Starting phenix.real_space_refine on Wed Nov 20 15:22:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8spw_40688/11_2024/8spw_40688.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8spw_40688/11_2024/8spw_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8spw_40688/11_2024/8spw_40688.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8spw_40688/11_2024/8spw_40688.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8spw_40688/11_2024/8spw_40688.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8spw_40688/11_2024/8spw_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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 21960 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 3636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3636 Classifications: {'peptide': 474} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 451} Chain: "B" Number of atoms: 3644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3644 Classifications: {'peptide': 475} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 452} Chain: "C" Number of atoms: 3650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3650 Classifications: {'peptide': 476} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 453} Chain: "D" Number of atoms: 3623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3623 Classifications: {'peptide': 470} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 446} Chain: "E" Number of atoms: 3623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3623 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 446} Chain: "F" Number of atoms: 3623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3623 Classifications: {'peptide': 470} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 446} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 13.47, per 1000 atoms: 0.61 Number of scatterers: 21960 At special positions: 0 Unit cell: (112.56, 120.12, 126.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 67 16.00 P 15 15.00 Mg 5 11.99 O 4223 8.00 N 3820 7.00 C 13830 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.34 Conformation dependent library (CDL) restraints added in 3.8 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: 2.69 Creating SS restraints... Processing helix chain 'A' and resid 100 through 104 removed outlier: 3.866A pdb=" N LEU A 103 " --> pdb=" O GLY A 100 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE A 104 " --> pdb=" O GLU A 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 100 through 104' Processing helix chain 'A' and resid 150 through 157 Processing helix chain 'A' and resid 175 through 186 removed outlier: 3.878A pdb=" N ALA A 179 " --> pdb=" O LYS A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 215 removed outlier: 3.602A pdb=" N HIS A 215 " --> pdb=" O THR A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 219 removed outlier: 4.346A pdb=" N ASP A 219 " --> pdb=" O GLY A 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 216 through 219' Processing helix chain 'A' and resid 231 through 253 removed outlier: 3.737A pdb=" N LEU A 235 " --> pdb=" O PRO A 231 " (cutoff:3.500A) Proline residue: A 239 - end of helix removed outlier: 3.989A pdb=" N MET A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY A 246 " --> pdb=" O GLY A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 277 removed outlier: 3.596A pdb=" N LEU A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 299 Processing helix chain 'A' and resid 322 through 325 Processing helix chain 'A' and resid 328 through 338 Processing helix chain 'A' and resid 345 through 351 Processing helix chain 'A' and resid 372 through 397 removed outlier: 4.185A pdb=" N THR A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA A 394 " --> pdb=" O ARG A 390 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N PHE A 395 " --> pdb=" O GLU A 391 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLN A 397 " --> pdb=" O GLU A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 421 removed outlier: 3.570A pdb=" N LEU A 420 " --> pdb=" O THR A 416 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS A 421 " --> pdb=" O VAL A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 442 Processing helix chain 'A' and resid 449 through 451 No H-bonds generated for 'chain 'A' and resid 449 through 451' Processing helix chain 'A' and resid 452 through 467 removed outlier: 3.547A pdb=" N LYS A 458 " --> pdb=" O ARG A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 479 removed outlier: 3.989A pdb=" N LEU A 472 " --> pdb=" O GLY A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 498 removed outlier: 3.748A pdb=" N THR A 497 " --> pdb=" O ALA A 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 157 Processing helix chain 'B' and resid 174 through 186 Processing helix chain 'B' and resid 201 through 214 Processing helix chain 'B' and resid 215 through 220 removed outlier: 5.803A pdb=" N LEU B 218 " --> pdb=" O HIS B 215 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR B 220 " --> pdb=" O ALA B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 253 Proline residue: B 239 - end of helix removed outlier: 3.697A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 277 removed outlier: 4.157A pdb=" N GLN B 266 " --> pdb=" O ASP B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 299 Processing helix chain 'B' and resid 305 through 309 Processing helix chain 'B' and resid 328 through 336 Processing helix chain 'B' and resid 345 through 352 Processing helix chain 'B' and resid 372 through 379 Processing helix chain 'B' and resid 380 through 399 removed outlier: 4.499A pdb=" N LEU B 384 " --> pdb=" O GLY B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 421 removed outlier: 3.623A pdb=" N LYS B 421 " --> pdb=" O VAL B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 442 Processing helix chain 'B' and resid 444 through 448 removed outlier: 4.058A pdb=" N ASP B 447 " --> pdb=" O PHE B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 467 removed outlier: 4.271A pdb=" N ARG B 455 " --> pdb=" O GLU B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 479 removed outlier: 3.527A pdb=" N LEU B 472 " --> pdb=" O GLY B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 498 Processing helix chain 'C' and resid 100 through 104 Processing helix chain 'C' and resid 150 through 156 Processing helix chain 'C' and resid 174 through 186 Processing helix chain 'C' and resid 201 through 215 Processing helix chain 'C' and resid 231 through 252 Proline residue: C 239 - end of helix removed outlier: 3.671A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS C 252 " --> pdb=" O TYR C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 277 Processing helix chain 'C' and resid 289 through 300 removed outlier: 4.013A pdb=" N ARG C 300 " --> pdb=" O ARG C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 325 Processing helix chain 'C' and resid 328 through 336 Processing helix chain 'C' and resid 345 through 352 removed outlier: 3.662A pdb=" N GLY C 352 " --> pdb=" O LEU C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 379 Processing helix chain 'C' and resid 379 through 399 removed outlier: 3.827A pdb=" N ARG C 383 " --> pdb=" O ALA C 379 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LEU C 384 " --> pdb=" O GLY C 380 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA C 394 " --> pdb=" O ARG C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 420 Processing helix chain 'C' and resid 429 through 443 removed outlier: 3.639A pdb=" N GLY C 443 " --> pdb=" O ALA C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 447 removed outlier: 4.141A pdb=" N ASP C 447 " --> pdb=" O PHE C 444 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 444 through 447' Processing helix chain 'C' and resid 449 through 467 removed outlier: 4.243A pdb=" N ARG C 454 " --> pdb=" O VAL C 450 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ARG C 455 " --> pdb=" O GLU C 451 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS C 458 " --> pdb=" O ARG C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 479 removed outlier: 3.944A pdb=" N LEU C 472 " --> pdb=" O GLY C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 498 Processing helix chain 'D' and resid 88 through 92 Processing helix chain 'D' and resid 124 through 128 Processing helix chain 'D' and resid 139 through 146 Processing helix chain 'D' and resid 163 through 179 removed outlier: 3.719A pdb=" N LEU D 167 " --> pdb=" O GLY D 163 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU D 178 " --> pdb=" O ASN D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 206 Processing helix chain 'D' and resid 207 through 209 No H-bonds generated for 'chain 'D' and resid 207 through 209' Processing helix chain 'D' and resid 221 through 242 removed outlier: 3.843A pdb=" N ARG D 225 " --> pdb=" O PRO D 221 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ALA D 229 " --> pdb=" O ARG D 225 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N LEU D 230 " --> pdb=" O MET D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 269 removed outlier: 4.096A pdb=" N THR D 258 " --> pdb=" O ILE D 254 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU D 267 " --> pdb=" O GLU D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 292 removed outlier: 3.687A pdb=" N ILE D 292 " --> pdb=" O LEU D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 323 removed outlier: 3.993A pdb=" N SER D 323 " --> pdb=" O ALA D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 339 Processing helix chain 'D' and resid 355 through 360 Processing helix chain 'D' and resid 360 through 388 removed outlier: 4.289A pdb=" N ASP D 382 " --> pdb=" O LYS D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 410 removed outlier: 3.692A pdb=" N ARG D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU D 410 " --> pdb=" O ILE D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 422 removed outlier: 4.161A pdb=" N PHE D 420 " --> pdb=" O VAL D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 442 Processing helix chain 'D' and resid 450 through 454 Processing helix chain 'D' and resid 458 through 470 Processing helix chain 'E' and resid 88 through 92 removed outlier: 3.584A pdb=" N THR E 91 " --> pdb=" O GLY E 88 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU E 92 " --> pdb=" O GLU E 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 88 through 92' Processing helix chain 'E' and resid 139 through 146 Processing helix chain 'E' and resid 163 through 179 Processing helix chain 'E' and resid 191 through 205 Processing helix chain 'E' and resid 207 through 209 No H-bonds generated for 'chain 'E' and resid 207 through 209' Processing helix chain 'E' and resid 221 through 243 removed outlier: 3.600A pdb=" N ARG E 225 " --> pdb=" O PRO E 221 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ALA E 229 " --> pdb=" O ARG E 225 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LEU E 230 " --> pdb=" O MET E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 269 Processing helix chain 'E' and resid 281 through 291 Processing helix chain 'E' and resid 315 through 323 Processing helix chain 'E' and resid 332 through 338 Processing helix chain 'E' and resid 355 through 360 Processing helix chain 'E' and resid 360 through 388 removed outlier: 4.365A pdb=" N ASP E 382 " --> pdb=" O LYS E 378 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ILE E 383 " --> pdb=" O GLU E 379 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE E 386 " --> pdb=" O ASP E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 393 through 410 removed outlier: 3.758A pdb=" N ARG E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 416 No H-bonds generated for 'chain 'E' and resid 414 through 416' Processing helix chain 'E' and resid 417 through 422 Processing helix chain 'E' and resid 429 through 443 Processing helix chain 'E' and resid 449 through 454 Processing helix chain 'E' and resid 458 through 470 Processing helix chain 'F' and resid 124 through 128 removed outlier: 3.533A pdb=" N LEU F 128 " --> pdb=" O PHE F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 145 Processing helix chain 'F' and resid 163 through 178 Processing helix chain 'F' and resid 193 through 205 removed outlier: 4.000A pdb=" N ASP F 197 " --> pdb=" O ARG F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 210 Processing helix chain 'F' and resid 221 through 242 removed outlier: 5.140A pdb=" N ALA F 229 " --> pdb=" O ARG F 225 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LEU F 230 " --> pdb=" O MET F 226 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA F 236 " --> pdb=" O GLY F 232 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE F 239 " --> pdb=" O MET F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 269 removed outlier: 3.936A pdb=" N THR F 258 " --> pdb=" O ILE F 254 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLU F 263 " --> pdb=" O GLN F 259 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA F 266 " --> pdb=" O SER F 262 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLY F 269 " --> pdb=" O SER F 265 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 290 removed outlier: 3.709A pdb=" N LEU F 288 " --> pdb=" O GLU F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 315 through 325 removed outlier: 3.908A pdb=" N HIS F 324 " --> pdb=" O THR F 320 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU F 325 " --> pdb=" O THR F 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 338 removed outlier: 3.647A pdb=" N MET F 338 " --> pdb=" O LYS F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 360 through 387 removed outlier: 3.554A pdb=" N ILE F 386 " --> pdb=" O ASP F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 410 removed outlier: 3.719A pdb=" N VAL F 399 " --> pdb=" O GLU F 395 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL F 400 " --> pdb=" O ASP F 396 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG F 405 " --> pdb=" O HIS F 401 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU F 410 " --> pdb=" O ILE F 406 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 420 removed outlier: 3.715A pdb=" N GLN F 419 " --> pdb=" O VAL F 416 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 443 removed outlier: 3.942A pdb=" N GLU F 439 " --> pdb=" O ARG F 435 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE F 440 " --> pdb=" O GLY F 436 " (cutoff:3.500A) Processing helix chain 'F' and resid 449 through 453 Processing helix chain 'F' and resid 458 through 469 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 35 removed outlier: 6.230A pdb=" N ARG A 40 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N VAL A 34 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL A 74 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N ALA A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY A 29 " --> pdb=" O VAL A 88 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 99 Processing sheet with id=AA3, first strand: chain 'A' and resid 107 through 108 removed outlier: 3.952A pdb=" N ILE A 222 " --> pdb=" O SER A 193 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ILE A 192 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N VAL A 259 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE A 194 " --> pdb=" O VAL A 259 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TYR A 260 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL A 363 " --> pdb=" O GLN A 341 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 28 through 33 removed outlier: 6.419A pdb=" N ARG B 40 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N VAL B 74 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N ALA B 63 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU B 76 " --> pdb=" O GLY B 61 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N GLY B 61 " --> pdb=" O LEU B 76 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 96 through 99 Processing sheet with id=AA6, first strand: chain 'B' and resid 107 through 108 removed outlier: 6.137A pdb=" N VAL B 108 " --> pdb=" O THR B 225 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 318 through 321 removed outlier: 6.704A pdb=" N ILE B 167 " --> pdb=" O VAL B 319 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N THR B 321 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N GLY B 169 " --> pdb=" O THR B 321 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASP B 170 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 28 through 31 removed outlier: 6.703A pdb=" N VAL C 74 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N ALA C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLU C 51 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N LEU C 52 " --> pdb=" O THR C 91 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 96 through 99 Processing sheet with id=AB1, first strand: chain 'C' and resid 107 through 108 removed outlier: 3.503A pdb=" N TYR C 260 " --> pdb=" O LEU C 316 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 318 through 320 removed outlier: 6.748A pdb=" N ILE C 167 " --> pdb=" O VAL C 319 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 3 through 10 removed outlier: 6.723A pdb=" N ASP D 15 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N VAL D 9 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL D 13 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N THR D 58 " --> pdb=" O HIS D 53 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N HIS D 53 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ARG D 60 " --> pdb=" O ALA D 51 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE D 44 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N GLN D 33 " --> pdb=" O GLU D 75 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLU D 75 " --> pdb=" O GLN D 33 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 84 through 86 Processing sheet with id=AB5, first strand: chain 'D' and resid 95 through 96 removed outlier: 6.822A pdb=" N PHE D 96 " --> pdb=" O PHE D 215 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N SER D 183 " --> pdb=" O ALA D 212 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N VAL D 214 " --> pdb=" O SER D 183 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N PHE D 185 " --> pdb=" O VAL D 214 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N GLY D 216 " --> pdb=" O PHE D 185 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N GLY D 187 " --> pdb=" O GLY D 216 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE D 182 " --> pdb=" O LEU D 248 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N PHE D 250 " --> pdb=" O ILE D 182 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL D 184 " --> pdb=" O PHE D 250 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N ASP D 252 " --> pdb=" O VAL D 184 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ALA D 186 " --> pdb=" O ASP D 252 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N VAL D 247 " --> pdb=" O THR D 301 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N ILE D 303 " --> pdb=" O VAL D 247 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU D 249 " --> pdb=" O ILE D 303 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N ALA D 305 " --> pdb=" O LEU D 249 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N ILE D 251 " --> pdb=" O ALA D 305 " (cutoff:3.500A) removed outlier: 8.777A pdb=" N TYR D 307 " --> pdb=" O ILE D 251 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE D 154 " --> pdb=" O GLN D 304 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ILE D 306 " --> pdb=" O ILE D 154 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU D 156 " --> pdb=" O ILE D 306 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 4 through 10 removed outlier: 5.928A pdb=" N VAL E 6 " --> pdb=" O LYS E 17 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N LYS E 17 " --> pdb=" O VAL E 6 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN E 8 " --> pdb=" O ASP E 15 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N VAL E 13 " --> pdb=" O MET E 10 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N THR E 58 " --> pdb=" O HIS E 53 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N HIS E 53 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ARG E 60 " --> pdb=" O ALA E 51 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N GLN E 33 " --> pdb=" O GLU E 75 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLU E 75 " --> pdb=" O GLN E 33 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 84 through 87 removed outlier: 3.704A pdb=" N ARG E 114 " --> pdb=" O VAL E 87 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 95 through 96 removed outlier: 6.122A pdb=" N PHE E 96 " --> pdb=" O PHE E 215 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N GLN E 217 " --> pdb=" O PHE E 96 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL E 184 " --> pdb=" O PHE E 250 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA E 305 " --> pdb=" O ILE E 251 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE E 154 " --> pdb=" O GLN E 304 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ILE E 306 " --> pdb=" O ILE E 154 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N LEU E 156 " --> pdb=" O ILE E 306 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LYS E 153 " --> pdb=" O ALA E 327 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N THR E 329 " --> pdb=" O LYS E 153 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N GLY E 155 " --> pdb=" O THR E 329 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N LEU E 331 " --> pdb=" O GLY E 155 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N PHE E 157 " --> pdb=" O LEU E 331 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 134 through 135 removed outlier: 4.258A pdb=" N TYR E 148 " --> pdb=" O LEU E 135 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 3 through 5 removed outlier: 5.891A pdb=" N GLU F 75 " --> pdb=" O GLN F 33 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N GLN F 33 " --> pdb=" O GLU F 75 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ARG F 60 " --> pdb=" O ALA F 51 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 84 through 86 Processing sheet with id=AC3, first strand: chain 'F' and resid 134 through 135 removed outlier: 4.591A pdb=" N TYR F 148 " --> pdb=" O LEU F 135 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 304 through 306 Processing sheet with id=AC5, first strand: chain 'F' and resid 183 through 184 985 hydrogen bonds defined for protein. 2841 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.53 Time building geometry restraints manager: 7.06 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: 0.700 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: 0.010 Extract box with map and model: 0.880 Check model and map are aligned: 0.160 Set scattering table: 0.160 Process input model: 51.120 Find NCS groups from input model: 1.370 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6530 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 22330 Z= 0.227 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 *********************** 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 : 2.526 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: 0.3483 time to fit residues: 311.0896 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 : 1.817 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6653 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= 0.206 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 *********************** 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 : 2.651 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: 0.5859 (OUTLIER) cc_final: 0.5517 (ttm) REVERT: A 444 PHE cc_start: 0.6275 (m-80) cc_final: 0.6035 (m-80) REVERT: B 406 THR cc_start: 0.8252 (OUTLIER) cc_final: 0.8012 (t) REVERT: B 438 TYR cc_start: 0.7626 (t80) cc_final: 0.7312 (t80) REVERT: D 235 MET cc_start: 0.6545 (mtt) cc_final: 0.6225 (mtp) REVERT: D 271 MET cc_start: 0.6665 (mtt) cc_final: 0.6261 (mtt) REVERT: E 126 GLU cc_start: 0.5614 (pm20) cc_final: 0.5163 (pm20) REVERT: E 202 MET cc_start: 0.5677 (mmt) cc_final: 0.3902 (mtp) REVERT: F 235 MET cc_start: 0.6231 (mmt) cc_final: 0.6016 (mmt) REVERT: F 253 ASN cc_start: 0.4729 (OUTLIER) cc_final: 0.4290 (p0) REVERT: F 256 ARG cc_start: 0.4934 (OUTLIER) cc_final: 0.4533 (mtm-85) REVERT: F 264 VAL cc_start: 0.3041 (t) cc_final: 0.2472 (t) REVERT: F 404 ARG cc_start: 0.7881 (mmm-85) cc_final: 0.7461 (tpp80) outliers start: 70 outliers final: 38 residues processed: 411 average time/residue: 0.3396 time to fit residues: 214.0199 Evaluate side-chains 341 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 299 time to evaluate : 2.471 ------------------------------------------------------------------------------- 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 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 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 142 optimal weight: 7.9990 chunk 79 optimal weight: 3.9990 chunk 213 optimal weight: 8.9990 chunk 174 optimal weight: 9.9990 chunk 70 optimal weight: 5.9990 chunk 256 optimal weight: 10.0000 chunk 277 optimal weight: 10.0000 chunk 228 optimal weight: 9.9990 chunk 254 optimal weight: 7.9990 chunk 87 optimal weight: 3.9990 chunk 205 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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 358 ASN A 474 HIS B 185 ASN ** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 ASN C 294 HIS C 333 ASN C 425 HIS D 22 HIS D 219 ASN ** E 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 259 GLN F 169 GLN ** F 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 324 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7026 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 22330 Z= 0.476 Angle : 0.799 8.853 30283 Z= 0.426 Chirality : 0.053 0.255 3480 Planarity : 0.007 0.071 3960 Dihedral : 9.107 114.228 3244 Min Nonbonded Distance : 1.700 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 5.82 % Allowed : 16.00 % Favored : 78.18 % 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: -0.80 (0.15), residues: 2823 helix: 0.29 (0.15), residues: 1111 sheet: -0.32 (0.24), residues: 438 loop : -1.30 (0.16), residues: 1274 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS A 255 PHE 0.058 0.003 PHE E 414 TYR 0.028 0.003 TYR A 329 ARG 0.007 0.001 ARG D 256 *********************** 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 455 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 320 time to evaluate : 2.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 32 ILE cc_start: 0.8083 (OUTLIER) cc_final: 0.7799 (mm) REVERT: B 406 THR cc_start: 0.8327 (OUTLIER) cc_final: 0.8038 (t) REVERT: D 271 MET cc_start: 0.6851 (mtt) cc_final: 0.6507 (mtt) REVERT: D 368 ARG cc_start: 0.8004 (OUTLIER) cc_final: 0.7248 (tpp-160) REVERT: E 259 GLN cc_start: 0.7334 (OUTLIER) cc_final: 0.6411 (mp-120) REVERT: E 268 LEU cc_start: 0.6526 (OUTLIER) cc_final: 0.6064 (mm) REVERT: E 328 THR cc_start: 0.7996 (OUTLIER) cc_final: 0.7673 (p) REVERT: E 469 MET cc_start: 0.5854 (ttm) cc_final: 0.5512 (ttm) REVERT: F 48 LEU cc_start: 0.6803 (OUTLIER) cc_final: 0.6568 (mt) REVERT: F 191 ARG cc_start: 0.5392 (OUTLIER) cc_final: 0.2656 (mmm160) REVERT: F 201 GLU cc_start: 0.5918 (OUTLIER) cc_final: 0.5531 (mm-30) outliers start: 135 outliers final: 81 residues processed: 426 average time/residue: 0.3223 time to fit residues: 212.8414 Evaluate side-chains 365 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 275 time to evaluate : 2.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ILE 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 410 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 166 LEU Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 200 GLN Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 236 PHE Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 294 HIS Chi-restraints excluded: chain C residue 406 THR Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 34 HIS Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 70 LEU 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 322 PHE Chi-restraints excluded: chain D residue 368 ARG Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 419 GLN Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 205 SER 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 328 THR 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 47 THR Chi-restraints excluded: chain F residue 48 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 162 VAL Chi-restraints excluded: chain F residue 191 ARG Chi-restraints excluded: chain F residue 201 GLU Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 251 ILE Chi-restraints excluded: chain F residue 253 ASN Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 456 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 253 optimal weight: 8.9990 chunk 192 optimal weight: 10.0000 chunk 133 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 172 optimal weight: 7.9990 chunk 257 optimal weight: 1.9990 chunk 272 optimal weight: 10.0000 chunk 134 optimal weight: 5.9990 chunk 244 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 HIS B 474 HIS ** C 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 330 ASN E 173 HIS ** E 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 253 ASN ** F 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 407 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 moved from start: 0.4096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 22330 Z= 0.281 Angle : 0.642 8.855 30283 Z= 0.342 Chirality : 0.047 0.267 3480 Planarity : 0.005 0.053 3960 Dihedral : 8.540 92.979 3239 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 5.13 % Allowed : 18.54 % Favored : 76.33 % 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: -0.65 (0.15), residues: 2823 helix: 0.52 (0.15), residues: 1101 sheet: -0.38 (0.24), residues: 431 loop : -1.25 (0.17), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.027 0.001 HIS C 294 PHE 0.022 0.002 PHE C 494 TYR 0.015 0.002 TYR B 438 ARG 0.017 0.001 ARG C 127 *********************** 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 421 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 302 time to evaluate : 2.477 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 150 ILE cc_start: 0.7440 (OUTLIER) cc_final: 0.7133 (mt) REVERT: A 245 MET cc_start: 0.6232 (mmm) cc_final: 0.5280 (ptt) REVERT: C 198 ILE cc_start: 0.5487 (OUTLIER) cc_final: 0.5138 (mt) REVERT: D 235 MET cc_start: 0.6635 (mtt) cc_final: 0.6330 (mtp) REVERT: D 271 MET cc_start: 0.6751 (mtt) cc_final: 0.6403 (mtt) REVERT: E 268 LEU cc_start: 0.6591 (OUTLIER) cc_final: 0.6171 (mm) REVERT: E 285 MET cc_start: 0.8206 (tpp) cc_final: 0.7814 (tpp) REVERT: E 469 MET cc_start: 0.5839 (ttm) cc_final: 0.5580 (mtt) REVERT: F 191 ARG cc_start: 0.5381 (OUTLIER) cc_final: 0.2718 (mmm160) REVERT: F 201 GLU cc_start: 0.6044 (OUTLIER) cc_final: 0.5765 (mm-30) REVERT: F 404 ARG cc_start: 0.7817 (mmm-85) cc_final: 0.7387 (tpp80) outliers start: 119 outliers final: 83 residues processed: 401 average time/residue: 0.3227 time to fit residues: 203.0492 Evaluate side-chains 351 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 263 time to evaluate : 2.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 150 ILE 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 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 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 198 ILE Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 260 TYR Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 200 GLN Chi-restraints excluded: chain C residue 236 PHE Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 406 THR Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 34 HIS Chi-restraints excluded: chain D residue 70 LEU 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 219 ASN Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 251 ILE 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 322 PHE Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 419 GLN Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 197 ASP Chi-restraints excluded: chain E residue 205 SER 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 374 LEU 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 66 SER Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 191 ARG Chi-restraints excluded: chain F residue 193 ARG Chi-restraints excluded: chain F residue 201 GLU Chi-restraints excluded: chain F residue 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 306 ILE Chi-restraints excluded: chain F residue 321 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 227 optimal weight: 0.0370 chunk 154 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 202 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 chunk 232 optimal weight: 10.0000 chunk 188 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 139 optimal weight: 5.9990 chunk 244 optimal weight: 7.9990 chunk 68 optimal weight: 4.9990 overall best weight: 2.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 GLN A 474 HIS ** C 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 294 HIS D 330 ASN E 259 GLN ** F 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6925 moved from start: 0.4319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22330 Z= 0.210 Angle : 0.598 9.772 30283 Z= 0.313 Chirality : 0.045 0.202 3480 Planarity : 0.005 0.060 3960 Dihedral : 8.164 87.965 3239 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 4.36 % Allowed : 20.31 % Favored : 75.33 % 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: -0.52 (0.15), residues: 2823 helix: 0.68 (0.15), residues: 1110 sheet: -0.38 (0.25), residues: 426 loop : -1.22 (0.17), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 294 PHE 0.034 0.002 PHE C 460 TYR 0.017 0.001 TYR B 438 ARG 0.005 0.000 ARG A 278 *********************** 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 390 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 289 time to evaluate : 2.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 250 MET cc_start: 0.5914 (tpt) cc_final: 0.5641 (tpt) REVERT: D 64 MET cc_start: 0.6118 (mmm) cc_final: 0.5445 (mmp) REVERT: D 235 MET cc_start: 0.6586 (mtt) cc_final: 0.6287 (mtp) REVERT: D 368 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.7323 (tpp-160) REVERT: E 268 LEU cc_start: 0.6577 (OUTLIER) cc_final: 0.6248 (mm) REVERT: E 369 LYS cc_start: 0.6670 (pttm) cc_final: 0.6321 (tttp) REVERT: E 469 MET cc_start: 0.5840 (ttm) cc_final: 0.5602 (mtt) REVERT: F 191 ARG cc_start: 0.5546 (OUTLIER) cc_final: 0.2663 (mmm160) REVERT: F 285 MET cc_start: 0.7579 (ttm) cc_final: 0.7021 (tpp) REVERT: F 404 ARG cc_start: 0.7830 (mmm-85) cc_final: 0.7368 (tpp80) outliers start: 101 outliers final: 75 residues processed: 369 average time/residue: 0.3335 time to fit residues: 192.6910 Evaluate side-chains 340 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 262 time to evaluate : 2.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 372 ILE Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 467 ASN 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 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 319 VAL 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 C residue 48 MET Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 200 GLN Chi-restraints excluded: chain C residue 236 PHE Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 294 HIS Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 34 HIS Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 77 ILE 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 219 ASN Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 359 VAL 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 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 132 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 197 ASP Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 259 GLN Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 411 SER Chi-restraints excluded: chain E residue 423 GLN Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 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 247 VAL Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain F residue 406 ILE Chi-restraints excluded: chain F residue 437 PHE Chi-restraints excluded: chain F residue 456 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 91 optimal weight: 20.0000 chunk 245 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 160 optimal weight: 6.9990 chunk 67 optimal weight: 7.9990 chunk 272 optimal weight: 7.9990 chunk 226 optimal weight: 5.9990 chunk 126 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 90 optimal weight: 10.0000 chunk 143 optimal weight: 7.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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 474 HIS B 294 HIS ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 330 ASN ** E 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 259 GLN ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.4940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.079 22330 Z= 0.514 Angle : 0.802 9.829 30283 Z= 0.428 Chirality : 0.053 0.211 3480 Planarity : 0.007 0.058 3960 Dihedral : 8.817 89.887 3239 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 6.60 % Allowed : 19.32 % Favored : 74.08 % 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: -1.27 (0.15), residues: 2823 helix: 0.12 (0.15), residues: 1098 sheet: -0.85 (0.25), residues: 420 loop : -1.66 (0.16), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.025 0.002 HIS C 294 PHE 0.030 0.003 PHE A 494 TYR 0.030 0.003 TYR B 240 ARG 0.007 0.001 ARG D 270 *********************** 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 444 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 291 time to evaluate : 2.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 250 MET cc_start: 0.5972 (tpt) cc_final: 0.5737 (tpt) REVERT: B 406 THR cc_start: 0.8434 (OUTLIER) cc_final: 0.8034 (t) REVERT: C 198 ILE cc_start: 0.5720 (OUTLIER) cc_final: 0.5428 (mt) REVERT: C 361 LEU cc_start: 0.7661 (OUTLIER) cc_final: 0.7424 (tp) REVERT: D 235 MET cc_start: 0.6737 (mtt) cc_final: 0.6336 (mtp) REVERT: D 368 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.7642 (tpp-160) REVERT: E 268 LEU cc_start: 0.6671 (OUTLIER) cc_final: 0.6153 (mm) REVERT: E 469 MET cc_start: 0.5902 (ttm) cc_final: 0.5553 (ttm) REVERT: F 48 LEU cc_start: 0.6942 (OUTLIER) cc_final: 0.6715 (mt) REVERT: F 191 ARG cc_start: 0.5395 (OUTLIER) cc_final: 0.3343 (tpp-160) outliers start: 153 outliers final: 113 residues processed: 411 average time/residue: 0.3333 time to fit residues: 216.4064 Evaluate side-chains 384 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 264 time to evaluate : 2.532 ------------------------------------------------------------------------------- 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 115 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 182 THR 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 62 MET 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 204 THR Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 260 TYR Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 319 VAL 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 406 THR Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 200 GLN Chi-restraints excluded: chain C residue 236 PHE Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 294 HIS Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 406 THR Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 34 HIS Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 251 ILE 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 322 PHE 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 434 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 74 MET Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 174 ASN Chi-restraints excluded: chain E residue 177 GLN 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 268 LEU Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 374 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 48 LEU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 191 ARG Chi-restraints excluded: chain F residue 193 ARG Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 251 ILE Chi-restraints excluded: chain F residue 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 433 THR 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 263 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 155 optimal weight: 0.9980 chunk 199 optimal weight: 6.9990 chunk 154 optimal weight: 3.9990 chunk 229 optimal weight: 6.9990 chunk 152 optimal weight: 7.9990 chunk 271 optimal weight: 5.9990 chunk 170 optimal weight: 0.2980 chunk 165 optimal weight: 3.9990 chunk 125 optimal weight: 0.9980 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 294 HIS C 345 GLN E 174 ASN E 177 GLN E 412 GLN ** F 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6912 moved from start: 0.4952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22330 Z= 0.178 Angle : 0.619 12.229 30283 Z= 0.320 Chirality : 0.045 0.250 3480 Planarity : 0.005 0.063 3960 Dihedral : 8.019 88.938 3238 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.06 % Allowed : 23.33 % Favored : 73.61 % 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: -0.72 (0.15), residues: 2823 helix: 0.60 (0.15), residues: 1112 sheet: -0.71 (0.24), residues: 418 loop : -1.33 (0.16), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS C 294 PHE 0.032 0.001 PHE C 460 TYR 0.021 0.001 TYR B 461 ARG 0.009 0.001 ARG A 278 *********************** 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 352 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 281 time to evaluate : 2.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 GLN cc_start: 0.8363 (tm-30) cc_final: 0.7968 (tm-30) REVERT: B 176 THR cc_start: 0.8257 (m) cc_final: 0.8050 (p) REVERT: C 95 MET cc_start: 0.5743 (tpp) cc_final: 0.5532 (mmm) REVERT: D 235 MET cc_start: 0.6617 (mtt) cc_final: 0.6344 (mtp) REVERT: D 368 ARG cc_start: 0.7979 (OUTLIER) cc_final: 0.7288 (tpp-160) REVERT: E 469 MET cc_start: 0.5883 (ttm) cc_final: 0.5630 (mtt) REVERT: F 191 ARG cc_start: 0.5261 (OUTLIER) cc_final: 0.3226 (tpp-160) REVERT: F 404 ARG cc_start: 0.7842 (mmm-85) cc_final: 0.7465 (mmm-85) outliers start: 71 outliers final: 54 residues processed: 338 average time/residue: 0.3480 time to fit residues: 185.4669 Evaluate side-chains 308 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 252 time to evaluate : 2.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 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 130 GLU Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 200 GLN Chi-restraints excluded: chain C residue 236 PHE Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 34 HIS Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 368 ARG Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 174 ASN Chi-restraints excluded: chain E residue 197 ASP Chi-restraints excluded: chain E residue 259 GLN Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 384 ILE 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 228 VAL Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 406 ILE Chi-restraints excluded: chain F residue 437 PHE Chi-restraints excluded: chain F residue 456 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 168 optimal weight: 9.9990 chunk 108 optimal weight: 2.9990 chunk 162 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 chunk 52 optimal weight: 9.9990 chunk 172 optimal weight: 0.0980 chunk 185 optimal weight: 10.0000 chunk 134 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 213 optimal weight: 5.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 HIS D 365 GLN F 119 HIS ** F 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.5083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 22330 Z= 0.244 Angle : 0.641 13.166 30283 Z= 0.329 Chirality : 0.046 0.203 3480 Planarity : 0.005 0.062 3960 Dihedral : 7.980 88.587 3238 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 3.49 % Allowed : 23.50 % Favored : 73.01 % 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: -0.73 (0.15), residues: 2823 helix: 0.58 (0.15), residues: 1112 sheet: -0.70 (0.24), residues: 423 loop : -1.33 (0.17), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 415 PHE 0.031 0.002 PHE A 494 TYR 0.014 0.002 TYR B 461 ARG 0.008 0.000 ARG E 3 *********************** 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 351 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 270 time to evaluate : 2.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 GLN cc_start: 0.8339 (tm-30) cc_final: 0.7901 (tm-30) REVERT: A 245 MET cc_start: 0.6095 (mmm) cc_final: 0.5387 (ptt) REVERT: B 176 THR cc_start: 0.8277 (m) cc_final: 0.8054 (p) REVERT: D 235 MET cc_start: 0.6690 (mtt) cc_final: 0.6360 (mtp) REVERT: D 368 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.7440 (tpp-160) REVERT: D 450 GLU cc_start: 0.5312 (mm-30) cc_final: 0.5029 (mm-30) REVERT: E 174 ASN cc_start: 0.6156 (OUTLIER) cc_final: 0.5953 (m-40) REVERT: E 469 MET cc_start: 0.5867 (ttm) cc_final: 0.5589 (ttm) REVERT: F 191 ARG cc_start: 0.5268 (OUTLIER) cc_final: 0.3245 (tpp-160) REVERT: F 404 ARG cc_start: 0.7896 (mmm-85) cc_final: 0.7533 (mmm-85) outliers start: 81 outliers final: 63 residues processed: 330 average time/residue: 0.3277 time to fit residues: 171.8882 Evaluate side-chains 325 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 259 time to evaluate : 2.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 260 TYR Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 200 GLN Chi-restraints excluded: chain C residue 236 PHE Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 34 HIS Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 368 ARG Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 74 MET 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 262 SER Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 384 ILE Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 191 ARG Chi-restraints excluded: chain F residue 193 ARG Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 304 GLN Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 437 PHE 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 247 optimal weight: 0.8980 chunk 260 optimal weight: 0.2980 chunk 237 optimal weight: 8.9990 chunk 253 optimal weight: 6.9990 chunk 152 optimal weight: 9.9990 chunk 110 optimal weight: 0.7980 chunk 198 optimal weight: 6.9990 chunk 77 optimal weight: 0.7980 chunk 228 optimal weight: 8.9990 chunk 239 optimal weight: 8.9990 chunk 252 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 GLN D 217 GLN E 412 GLN F 253 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 moved from start: 0.5173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 22330 Z= 0.168 Angle : 0.603 13.735 30283 Z= 0.305 Chirality : 0.044 0.213 3480 Planarity : 0.005 0.064 3960 Dihedral : 7.639 89.943 3238 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.98 % Allowed : 24.36 % Favored : 72.66 % 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: -0.49 (0.16), residues: 2823 helix: 0.77 (0.16), residues: 1108 sheet: -0.52 (0.24), residues: 428 loop : -1.19 (0.17), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS A 470 PHE 0.034 0.001 PHE C 460 TYR 0.013 0.001 TYR B 461 ARG 0.008 0.000 ARG A 278 *********************** 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 337 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 268 time to evaluate : 2.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 GLN cc_start: 0.8281 (tm-30) cc_final: 0.7884 (tm-30) REVERT: A 250 MET cc_start: 0.5804 (ttp) cc_final: 0.5415 (mtp) REVERT: D 235 MET cc_start: 0.6645 (mtt) cc_final: 0.6337 (mtp) REVERT: D 368 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.7550 (mmt180) REVERT: E 469 MET cc_start: 0.5858 (ttm) cc_final: 0.5634 (mtt) REVERT: F 191 ARG cc_start: 0.5089 (OUTLIER) cc_final: 0.3052 (tpp-160) REVERT: F 253 ASN cc_start: 0.4915 (OUTLIER) cc_final: 0.4579 (p0) REVERT: F 404 ARG cc_start: 0.7830 (mmm-85) cc_final: 0.7465 (mmm-85) outliers start: 69 outliers final: 52 residues processed: 325 average time/residue: 0.3370 time to fit residues: 172.0211 Evaluate side-chains 309 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 254 time to evaluate : 2.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 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 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 381 THR 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 173 THR Chi-restraints excluded: chain C residue 200 GLN Chi-restraints excluded: chain C residue 236 PHE Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 34 HIS Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 368 ARG Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 197 ASP Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 384 ILE 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 99 LEU Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 191 ARG Chi-restraints excluded: chain F residue 193 ARG Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 253 ASN Chi-restraints excluded: chain F residue 304 GLN Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 437 PHE Chi-restraints excluded: chain F residue 456 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 166 optimal weight: 0.8980 chunk 267 optimal weight: 2.9990 chunk 163 optimal weight: 0.9990 chunk 127 optimal weight: 7.9990 chunk 186 optimal weight: 20.0000 chunk 280 optimal weight: 9.9990 chunk 258 optimal weight: 7.9990 chunk 223 optimal weight: 9.9990 chunk 23 optimal weight: 0.9990 chunk 172 optimal weight: 1.9990 chunk 137 optimal weight: 6.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 GLN ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 ASN F 253 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 moved from start: 0.5188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.250 22330 Z= 0.288 Angle : 0.756 59.197 30283 Z= 0.417 Chirality : 0.046 0.308 3480 Planarity : 0.005 0.064 3960 Dihedral : 7.579 89.937 3236 Min Nonbonded Distance : 1.667 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.67 % Allowed : 25.05 % Favored : 72.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.16), residues: 2823 helix: 0.77 (0.16), residues: 1108 sheet: -0.48 (0.24), residues: 428 loop : -1.19 (0.17), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS A 470 PHE 0.054 0.002 PHE D 408 TYR 0.014 0.001 TYR A 461 ARG 0.064 0.001 ARG F 115 ********************** 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 316 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 254 time to evaluate : 2.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 GLN cc_start: 0.8303 (tm-30) cc_final: 0.7886 (tm-30) REVERT: A 250 MET cc_start: 0.5806 (ttp) cc_final: 0.5433 (mtp) REVERT: B 406 THR cc_start: 0.8308 (OUTLIER) cc_final: 0.7862 (t) REVERT: D 235 MET cc_start: 0.6645 (mtt) cc_final: 0.6348 (mtp) REVERT: D 368 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.7552 (mmt180) REVERT: E 3 ARG cc_start: 0.7550 (mmm-85) cc_final: 0.7176 (mmt90) REVERT: E 469 MET cc_start: 0.5845 (ttm) cc_final: 0.5558 (ttm) REVERT: F 191 ARG cc_start: 0.5089 (OUTLIER) cc_final: 0.3062 (tpp-160) REVERT: F 404 ARG cc_start: 0.7833 (mmm-85) cc_final: 0.7474 (mmm-85) outliers start: 62 outliers final: 55 residues processed: 306 average time/residue: 0.3319 time to fit residues: 160.9919 Evaluate side-chains 306 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 248 time to evaluate : 2.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 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 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 406 THR 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 173 THR Chi-restraints excluded: chain C residue 200 GLN Chi-restraints excluded: chain C residue 236 PHE Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 34 HIS Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 368 ARG Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain D residue 413 ASN Chi-restraints excluded: chain D residue 416 VAL 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 171 LEU Chi-restraints excluded: chain E residue 197 ASP Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 384 ILE Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 191 ARG Chi-restraints excluded: chain F residue 193 ARG Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 237 GLU Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 437 PHE Chi-restraints excluded: chain F residue 456 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 177 optimal weight: 4.9990 chunk 238 optimal weight: 20.0000 chunk 68 optimal weight: 0.8980 chunk 206 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 chunk 62 optimal weight: 0.8980 chunk 224 optimal weight: 0.5980 chunk 93 optimal weight: 8.9990 chunk 230 optimal weight: 40.0000 chunk 28 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 GLN ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.195195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.157845 restraints weight = 26298.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.161722 restraints weight = 15723.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.164472 restraints weight = 11241.044| |-----------------------------------------------------------------------------| r_work (final): 0.4037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6923 moved from start: 0.5192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.197 22330 Z= 0.296 Angle : 0.845 59.200 30283 Z= 0.484 Chirality : 0.047 0.655 3480 Planarity : 0.005 0.064 3960 Dihedral : 7.590 89.931 3236 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.02 % Allowed : 24.62 % Favored : 72.36 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.48 (0.16), residues: 2823 helix: 0.77 (0.16), residues: 1108 sheet: -0.48 (0.24), residues: 428 loop : -1.19 (0.17), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS A 470 PHE 0.040 0.002 PHE D 408 TYR 0.013 0.001 TYR C 195 ARG 0.044 0.001 ARG F 115 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4514.43 seconds wall clock time: 262 minutes 44.93 seconds (15764.93 seconds total)