLIER) cc_final: 0.7414 (mt) REVERT: F 191 ARG cc_start: 0.5010 (OUTLIER) cc_final: 0.2146 (mmm160) REVERT: F 404 ARG cc_start: 0.8257 (mmm-85) cc_final: 0.7530 (tpp-160) outliers start: 96 outliers final: 74 residues processed: 365 average time/residue: 0.3123 time to fit residues: 179.2176 Evaluate side-chains 355 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 275 time to evaluate : 2.680 ------------------------------------------------------------------------------- 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 198 ILE 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 435 LEU 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 130 GLU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain C residue 48 MET 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 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 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 32 ILE 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 268 LEU Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 368 ARG Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 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 58 THR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 74 MET Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 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 392 LEU Chi-restraints excluded: chain E residue 423 GLN Chi-restraints excluded: chain E residue 456 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 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 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: 10.0000 chunk 26 optimal weight: 3.9990 chunk 174 optimal weight: 10.0000 chunk 279 optimal weight: 20.0000 chunk 241 optimal weight: 0.9980 chunk 208 optimal weight: 8.9990 chunk 193 optimal weight: 10.0000 chunk 104 optimal weight: 9.9990 chunk 75 optimal weight: 3.9990 chunk 183 optimal weight: 8.9990 chunk 249 optimal weight: 10.0000 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 294 HIS ** C 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 330 ASN ** E 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 365 GLN ** F 253 ASN ** 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 = 0.4325 r_free = 0.4325 target = 0.187729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.151779 restraints weight = 26753.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.153588 restraints weight = 20296.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.155457 restraints weight = 14849.675| |-----------------------------------------------------------------------------| r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.4909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 22330 Z= 0.281 Angle : 0.770 11.842 30283 Z= 0.409 Chirality : 0.051 0.200 3480 Planarity : 0.007 0.057 3960 Dihedral : 8.631 89.583 3238 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 5.13 % Allowed : 19.84 % Favored : 75.03 % 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: -0.98 (0.15), residues: 2823 helix: 0.32 (0.15), residues: 1097 sheet: -0.59 (0.24), residues: 417 loop : -1.49 (0.16), residues: 1309 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.002 HIS E 173 PHE 0.037 0.003 PHE C 460 TYR 0.028 0.003 TYR C 240 ARG 0.011 0.001 ARG C 127 Details of bonding type rmsd hydrogen bonds : bond 0.06156 ( 985) hydrogen bonds : angle 5.52095 ( 2841) covalent geometry : bond 0.00687 (22330) covalent geometry : angle 0.76971 (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 417 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 298 time to evaluate : 2.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 GLN cc_start: 0.8738 (tm-30) cc_final: 0.8425 (tm-30) REVERT: A 245 MET cc_start: 0.5285 (ptp) cc_final: 0.4665 (mmm) REVERT: B 32 ILE cc_start: 0.7882 (OUTLIER) cc_final: 0.7456 (mm) REVERT: B 176 THR cc_start: 0.8016 (m) cc_final: 0.7723 (p) REVERT: C 62 MET cc_start: 0.6794 (ptm) cc_final: 0.6587 (ptt) REVERT: C 93 ARG cc_start: 0.7390 (ptt-90) cc_final: 0.7177 (ptt-90) REVERT: C 137 MET cc_start: 0.5657 (mmm) cc_final: 0.5255 (mtp) REVERT: C 415 ARG cc_start: 0.8216 (mtt90) cc_final: 0.7863 (mpt-90) REVERT: D 218 MET cc_start: 0.7918 (ptt) cc_final: 0.7692 (ptt) REVERT: D 235 MET cc_start: 0.7251 (mtt) cc_final: 0.6688 (mtp) REVERT: D 271 MET cc_start: 0.7582 (mtt) cc_final: 0.7229 (mtt) REVERT: D 368 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7150 (tpp-160) REVERT: E 268 LEU cc_start: 0.6707 (OUTLIER) cc_final: 0.6136 (mm) REVERT: E 337 GLU cc_start: 0.6841 (pt0) cc_final: 0.6307 (mt-10) REVERT: E 369 LYS cc_start: 0.7528 (pttm) cc_final: 0.7281 (pttm) REVERT: E 469 MET cc_start: 0.5836 (ttm) cc_final: 0.5570 (ttm) REVERT: F 191 ARG cc_start: 0.4998 (OUTLIER) cc_final: 0.2740 (tpp-160) REVERT: F 288 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8538 (tp) REVERT: F 402 ARG cc_start: 0.8266 (ttp-170) cc_final: 0.8017 (ttm-80) REVERT: F 404 ARG cc_start: 0.8256 (mmm-85) cc_final: 0.8001 (mmm-85) outliers start: 119 outliers final: 85 residues processed: 388 average time/residue: 0.3168 time to fit residues: 194.4735 Evaluate side-chains 354 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 264 time to evaluate : 2.299 ------------------------------------------------------------------------------- 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 198 ILE Chi-restraints excluded: chain A residue 293 LEU 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 435 LEU 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 130 GLU Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 260 TYR Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain C residue 48 MET 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 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 197 ASP Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 368 ARG Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 419 GLN Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 74 MET Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 197 ASP Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 392 LEU Chi-restraints excluded: chain E residue 411 SER Chi-restraints excluded: chain E residue 423 GLN Chi-restraints excluded: chain E residue 447 HIS Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 18 PHE 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 162 VAL Chi-restraints excluded: chain F residue 191 ARG Chi-restraints excluded: chain F residue 193 ARG Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 288 LEU Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 437 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 69 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 90 optimal weight: 9.9990 chunk 225 optimal weight: 10.0000 chunk 277 optimal weight: 10.0000 chunk 192 optimal weight: 0.0060 chunk 215 optimal weight: 1.9990 chunk 243 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 122 optimal weight: 7.9990 overall best weight: 2.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 HIS ** B 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 ASN ** F 253 ASN ** 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 = 0.4362 r_free = 0.4362 target = 0.191987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.155033 restraints weight = 26447.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.157829 restraints weight = 18087.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.159516 restraints weight = 11998.701| |-----------------------------------------------------------------------------| r_work (final): 0.3990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.5033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22330 Z= 0.162 Angle : 0.650 14.006 30283 Z= 0.337 Chirality : 0.046 0.208 3480 Planarity : 0.005 0.062 3960 Dihedral : 8.189 89.236 3238 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 4.61 % Allowed : 21.69 % Favored : 73.70 % 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: -0.79 (0.15), residues: 2823 helix: 0.54 (0.15), residues: 1108 sheet: -0.62 (0.25), residues: 409 loop : -1.41 (0.16), residues: 1306 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 179 PHE 0.029 0.002 PHE A 494 TYR 0.033 0.002 TYR E 148 ARG 0.006 0.000 ARG C 127 Details of bonding type rmsd hydrogen bonds : bond 0.04878 ( 985) hydrogen bonds : angle 5.19790 ( 2841) covalent geometry : bond 0.00382 (22330) covalent geometry : angle 0.64950 (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 389 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 282 time to evaluate : 2.539 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: 0.8691 (tm-30) cc_final: 0.7957 (tm-30) REVERT: A 245 MET cc_start: 0.5151 (ptp) cc_final: 0.4583 (mmm) REVERT: A 444 PHE cc_start: 0.7083 (m-80) cc_final: 0.6756 (m-80) REVERT: B 32 ILE cc_start: 0.8027 (OUTLIER) cc_final: 0.7702 (mm) REVERT: B 176 THR cc_start: 0.7963 (m) cc_final: 0.7694 (p) REVERT: B 349 PHE cc_start: 0.3944 (t80) cc_final: 0.3435 (t80) REVERT: B 406 THR cc_start: 0.8623 (p) cc_final: 0.8229 (t) REVERT: C 415 ARG cc_start: 0.8169 (mtt90) cc_final: 0.7825 (mpt-90) REVERT: D 218 MET cc_start: 0.7970 (ptt) cc_final: 0.7705 (ptt) REVERT: D 235 MET cc_start: 0.7184 (mtt) cc_final: 0.6665 (mtp) REVERT: D 288 LEU cc_start: 0.7797 (tp) cc_final: 0.7340 (tp) REVERT: D 368 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7707 (mmt180) REVERT: E 64 MET cc_start: 0.5368 (mmp) cc_final: 0.4573 (mmm) REVERT: E 268 LEU cc_start: 0.6618 (OUTLIER) cc_final: 0.6205 (mm) REVERT: E 369 LYS cc_start: 0.7628 (pttm) cc_final: 0.7327 (pttm) REVERT: E 469 MET cc_start: 0.5762 (ttm) cc_final: 0.5525 (mtt) REVERT: F 154 ILE cc_start: 0.7893 (OUTLIER) cc_final: 0.7543 (mt) REVERT: F 191 ARG cc_start: 0.4863 (OUTLIER) cc_final: 0.2830 (tpp-160) REVERT: F 285 MET cc_start: 0.7507 (ttm) cc_final: 0.7108 (tpp) REVERT: F 288 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8560 (tp) REVERT: F 402 ARG cc_start: 0.8307 (ttp-170) cc_final: 0.7976 (ttm-80) REVERT: F 404 ARG cc_start: 0.8260 (mmm-85) cc_final: 0.8021 (mmm-85) outliers start: 107 outliers final: 81 residues processed: 364 average time/residue: 0.3128 time to fit residues: 180.7491 Evaluate side-chains 354 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 267 time to evaluate : 2.352 ------------------------------------------------------------------------------- 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 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 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 130 GLU Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 260 TYR Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 466 GLN Chi-restraints excluded: chain C residue 48 MET 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 276 LEU Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 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 268 LEU Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 368 ARG Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 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 35 LYS Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 74 MET Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 174 ASN Chi-restraints excluded: chain E residue 177 GLN Chi-restraints excluded: chain E residue 197 ASP Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 384 ILE Chi-restraints excluded: chain E residue 447 HIS Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 18 PHE 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 193 ARG Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 288 LEU Chi-restraints excluded: chain F residue 304 GLN Chi-restraints excluded: chain F residue 437 PHE Chi-restraints excluded: chain F residue 456 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 249 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 179 optimal weight: 9.9990 chunk 171 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 248 optimal weight: 3.9990 chunk 231 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 132 optimal weight: 20.0000 chunk 102 optimal weight: 0.0170 chunk 188 optimal weight: 3.9990 overall best weight: 1.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 474 HIS ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 ASN ** F 253 ASN ** 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 = 0.4389 r_free = 0.4389 target = 0.194831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.157948 restraints weight = 26150.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.162897 restraints weight = 16478.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.164586 restraints weight = 10149.744| |-----------------------------------------------------------------------------| r_work (final): 0.4047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 moved from start: 0.5119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22330 Z= 0.129 Angle : 0.619 14.469 30283 Z= 0.317 Chirality : 0.045 0.259 3480 Planarity : 0.005 0.064 3960 Dihedral : 7.804 89.903 3238 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.71 % Allowed : 22.64 % Favored : 73.65 % 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: -0.53 (0.16), residues: 2823 helix: 0.76 (0.16), residues: 1111 sheet: -0.57 (0.24), residues: 421 loop : -1.24 (0.17), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS E 179 PHE 0.035 0.001 PHE C 460 TYR 0.014 0.001 TYR B 461 ARG 0.007 0.000 ARG E 352 Details of bonding type rmsd hydrogen bonds : bond 0.04281 ( 985) hydrogen bonds : angle 5.03198 ( 2841) covalent geometry : bond 0.00295 (22330) covalent geometry : angle 0.61869 (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 371 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 285 time to evaluate : 2.580 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: 0.8619 (tm-30) cc_final: 0.7892 (tm-30) REVERT: A 245 MET cc_start: 0.5089 (ptp) cc_final: 0.4583 (mmm) REVERT: A 444 PHE cc_start: 0.6941 (m-80) cc_final: 0.6642 (m-80) REVERT: B 32 ILE cc_start: 0.7868 (OUTLIER) cc_final: 0.7517 (mm) REVERT: B 176 THR cc_start: 0.7968 (m) cc_final: 0.7741 (p) REVERT: B 349 PHE cc_start: 0.3794 (t80) cc_final: 0.3303 (t80) REVERT: C 415 ARG cc_start: 0.8174 (mtt90) cc_final: 0.7835 (mpt-90) REVERT: D 218 MET cc_start: 0.7977 (ptt) cc_final: 0.7711 (ptt) REVERT: D 235 MET cc_start: 0.7263 (mtt) cc_final: 0.6751 (mtp) REVERT: D 332 GLU cc_start: 0.7520 (mm-30) cc_final: 0.7306 (mm-30) REVERT: D 368 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.7588 (mmt180) REVERT: E 64 MET cc_start: 0.5371 (mmp) cc_final: 0.4632 (mmm) REVERT: E 268 LEU cc_start: 0.6699 (OUTLIER) cc_final: 0.6336 (mm) REVERT: E 369 LYS cc_start: 0.7374 (pttm) cc_final: 0.6515 (tptm) REVERT: F 154 ILE cc_start: 0.7885 (OUTLIER) cc_final: 0.7502 (mt) REVERT: F 191 ARG cc_start: 0.4802 (OUTLIER) cc_final: 0.2874 (tpp-160) REVERT: F 285 MET cc_start: 0.7403 (ttm) cc_final: 0.7088 (tpp) REVERT: F 402 ARG cc_start: 0.8296 (ttp-170) cc_final: 0.7926 (ttm-80) REVERT: F 404 ARG cc_start: 0.8225 (mmm-85) cc_final: 0.7986 (mmm-85) outliers start: 86 outliers final: 65 residues processed: 353 average time/residue: 0.3200 time to fit residues: 179.6328 Evaluate side-chains 339 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 269 time to evaluate : 2.369 ------------------------------------------------------------------------------- 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 406 THR Chi-restraints excluded: chain A residue 435 LEU 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 130 GLU Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 260 TYR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain C residue 48 MET 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 276 LEU Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 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 268 LEU Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 368 ARG Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 419 GLN Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 74 MET Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 174 ASN Chi-restraints excluded: chain E residue 197 ASP Chi-restraints excluded: chain E residue 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 384 ILE Chi-restraints excluded: chain E residue 447 HIS Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 52 LEU 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 193 ARG Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 248 LEU 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: 10.0000 chunk 20 optimal weight: 10.0000 chunk 258 optimal weight: 7.9990 chunk 142 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 chunk 188 optimal weight: 5.9990 chunk 250 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 141 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 198 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.189202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.152991 restraints weight = 26701.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.155652 restraints weight = 17830.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.156815 restraints weight = 12908.861| |-----------------------------------------------------------------------------| r_work (final): 0.3952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 moved from start: 0.5300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 22330 Z= 0.206 Angle : 0.705 14.212 30283 Z= 0.364 Chirality : 0.048 0.194 3480 Planarity : 0.006 0.060 3960 Dihedral : 8.068 88.129 3238 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 3.75 % Allowed : 22.94 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.83 (0.15), residues: 2823 helix: 0.57 (0.15), residues: 1109 sheet: -0.76 (0.25), residues: 417 loop : -1.45 (0.16), residues: 1297 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS B 474 PHE 0.026 0.002 PHE A 494 TYR 0.018 0.002 TYR C 240 ARG 0.006 0.001 ARG C 127 Details of bonding type rmsd hydrogen bonds : bond 0.05121 ( 985) hydrogen bonds : angle 5.26553 ( 2841) covalent geometry : bond 0.00498 (22330) covalent geometry : angle 0.70520 (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 369 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 282 time to evaluate : 2.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 GLN cc_start: 0.8720 (tm-30) cc_final: 0.7920 (tm-30) REVERT: A 245 MET cc_start: 0.5209 (ptp) cc_final: 0.4624 (mmm) REVERT: A 444 PHE cc_start: 0.7149 (m-80) cc_final: 0.6682 (m-80) REVERT: B 32 ILE cc_start: 0.7823 (OUTLIER) cc_final: 0.7481 (mm) REVERT: B 176 THR cc_start: 0.7994 (m) cc_final: 0.7730 (p) REVERT: B 406 THR cc_start: 0.8628 (p) cc_final: 0.8232 (t) REVERT: C 415 ARG cc_start: 0.8155 (mtt90) cc_final: 0.7825 (mpt-90) REVERT: D 218 MET cc_start: 0.7978 (ptt) cc_final: 0.7697 (ptt) REVERT: D 235 MET cc_start: 0.7318 (mtt) cc_final: 0.6743 (mtp) REVERT: D 271 MET cc_start: 0.7711 (mtm) cc_final: 0.7406 (mtt) REVERT: D 288 LEU cc_start: 0.7697 (tp) cc_final: 0.7290 (tp) REVERT: D 332 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7488 (mm-30) REVERT: D 368 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.6991 (tpp-160) REVERT: E 64 MET cc_start: 0.5377 (mmp) cc_final: 0.4591 (mmm) REVERT: E 268 LEU cc_start: 0.6725 (OUTLIER) cc_final: 0.6255 (mm) REVERT: F 154 ILE cc_start: 0.7954 (OUTLIER) cc_final: 0.7536 (mt) REVERT: F 191 ARG cc_start: 0.4857 (OUTLIER) cc_final: 0.2955 (tpp-160) REVERT: F 402 ARG cc_start: 0.8355 (ttp-170) cc_final: 0.8098 (ttm-80) outliers start: 87 outliers final: 74 residues processed: 348 average time/residue: 0.3091 time to fit residues: 171.6143 Evaluate side-chains 354 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 275 time to evaluate : 2.371 ------------------------------------------------------------------------------- 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 406 THR Chi-restraints excluded: chain A residue 435 LEU 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 123 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 198 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 321 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain C residue 48 MET 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 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 268 LEU Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 368 ARG Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 419 GLN Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 74 MET Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 174 ASN Chi-restraints excluded: chain E residue 197 ASP Chi-restraints excluded: chain E residue 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 384 ILE Chi-restraints excluded: chain E residue 447 HIS Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 18 PHE Chi-restraints excluded: chain F residue 52 LEU 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 193 ARG Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 304 GLN 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: 1.9990 chunk 78 optimal weight: 0.0030 chunk 246 optimal weight: 6.9990 chunk 126 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 27 optimal weight: 8.9990 chunk 125 optimal weight: 1.9990 chunk 47 optimal weight: 8.9990 chunk 3 optimal weight: 5.9990 chunk 242 optimal weight: 7.9990 overall best weight: 2.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 345 GLN ** D 217 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 = 0.4363 r_free = 0.4363 target = 0.191945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.154530 restraints weight = 26504.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.157825 restraints weight = 17201.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.159584 restraints weight = 11297.727| |-----------------------------------------------------------------------------| r_work (final): 0.3988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.5356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22330 Z= 0.149 Angle : 0.655 14.828 30283 Z= 0.335 Chirality : 0.046 0.205 3480 Planarity : 0.005 0.062 3960 Dihedral : 7.890 87.996 3238 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.62 % Allowed : 23.16 % Favored : 73.22 % 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: -0.69 (0.15), residues: 2823 helix: 0.68 (0.15), residues: 1110 sheet: -0.74 (0.24), residues: 419 loop : -1.35 (0.16), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS E 173 PHE 0.033 0.002 PHE C 460 TYR 0.017 0.002 TYR B 438 ARG 0.010 0.000 ARG C 476 Details of bonding type rmsd hydrogen bonds : bond 0.04532 ( 985) hydrogen bonds : angle 5.13897 ( 2841) covalent geometry : bond 0.00352 (22330) covalent geometry : angle 0.65509 (30283) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6949.62 seconds wall clock time: 120 minutes 51.89 seconds (7251.89 seconds total)