Starting phenix.real_space_refine on Mon Aug 25 03:29:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zi1_60118/08_2025/8zi1_60118.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zi1_60118/08_2025/8zi1_60118.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zi1_60118/08_2025/8zi1_60118.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zi1_60118/08_2025/8zi1_60118.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zi1_60118/08_2025/8zi1_60118.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zi1_60118/08_2025/8zi1_60118.map" } resolution = 2.92 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.016 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 11 5.49 5 Mg 3 5.21 5 S 99 5.16 5 C 15720 2.51 5 N 4294 2.21 5 O 4881 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25008 Number of models: 1 Model: "" Number of chains: 12 Chain: "e" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 959 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "A" Number of atoms: 3702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3702 Classifications: {'peptide': 489} Link IDs: {'PTRANS': 17, 'TRANS': 471} Chain: "B" Number of atoms: 3703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3703 Classifications: {'peptide': 489} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 471} Chain: "C" Number of atoms: 3703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3703 Classifications: {'peptide': 489} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 471} Chain: "D" Number of atoms: 3525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3525 Classifications: {'peptide': 463} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 440} Chain: "E" Number of atoms: 3525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3525 Classifications: {'peptide': 463} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 440} Chain: "F" Number of atoms: 3525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3525 Classifications: {'peptide': 463} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 440} Chain: "g" Number of atoms: 2243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2243 Classifications: {'peptide': 288} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 279} 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: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.91, per 1000 atoms: 0.20 Number of scatterers: 25008 At special positions: 0 Unit cell: (138.138, 139.854, 148.434, 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 99 16.00 P 11 15.00 Mg 3 11.99 O 4881 8.00 N 4294 7.00 C 15720 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: 2.02 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5958 Finding SS restraints... Secondary structure from input PDB file: 138 helices and 28 sheets defined 46.7% alpha, 15.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'e' and resid 90 through 101 removed outlier: 4.338A pdb=" N GLU e 96 " --> pdb=" O ALA e 92 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ALA e 97 " --> pdb=" O ALA e 93 " (cutoff:3.500A) Processing helix chain 'e' and resid 101 through 109 removed outlier: 4.139A pdb=" N LEU e 105 " --> pdb=" O ALA e 101 " (cutoff:3.500A) Processing helix chain 'e' and resid 119 through 132 removed outlier: 3.503A pdb=" N ARG e 132 " --> pdb=" O LEU e 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 83 removed outlier: 4.236A pdb=" N SER A 82 " --> pdb=" O ASN A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 105 removed outlier: 3.776A pdb=" N LEU A 104 " --> pdb=" O GLY A 101 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A 105 " --> pdb=" O PRO A 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 101 through 105' Processing helix chain 'A' and resid 136 through 140 removed outlier: 3.687A pdb=" N ARG A 140 " --> pdb=" O VAL A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 158 Processing helix chain 'A' and resid 175 through 187 removed outlier: 3.799A pdb=" N GLN A 187 " --> pdb=" O ALA A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 216 Processing helix chain 'A' and resid 217 through 220 Processing helix chain 'A' and resid 232 through 252 Proline residue: A 240 - end of helix removed outlier: 3.703A pdb=" N TYR A 249 " --> pdb=" O THR A 245 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N PHE A 250 " --> pdb=" O MET A 246 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ARG A 251 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP A 252 " --> pdb=" O GLU A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 278 removed outlier: 3.948A pdb=" N GLN A 267 " --> pdb=" O ASP A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 301 removed outlier: 4.017A pdb=" N LEU A 298 " --> pdb=" O LEU A 294 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU A 299 " --> pdb=" O HIS A 295 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ARG A 301 " --> pdb=" O ARG A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 315 Processing helix chain 'A' and resid 340 through 348 Processing helix chain 'A' and resid 357 through 363 Processing helix chain 'A' and resid 384 through 391 Processing helix chain 'A' and resid 391 through 405 removed outlier: 3.780A pdb=" N ARG A 395 " --> pdb=" O SER A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 420 Processing helix chain 'A' and resid 420 through 433 removed outlier: 4.099A pdb=" N LYS A 433 " --> pdb=" O THR A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 454 Processing helix chain 'A' and resid 455 through 458 Processing helix chain 'A' and resid 461 through 479 removed outlier: 4.444A pdb=" N VAL A 466 " --> pdb=" O VAL A 462 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ASP A 467 " --> pdb=" O LYS A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 490 removed outlier: 3.639A pdb=" N GLU A 489 " --> pdb=" O LYS A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 512 removed outlier: 4.857A pdb=" N ALA A 510 " --> pdb=" O GLU A 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 83 removed outlier: 4.058A pdb=" N SER B 82 " --> pdb=" O ASN B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 105 removed outlier: 3.745A pdb=" N LEU B 104 " --> pdb=" O GLY B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 140 removed outlier: 3.675A pdb=" N ARG B 140 " --> pdb=" O VAL B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 158 Processing helix chain 'B' and resid 175 through 186 removed outlier: 3.580A pdb=" N MET B 179 " --> pdb=" O GLY B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 218 through 220 No H-bonds generated for 'chain 'B' and resid 218 through 220' Processing helix chain 'B' and resid 232 through 248 Proline residue: B 240 - end of helix Processing helix chain 'B' and resid 248 through 253 removed outlier: 3.729A pdb=" N ARG B 253 " --> pdb=" O TYR B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 278 removed outlier: 3.894A pdb=" N GLN B 267 " --> pdb=" O ASP B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 287 Processing helix chain 'B' and resid 291 through 300 removed outlier: 3.656A pdb=" N HIS B 295 " --> pdb=" O VAL B 291 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU B 298 " --> pdb=" O LEU B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 314 Processing helix chain 'B' and resid 340 through 348 removed outlier: 3.550A pdb=" N SER B 348 " --> pdb=" O THR B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 364 Processing helix chain 'B' and resid 378 through 383 removed outlier: 3.891A pdb=" N SER B 381 " --> pdb=" O VAL B 378 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN B 383 " --> pdb=" O GLY B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 404 removed outlier: 4.595A pdb=" N GLY B 392 " --> pdb=" O LYS B 388 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N GLY B 393 " --> pdb=" O LYS B 389 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ILE B 394 " --> pdb=" O LEU B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 409 removed outlier: 4.116A pdb=" N GLN B 409 " --> pdb=" O ALA B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 414 Processing helix chain 'B' and resid 415 through 432 Processing helix chain 'B' and resid 441 through 454 Processing helix chain 'B' and resid 455 through 459 removed outlier: 4.091A pdb=" N ASP B 459 " --> pdb=" O TYR B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 463 No H-bonds generated for 'chain 'B' and resid 461 through 463' Processing helix chain 'B' and resid 464 through 476 Processing helix chain 'B' and resid 480 through 491 Processing helix chain 'B' and resid 494 through 511 Processing helix chain 'C' and resid 79 through 83 removed outlier: 4.140A pdb=" N SER C 82 " --> pdb=" O ASN C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 105 removed outlier: 3.695A pdb=" N LEU C 104 " --> pdb=" O GLY C 101 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU C 105 " --> pdb=" O PRO C 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 101 through 105' Processing helix chain 'C' and resid 136 through 140 Processing helix chain 'C' and resid 151 through 158 removed outlier: 3.578A pdb=" N MET C 157 " --> pdb=" O SER C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 186 removed outlier: 3.866A pdb=" N MET C 179 " --> pdb=" O GLY C 175 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA C 180 " --> pdb=" O LYS C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 216 Processing helix chain 'C' and resid 217 through 220 removed outlier: 3.841A pdb=" N ALA C 220 " --> pdb=" O GLY C 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 217 through 220' Processing helix chain 'C' and resid 232 through 238 Processing helix chain 'C' and resid 238 through 252 removed outlier: 3.831A pdb=" N TYR C 249 " --> pdb=" O THR C 245 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N PHE C 250 " --> pdb=" O MET C 246 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG C 251 " --> pdb=" O GLY C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 277 Processing helix chain 'C' and resid 290 through 300 removed outlier: 3.906A pdb=" N LEU C 298 " --> pdb=" O LEU C 294 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU C 299 " --> pdb=" O HIS C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 315 removed outlier: 3.509A pdb=" N VAL C 310 " --> pdb=" O SER C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 348 removed outlier: 3.704A pdb=" N SER C 348 " --> pdb=" O THR C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 364 Processing helix chain 'C' and resid 378 through 383 removed outlier: 3.945A pdb=" N SER C 381 " --> pdb=" O VAL C 378 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA C 382 " --> pdb=" O GLY C 379 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN C 383 " --> pdb=" O GLY C 380 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 378 through 383' Processing helix chain 'C' and resid 384 through 391 Processing helix chain 'C' and resid 393 through 409 removed outlier: 3.935A pdb=" N ALA C 397 " --> pdb=" O GLY C 393 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU C 403 " --> pdb=" O ALA C 399 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLN C 409 " --> pdb=" O ALA C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 432 Processing helix chain 'C' and resid 441 through 455 Processing helix chain 'C' and resid 464 through 479 removed outlier: 3.647A pdb=" N PHE C 468 " --> pdb=" O LYS C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 490 Processing helix chain 'C' and resid 494 through 510 removed outlier: 3.640A pdb=" N ALA C 500 " --> pdb=" O ASP C 496 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE C 501 " --> pdb=" O ILE C 497 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA C 510 " --> pdb=" O GLU C 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.699A pdb=" N THR D 82 " --> pdb=" O GLY D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 136 removed outlier: 3.664A pdb=" N LEU D 134 " --> pdb=" O LYS D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 166 Processing helix chain 'D' and resid 183 through 196 removed outlier: 3.652A pdb=" N ASP D 187 " --> pdb=" O ARG D 183 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N TYR D 189 " --> pdb=" O GLY D 185 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER D 195 " --> pdb=" O GLU D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 201 Processing helix chain 'D' and resid 211 through 218 removed outlier: 3.515A pdb=" N ARG D 215 " --> pdb=" O PRO D 211 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARG D 217 " --> pdb=" O GLY D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 232 removed outlier: 3.705A pdb=" N GLY D 222 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR D 228 " --> pdb=" O THR D 224 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE D 229 " --> pdb=" O MET D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 264 removed outlier: 3.655A pdb=" N TYR D 252 " --> pdb=" O ASN D 248 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR D 253 " --> pdb=" O ILE D 249 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA D 261 " --> pdb=" O THR D 257 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LEU D 262 " --> pdb=" O GLU D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 285 removed outlier: 3.671A pdb=" N LEU D 283 " --> pdb=" O GLU D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 307 Processing helix chain 'D' and resid 310 through 317 removed outlier: 3.565A pdb=" N THR D 315 " --> pdb=" O PRO D 311 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR D 316 " --> pdb=" O SER D 312 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE D 317 " --> pdb=" O PRO D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 320 No H-bonds generated for 'chain 'D' and resid 318 through 320' Processing helix chain 'D' and resid 327 through 333 Processing helix chain 'D' and resid 356 through 374 Processing helix chain 'D' and resid 375 through 382 Processing helix chain 'D' and resid 388 through 405 Processing helix chain 'D' and resid 412 through 417 removed outlier: 3.563A pdb=" N THR D 416 " --> pdb=" O ALA D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 438 removed outlier: 3.666A pdb=" N GLY D 438 " --> pdb=" O GLY D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 444 through 449 removed outlier: 3.527A pdb=" N PHE D 448 " --> pdb=" O GLU D 445 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR D 449 " --> pdb=" O GLN D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 464 removed outlier: 3.559A pdb=" N VAL D 457 " --> pdb=" O GLY D 453 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLU D 462 " --> pdb=" O ILE D 458 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LYS D 463 " --> pdb=" O ALA D 459 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 118 removed outlier: 3.605A pdb=" N GLN E 118 " --> pdb=" O TYR E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 136 removed outlier: 3.572A pdb=" N LEU E 134 " --> pdb=" O LYS E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 170 removed outlier: 3.647A pdb=" N ALA E 166 " --> pdb=" O ILE E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 194 Processing helix chain 'E' and resid 195 through 196 No H-bonds generated for 'chain 'E' and resid 195 through 196' Processing helix chain 'E' and resid 197 through 199 No H-bonds generated for 'chain 'E' and resid 197 through 199' Processing helix chain 'E' and resid 211 through 216 removed outlier: 3.713A pdb=" N ARG E 215 " --> pdb=" O PRO E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 217 through 232 Processing helix chain 'E' and resid 251 through 259 removed outlier: 5.115A pdb=" N THR E 257 " --> pdb=" O THR E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 263 Processing helix chain 'E' and resid 278 through 283 removed outlier: 4.146A pdb=" N VAL E 282 " --> pdb=" O GLU E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 332 Processing helix chain 'E' and resid 350 through 355 Processing helix chain 'E' and resid 355 through 362 Processing helix chain 'E' and resid 364 through 382 removed outlier: 4.535A pdb=" N ASP E 377 " --> pdb=" O LYS E 373 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ILE E 378 " --> pdb=" O GLU E 374 " (cutoff:3.500A) Processing helix chain 'E' and resid 391 through 405 Processing helix chain 'E' and resid 424 through 437 Processing helix chain 'E' and resid 438 through 443 removed outlier: 4.122A pdb=" N HIS E 442 " --> pdb=" O GLU E 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 453 through 464 Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.956A pdb=" N THR F 82 " --> pdb=" O GLY F 79 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU F 83 " --> pdb=" O THR F 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 79 through 83' Processing helix chain 'F' and resid 129 through 136 Processing helix chain 'F' and resid 153 through 169 removed outlier: 3.621A pdb=" N ALA F 166 " --> pdb=" O ILE F 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 195 Processing helix chain 'F' and resid 197 through 199 No H-bonds generated for 'chain 'F' and resid 197 through 199' Processing helix chain 'F' and resid 211 through 217 removed outlier: 3.537A pdb=" N ARG F 215 " --> pdb=" O PRO F 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 218 through 232 removed outlier: 3.768A pdb=" N GLY F 222 " --> pdb=" O VAL F 218 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 264 Processing helix chain 'F' and resid 268 through 272 Processing helix chain 'F' and resid 276 through 285 removed outlier: 3.637A pdb=" N LEU F 283 " --> pdb=" O GLU F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 307 removed outlier: 3.593A pdb=" N ASP F 306 " --> pdb=" O VAL F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 317 Processing helix chain 'F' and resid 327 through 334 removed outlier: 3.546A pdb=" N ALA F 331 " --> pdb=" O SER F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 382 removed outlier: 3.730A pdb=" N TYR F 359 " --> pdb=" O GLY F 355 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ASP F 377 " --> pdb=" O LYS F 373 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ILE F 378 " --> pdb=" O GLU F 374 " (cutoff:3.500A) Processing helix chain 'F' and resid 388 through 406 removed outlier: 3.839A pdb=" N LYS F 392 " --> pdb=" O ALA F 388 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N SER F 406 " --> pdb=" O GLN F 402 " (cutoff:3.500A) Processing helix chain 'F' and resid 412 through 417 Processing helix chain 'F' and resid 424 through 438 Processing helix chain 'F' and resid 444 through 449 removed outlier: 3.788A pdb=" N TYR F 449 " --> pdb=" O GLN F 446 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 464 Processing helix chain 'g' and resid 3 through 60 removed outlier: 3.642A pdb=" N ALA g 12 " --> pdb=" O ARG g 8 " (cutoff:3.500A) Proline residue: g 44 - end of helix Processing helix chain 'g' and resid 65 through 69 removed outlier: 3.775A pdb=" N VAL g 69 " --> pdb=" O ARG g 66 " (cutoff:3.500A) Processing helix chain 'g' and resid 90 through 109 Processing helix chain 'g' and resid 119 through 125 Processing helix chain 'g' and resid 125 through 130 removed outlier: 4.325A pdb=" N TYR g 129 " --> pdb=" O PHE g 125 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLY g 130 " --> pdb=" O PHE g 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 125 through 130' Processing helix chain 'g' and resid 145 through 162 removed outlier: 3.572A pdb=" N LEU g 149 " --> pdb=" O SER g 145 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLY g 151 " --> pdb=" O GLU g 147 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N SER g 152 " --> pdb=" O GLN g 148 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N MET g 156 " --> pdb=" O SER g 152 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE g 160 " --> pdb=" O MET g 156 " (cutoff:3.500A) Processing helix chain 'g' and resid 217 through 288 removed outlier: 3.673A pdb=" N LEU g 221 " --> pdb=" O LEU g 217 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL g 230 " --> pdb=" O ILE g 226 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TYR g 231 " --> pdb=" O GLU g 227 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU g 236 " --> pdb=" O GLN g 232 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU g 278 " --> pdb=" O ALA g 274 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'e' and resid 7 through 9 Processing sheet with id=AA2, first strand: chain 'e' and resid 22 through 24 Processing sheet with id=AA3, first strand: chain 'A' and resid 29 through 36 removed outlier: 5.877A pdb=" N ILE A 32 " --> pdb=" O HIS A 43 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N HIS A 43 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N MET A 34 " --> pdb=" O ARG A 41 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N GLY A 73 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N PHE A 61 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA A 64 " --> pdb=" O GLU A 52 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N GLU A 52 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N MET A 53 " --> pdb=" O THR A 92 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 97 through 100 removed outlier: 3.808A pdb=" N LEU A 126 " --> pdb=" O VAL A 100 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 107 through 109 removed outlier: 3.766A pdb=" N ARG A 107 " --> pdb=" O THR A 222 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N CYS A 194 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N VAL A 225 " --> pdb=" O CYS A 194 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N TYR A 196 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N ALA A 227 " --> pdb=" O TYR A 196 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ALA A 198 " --> pdb=" O ALA A 227 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 146 through 147 removed outlier: 4.480A pdb=" N VAL A 160 " --> pdb=" O VAL A 147 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 330 through 332 removed outlier: 6.422A pdb=" N ILE A 168 " --> pdb=" O ILE A 331 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 29 through 36 removed outlier: 3.601A pdb=" N THR B 31 " --> pdb=" O HIS B 43 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ARG B 41 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N VAL B 35 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE B 39 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL B 75 " --> pdb=" O ALA B 64 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N ALA B 64 " --> pdb=" O VAL B 75 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA B 64 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N GLU B 52 " --> pdb=" O ALA B 64 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N MET B 53 " --> pdb=" O THR B 92 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 97 through 100 removed outlier: 4.036A pdb=" N LEU B 126 " --> pdb=" O VAL B 100 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 108 through 109 removed outlier: 6.601A pdb=" N CYS B 194 " --> pdb=" O THR B 223 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N VAL B 225 " --> pdb=" O CYS B 194 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N TYR B 196 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N ALA B 227 " --> pdb=" O TYR B 196 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ALA B 198 " --> pdb=" O ALA B 227 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR B 261 " --> pdb=" O LEU B 328 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LEU B 167 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N LEU B 356 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ILE B 169 " --> pdb=" O LEU B 356 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 146 through 147 removed outlier: 4.544A pdb=" N VAL B 160 " --> pdb=" O VAL B 147 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 29 through 36 removed outlier: 6.497A pdb=" N ARG C 41 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL C 35 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE C 39 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N GLY C 73 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N PHE C 61 " --> pdb=" O LEU C 77 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU C 60 " --> pdb=" O PHE C 56 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLU C 52 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N MET C 53 " --> pdb=" O THR C 92 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 97 through 100 removed outlier: 3.735A pdb=" N LEU C 126 " --> pdb=" O VAL C 100 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 107 through 109 removed outlier: 3.706A pdb=" N ARG C 107 " --> pdb=" O THR C 222 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N CYS C 194 " --> pdb=" O THR C 223 " (cutoff:3.500A) removed outlier: 8.463A pdb=" N VAL C 225 " --> pdb=" O CYS C 194 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TYR C 196 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N ALA C 227 " --> pdb=" O TYR C 196 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ALA C 198 " --> pdb=" O ALA C 227 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 330 through 332 removed outlier: 6.401A pdb=" N ILE C 168 " --> pdb=" O ILE C 331 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 3 through 10 removed outlier: 6.344A pdb=" N ILE D 6 " --> pdb=" O GLU D 17 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N GLU D 17 " --> pdb=" O ILE D 6 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLN D 8 " --> pdb=" O ASP D 15 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N VAL D 49 " --> pdb=" O GLN D 44 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N GLN D 44 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ARG D 51 " --> pdb=" O GLN D 42 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THR D 38 " --> pdb=" O MET D 55 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 75 through 77 Processing sheet with id=AB9, first strand: chain 'D' and resid 86 through 87 removed outlier: 5.779A pdb=" N MET D 87 " --> pdb=" O TYR D 205 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL D 204 " --> pdb=" O ALA D 176 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 124 through 125 removed outlier: 4.254A pdb=" N PHE D 138 " --> pdb=" O LEU D 125 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 242 through 246 removed outlier: 6.817A pdb=" N VAL D 144 " --> pdb=" O GLN D 299 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N VAL D 301 " --> pdb=" O VAL D 144 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N LEU D 146 " --> pdb=" O VAL D 301 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR D 345 " --> pdb=" O THR D 323 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 4 through 10 removed outlier: 5.954A pdb=" N ILE E 6 " --> pdb=" O GLU E 17 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLU E 17 " --> pdb=" O ILE E 6 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN E 8 " --> pdb=" O ASP E 15 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N VAL E 49 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN E 43 " --> pdb=" O ARG E 51 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ILE E 53 " --> pdb=" O VAL E 41 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N VAL E 41 " --> pdb=" O ILE E 53 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ASP E 28 " --> pdb=" O VAL E 41 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ALA E 29 " --> pdb=" O THR E 70 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 75 through 77 Processing sheet with id=AC5, first strand: chain 'E' and resid 86 through 87 removed outlier: 6.436A pdb=" N MET E 87 " --> pdb=" O TYR E 205 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL E 174 " --> pdb=" O PHE E 245 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL E 242 " --> pdb=" O THR E 296 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N ILE E 298 " --> pdb=" O VAL E 242 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU E 244 " --> pdb=" O ILE E 298 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N ALA E 300 " --> pdb=" O LEU E 244 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N VAL E 246 " --> pdb=" O ALA E 300 " (cutoff:3.500A) removed outlier: 10.455A pdb=" N TYR E 302 " --> pdb=" O VAL E 246 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N VAL E 144 " --> pdb=" O GLN E 299 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N VAL E 301 " --> pdb=" O VAL E 144 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N LEU E 146 " --> pdb=" O VAL E 301 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LYS E 143 " --> pdb=" O ALA E 322 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N VAL E 324 " --> pdb=" O LYS E 143 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N GLY E 145 " --> pdb=" O VAL E 324 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 4 through 10 removed outlier: 6.597A pdb=" N ASP F 15 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ILE F 9 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N VAL F 13 " --> pdb=" O ILE F 9 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ILE F 53 " --> pdb=" O VAL F 41 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N VAL F 41 " --> pdb=" O ILE F 53 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N MET F 55 " --> pdb=" O LEU F 39 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N LEU F 39 " --> pdb=" O MET F 55 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N THR F 37 " --> pdb=" O VAL F 32 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL F 67 " --> pdb=" O GLY F 4 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 75 through 77 Processing sheet with id=AC8, first strand: chain 'F' and resid 86 through 87 removed outlier: 6.490A pdb=" N MET F 87 " --> pdb=" O TYR F 205 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N GLN F 207 " --> pdb=" O MET F 87 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU F 172 " --> pdb=" O LEU F 243 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N PHE F 245 " --> pdb=" O LEU F 172 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N VAL F 174 " --> pdb=" O PHE F 245 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL F 242 " --> pdb=" O THR F 296 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N ILE F 298 " --> pdb=" O VAL F 242 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU F 244 " --> pdb=" O ILE F 298 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N ALA F 300 " --> pdb=" O LEU F 244 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N VAL F 246 " --> pdb=" O ALA F 300 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 124 through 125 removed outlier: 4.587A pdb=" N PHE F 138 " --> pdb=" O LEU F 125 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'g' and resid 133 through 136 removed outlier: 6.533A pdb=" N VAL g 133 " --> pdb=" O VAL g 113 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N PHE g 115 " --> pdb=" O VAL g 133 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLY g 135 " --> pdb=" O PHE g 115 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLY g 77 " --> pdb=" O TYR g 169 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N VAL g 171 " --> pdb=" O GLY g 77 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE g 79 " --> pdb=" O VAL g 171 " (cutoff:3.500A) removed outlier: 8.711A pdb=" N ASN g 173 " --> pdb=" O ILE g 79 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N THR g 180 " --> pdb=" O VAL g 176 " (cutoff:3.500A) 1105 hydrogen bonds defined for protein. 3162 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: 4.28 Time building geometry restraints manager: 2.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 4348 1.31 - 1.44: 6053 1.44 - 1.56: 14785 1.56 - 1.69: 20 1.69 - 1.81: 184 Bond restraints: 25390 Sorted by residual: bond pdb=" CA VAL D 178 " pdb=" C VAL D 178 " ideal model delta sigma weight residual 1.523 1.569 -0.046 1.17e-02 7.31e+03 1.55e+01 bond pdb=" C PRO D 341 " pdb=" O PRO D 341 " ideal model delta sigma weight residual 1.238 1.188 0.050 1.35e-02 5.49e+03 1.35e+01 bond pdb=" CA GLN D 118 " pdb=" C GLN D 118 " ideal model delta sigma weight residual 1.521 1.566 -0.045 1.24e-02 6.50e+03 1.33e+01 bond pdb=" N ARG E 286 " pdb=" CA ARG E 286 " ideal model delta sigma weight residual 1.456 1.504 -0.048 1.33e-02 5.65e+03 1.31e+01 bond pdb=" N VAL E 201 " pdb=" CA VAL E 201 " ideal model delta sigma weight residual 1.456 1.497 -0.040 1.14e-02 7.69e+03 1.24e+01 ... (remaining 25385 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 32362 1.90 - 3.80: 1842 3.80 - 5.70: 197 5.70 - 7.60: 10 7.60 - 9.50: 1 Bond angle restraints: 34412 Sorted by residual: angle pdb=" N ILE C 505 " pdb=" CA ILE C 505 " pdb=" C ILE C 505 " ideal model delta sigma weight residual 110.62 106.54 4.08 1.02e+00 9.61e-01 1.60e+01 angle pdb=" N VAL E 451 " pdb=" CA VAL E 451 " pdb=" C VAL E 451 " ideal model delta sigma weight residual 112.29 108.53 3.76 9.40e-01 1.13e+00 1.60e+01 angle pdb=" CA ILE E 26 " pdb=" C ILE E 26 " pdb=" O ILE E 26 " ideal model delta sigma weight residual 121.23 116.98 4.25 1.07e+00 8.73e-01 1.58e+01 angle pdb=" N GLU B 479 " pdb=" CA GLU B 479 " pdb=" C GLU B 479 " ideal model delta sigma weight residual 114.31 109.19 5.12 1.29e+00 6.01e-01 1.58e+01 angle pdb=" CA GLY e 66 " pdb=" C GLY e 66 " pdb=" O GLY e 66 " ideal model delta sigma weight residual 121.86 117.73 4.13 1.04e+00 9.25e-01 1.57e+01 ... (remaining 34407 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 14176 17.85 - 35.70: 1038 35.70 - 53.56: 213 53.56 - 71.41: 41 71.41 - 89.26: 17 Dihedral angle restraints: 15485 sinusoidal: 6134 harmonic: 9351 Sorted by residual: dihedral pdb=" CA GLU D 184 " pdb=" C GLU D 184 " pdb=" N GLY D 185 " pdb=" CA GLY D 185 " ideal model delta harmonic sigma weight residual 180.00 161.23 18.77 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA TYR D 336 " pdb=" C TYR D 336 " pdb=" N PRO D 337 " pdb=" CA PRO D 337 " ideal model delta harmonic sigma weight residual 0.00 17.38 -17.38 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA ASP D 310 " pdb=" CB ASP D 310 " pdb=" CG ASP D 310 " pdb=" OD1 ASP D 310 " ideal model delta sinusoidal sigma weight residual -30.00 -89.73 59.73 1 2.00e+01 2.50e-03 1.19e+01 ... (remaining 15482 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2855 0.053 - 0.106: 758 0.106 - 0.159: 272 0.159 - 0.212: 67 0.212 - 0.265: 23 Chirality restraints: 3975 Sorted by residual: chirality pdb=" CA ILE E 9 " pdb=" N ILE E 9 " pdb=" C ILE E 9 " pdb=" CB ILE E 9 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CA GLN D 118 " pdb=" N GLN D 118 " pdb=" C GLN D 118 " pdb=" CB GLN D 118 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CA VAL A 108 " pdb=" N VAL A 108 " pdb=" C VAL A 108 " pdb=" CB VAL A 108 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 3972 not shown) Planarity restraints: 4484 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 255 " 0.019 2.00e-02 2.50e+03 3.71e-02 1.38e+01 pdb=" C GLU B 255 " -0.064 2.00e-02 2.50e+03 pdb=" O GLU B 255 " 0.024 2.00e-02 2.50e+03 pdb=" N ASP B 256 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 462 " 0.019 2.00e-02 2.50e+03 3.71e-02 1.37e+01 pdb=" C VAL B 462 " -0.064 2.00e-02 2.50e+03 pdb=" O VAL B 462 " 0.024 2.00e-02 2.50e+03 pdb=" N LYS B 463 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 171 " 0.016 2.00e-02 2.50e+03 3.31e-02 1.09e+01 pdb=" C GLY D 171 " -0.057 2.00e-02 2.50e+03 pdb=" O GLY D 171 " 0.021 2.00e-02 2.50e+03 pdb=" N LEU D 172 " 0.019 2.00e-02 2.50e+03 ... (remaining 4481 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 67 2.41 - 3.04: 15504 3.04 - 3.66: 35826 3.66 - 4.28: 53025 4.28 - 4.90: 90847 Nonbonded interactions: 195269 Sorted by model distance: nonbonded pdb="MG MG C 601 " pdb=" O2G ATP C 602 " model vdw 1.792 2.170 nonbonded pdb=" O2B ATP B 601 " pdb="MG MG B 602 " model vdw 1.866 2.170 nonbonded pdb=" O1G ATP B 601 " pdb="MG MG B 602 " model vdw 1.904 2.170 nonbonded pdb=" O GLU D 235 " pdb=" OD1 ASN D 236 " model vdw 1.958 3.040 nonbonded pdb=" OG1 THR A 177 " pdb="MG MG A 602 " model vdw 1.995 2.170 ... (remaining 195264 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 26 through 514) selection = (chain 'B' and (resid 26 through 513 or (resid 514 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name \ CE2 or name CZ or name OH )))) selection = (chain 'C' and (resid 26 through 513 or (resid 514 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name \ CE2 or name CZ or name OH )))) } ncs_group { reference = (chain 'D' and resid 2 through 464) selection = chain 'E' selection = chain 'F' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.740 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: 0.380 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 19.740 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.060 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: 0.000 Load rotamer database and sin/cos tables:7.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 25390 Z= 0.443 Angle : 0.864 9.503 34412 Z= 0.611 Chirality : 0.059 0.265 3975 Planarity : 0.004 0.092 4484 Dihedral : 13.344 89.260 9527 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.15), residues: 3260 helix: 1.08 (0.15), residues: 1259 sheet: 0.70 (0.23), residues: 484 loop : -1.01 (0.15), residues: 1517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG g 75 TYR 0.016 0.001 TYR e 16 PHE 0.020 0.001 PHE C 476 TRP 0.006 0.001 TRP C 139 HIS 0.004 0.001 HIS e 38 Details of bonding type rmsd covalent geometry : bond 0.00618 (25390) covalent geometry : angle 0.86389 (34412) hydrogen bonds : bond 0.19673 ( 1105) hydrogen bonds : angle 7.09221 ( 3162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 307 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 7 ASP cc_start: 0.8509 (m-30) cc_final: 0.7862 (p0) REVERT: A 290 ASP cc_start: 0.7530 (t70) cc_final: 0.7278 (t0) REVERT: C 49 MET cc_start: 0.8621 (mtm) cc_final: 0.8174 (mtp) REVERT: D 376 LYS cc_start: 0.8848 (pttt) cc_final: 0.8632 (mttt) REVERT: E 59 GLU cc_start: 0.7856 (pm20) cc_final: 0.7418 (pm20) REVERT: E 266 MET cc_start: 0.4691 (ptp) cc_final: 0.4425 (ptp) REVERT: E 284 GLN cc_start: 0.7643 (tt0) cc_final: 0.7302 (tm130) REVERT: g 49 MET cc_start: 0.8810 (mmt) cc_final: 0.8108 (mmm) REVERT: g 156 MET cc_start: 0.8199 (tpt) cc_final: 0.7217 (tpt) REVERT: g 229 MET cc_start: 0.9189 (mmm) cc_final: 0.8785 (mmm) outliers start: 0 outliers final: 0 residues processed: 307 average time/residue: 0.7250 time to fit residues: 249.9486 Evaluate side-chains 162 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 0.0060 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.0970 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 4.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 190 HIS D 407 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.112357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.080225 restraints weight = 49231.430| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.74 r_work: 0.3171 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25390 Z= 0.123 Angle : 0.553 11.422 34412 Z= 0.292 Chirality : 0.043 0.174 3975 Planarity : 0.004 0.059 4484 Dihedral : 6.712 79.732 3683 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.72 % Allowed : 9.27 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.15), residues: 3260 helix: 1.46 (0.15), residues: 1306 sheet: 0.62 (0.21), residues: 547 loop : -0.89 (0.16), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG g 33 TYR 0.017 0.001 TYR E 250 PHE 0.019 0.001 PHE D 405 TRP 0.007 0.001 TRP g 206 HIS 0.008 0.001 HIS e 74 Details of bonding type rmsd covalent geometry : bond 0.00251 (25390) covalent geometry : angle 0.55333 (34412) hydrogen bonds : bond 0.05183 ( 1105) hydrogen bonds : angle 5.17136 ( 3162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 188 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 7 ASP cc_start: 0.8564 (m-30) cc_final: 0.7962 (p0) REVERT: e 22 MET cc_start: 0.8432 (tpt) cc_final: 0.8214 (tpp) REVERT: e 46 GLN cc_start: 0.8008 (mp10) cc_final: 0.7464 (pp30) REVERT: A 34 MET cc_start: 0.7975 (tmm) cc_final: 0.7762 (tmt) REVERT: A 290 ASP cc_start: 0.7334 (t70) cc_final: 0.6920 (t0) REVERT: C 34 MET cc_start: 0.8134 (ttp) cc_final: 0.7859 (tmm) REVERT: D 376 LYS cc_start: 0.8882 (pttt) cc_final: 0.8620 (mttt) REVERT: E 59 GLU cc_start: 0.7883 (pm20) cc_final: 0.7425 (pm20) REVERT: E 62 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8330 (mttm) REVERT: E 266 MET cc_start: 0.4328 (ptp) cc_final: 0.3883 (ptp) REVERT: E 463 LYS cc_start: 0.8019 (ptmt) cc_final: 0.7756 (pttm) REVERT: F 110 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.7218 (ptm160) REVERT: F 371 ARG cc_start: 0.9154 (OUTLIER) cc_final: 0.7943 (tpm170) REVERT: g 49 MET cc_start: 0.8779 (mmt) cc_final: 0.8090 (mmm) REVERT: g 156 MET cc_start: 0.8098 (tpt) cc_final: 0.7493 (tpt) REVERT: g 229 MET cc_start: 0.9283 (mmm) cc_final: 0.8967 (mmm) outliers start: 45 outliers final: 14 residues processed: 219 average time/residue: 0.6298 time to fit residues: 157.4278 Evaluate side-chains 176 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 159 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 457 MET Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 332 GLU Chi-restraints excluded: chain C residue 334 GLN Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 62 LYS Chi-restraints excluded: chain D residue 203 MET Chi-restraints excluded: chain E residue 62 LYS Chi-restraints excluded: chain E residue 441 ASP Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 110 ARG Chi-restraints excluded: chain F residue 136 CYS Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 371 ARG Chi-restraints excluded: chain g residue 32 MET Chi-restraints excluded: chain g residue 115 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 18 optimal weight: 1.9990 chunk 112 optimal weight: 7.9990 chunk 295 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 157 optimal weight: 5.9990 chunk 302 optimal weight: 8.9990 chunk 143 optimal weight: 8.9990 chunk 287 optimal weight: 0.8980 chunk 282 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 54 optimal weight: 8.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 100 ASN ** e 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.108983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.076087 restraints weight = 50688.442| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.85 r_work: 0.3090 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 25390 Z= 0.188 Angle : 0.582 11.845 34412 Z= 0.306 Chirality : 0.046 0.227 3975 Planarity : 0.004 0.052 4484 Dihedral : 6.522 83.868 3683 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.95 % Allowed : 11.21 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.15), residues: 3260 helix: 1.55 (0.15), residues: 1278 sheet: 0.32 (0.21), residues: 549 loop : -0.90 (0.16), residues: 1433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 5 TYR 0.018 0.001 TYR g 208 PHE 0.024 0.001 PHE B 341 TRP 0.005 0.001 TRP C 139 HIS 0.006 0.001 HIS e 74 Details of bonding type rmsd covalent geometry : bond 0.00449 (25390) covalent geometry : angle 0.58206 (34412) hydrogen bonds : bond 0.05537 ( 1105) hydrogen bonds : angle 5.01249 ( 3162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 172 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 7 ASP cc_start: 0.8584 (m-30) cc_final: 0.8008 (p0) REVERT: e 46 GLN cc_start: 0.8083 (mp10) cc_final: 0.7438 (pm20) REVERT: A 34 MET cc_start: 0.8074 (tmm) cc_final: 0.7820 (tmt) REVERT: A 290 ASP cc_start: 0.7323 (t70) cc_final: 0.6994 (t0) REVERT: B 68 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8195 (mp0) REVERT: C 34 MET cc_start: 0.8200 (ttp) cc_final: 0.7770 (tmm) REVERT: D 5 ARG cc_start: 0.8169 (ttm110) cc_final: 0.7806 (tpp-160) REVERT: D 376 LYS cc_start: 0.8879 (pttt) cc_final: 0.8656 (mttt) REVERT: E 59 GLU cc_start: 0.8002 (pm20) cc_final: 0.7530 (pm20) REVERT: E 181 ARG cc_start: 0.7750 (OUTLIER) cc_final: 0.6858 (mtt90) REVERT: E 266 MET cc_start: 0.4300 (ptp) cc_final: 0.3762 (pmm) REVERT: E 463 LYS cc_start: 0.8130 (ptmt) cc_final: 0.7780 (pttm) REVERT: F 55 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.8328 (mmm) REVERT: F 371 ARG cc_start: 0.9164 (OUTLIER) cc_final: 0.7941 (tpm170) REVERT: g 49 MET cc_start: 0.8792 (mmt) cc_final: 0.8121 (mmm) REVERT: g 156 MET cc_start: 0.7945 (tpt) cc_final: 0.7402 (tpt) REVERT: g 229 MET cc_start: 0.9283 (mmm) cc_final: 0.9052 (mmm) outliers start: 51 outliers final: 15 residues processed: 205 average time/residue: 0.6474 time to fit residues: 151.5532 Evaluate side-chains 172 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 153 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 334 GLN Chi-restraints excluded: chain D residue 25 LYS Chi-restraints excluded: chain D residue 62 LYS Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain E residue 181 ARG Chi-restraints excluded: chain E residue 441 ASP Chi-restraints excluded: chain F residue 55 MET Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 136 CYS Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 371 ARG Chi-restraints excluded: chain g residue 32 MET Chi-restraints excluded: chain g residue 115 PHE Chi-restraints excluded: chain g residue 134 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 234 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 161 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 13 optimal weight: 0.1980 chunk 264 optimal weight: 0.6980 chunk 237 optimal weight: 1.9990 chunk 205 optimal weight: 4.9990 chunk 144 optimal weight: 7.9990 chunk 231 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 299 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.111843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.079263 restraints weight = 50191.166| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.84 r_work: 0.3137 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 25390 Z= 0.106 Angle : 0.509 11.921 34412 Z= 0.265 Chirality : 0.042 0.145 3975 Planarity : 0.004 0.065 4484 Dihedral : 6.023 85.361 3683 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.64 % Allowed : 12.62 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.15), residues: 3260 helix: 1.69 (0.15), residues: 1288 sheet: 0.51 (0.21), residues: 562 loop : -0.82 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 5 TYR 0.027 0.001 TYR g 208 PHE 0.011 0.001 PHE E 317 TRP 0.026 0.002 TRP g 206 HIS 0.003 0.000 HIS e 38 Details of bonding type rmsd covalent geometry : bond 0.00227 (25390) covalent geometry : angle 0.50883 (34412) hydrogen bonds : bond 0.04269 ( 1105) hydrogen bonds : angle 4.70055 ( 3162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 172 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 7 ASP cc_start: 0.8539 (m-30) cc_final: 0.7975 (p0) REVERT: e 46 GLN cc_start: 0.8052 (mp10) cc_final: 0.7530 (pp30) REVERT: A 34 MET cc_start: 0.8030 (tmm) cc_final: 0.7734 (tmt) REVERT: A 290 ASP cc_start: 0.7301 (t70) cc_final: 0.6879 (t0) REVERT: B 68 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8151 (mp0) REVERT: B 214 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8272 (mt-10) REVERT: C 34 MET cc_start: 0.8143 (ttp) cc_final: 0.7861 (tmm) REVERT: D 376 LYS cc_start: 0.8824 (pttt) cc_final: 0.8616 (mttt) REVERT: E 59 GLU cc_start: 0.7994 (pm20) cc_final: 0.7499 (pm20) REVERT: E 266 MET cc_start: 0.4239 (ptp) cc_final: 0.3481 (pmm) REVERT: F 371 ARG cc_start: 0.9147 (OUTLIER) cc_final: 0.7952 (tpm170) REVERT: F 374 GLU cc_start: 0.8340 (mt-10) cc_final: 0.7945 (mt-10) REVERT: g 49 MET cc_start: 0.8795 (mmt) cc_final: 0.8146 (mmm) REVERT: g 156 MET cc_start: 0.7967 (tpt) cc_final: 0.7454 (tpt) REVERT: g 229 MET cc_start: 0.9295 (mmm) cc_final: 0.9054 (mmm) outliers start: 43 outliers final: 16 residues processed: 204 average time/residue: 0.7595 time to fit residues: 176.8580 Evaluate side-chains 174 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 155 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 332 GLU Chi-restraints excluded: chain C residue 334 GLN Chi-restraints excluded: chain C residue 403 GLU Chi-restraints excluded: chain D residue 25 LYS Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 62 LYS Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 441 ASP Chi-restraints excluded: chain E residue 451 VAL Chi-restraints excluded: chain F residue 136 CYS Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 371 ARG Chi-restraints excluded: chain g residue 32 MET Chi-restraints excluded: chain g residue 100 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 16 optimal weight: 3.9990 chunk 176 optimal weight: 2.9990 chunk 150 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 73 optimal weight: 0.6980 chunk 164 optimal weight: 3.9990 chunk 217 optimal weight: 10.0000 chunk 153 optimal weight: 6.9990 chunk 245 optimal weight: 9.9990 chunk 127 optimal weight: 2.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.108909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.076639 restraints weight = 50041.167| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.77 r_work: 0.3099 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 25390 Z= 0.181 Angle : 0.565 15.541 34412 Z= 0.293 Chirality : 0.044 0.163 3975 Planarity : 0.004 0.052 4484 Dihedral : 6.155 87.213 3683 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.10 % Allowed : 13.42 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.15), residues: 3260 helix: 1.68 (0.15), residues: 1280 sheet: 0.34 (0.21), residues: 566 loop : -0.96 (0.16), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 5 TYR 0.016 0.001 TYR D 252 PHE 0.019 0.001 PHE E 415 TRP 0.012 0.002 TRP g 206 HIS 0.003 0.001 HIS F 190 Details of bonding type rmsd covalent geometry : bond 0.00436 (25390) covalent geometry : angle 0.56463 (34412) hydrogen bonds : bond 0.05079 ( 1105) hydrogen bonds : angle 4.80118 ( 3162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 162 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 7 ASP cc_start: 0.8567 (m-30) cc_final: 0.7971 (p0) REVERT: e 46 GLN cc_start: 0.8034 (mp10) cc_final: 0.7512 (pp30) REVERT: A 34 MET cc_start: 0.8089 (tmm) cc_final: 0.7815 (tmt) REVERT: A 290 ASP cc_start: 0.7322 (t70) cc_final: 0.7014 (t0) REVERT: A 377 ARG cc_start: 0.8004 (ptp-170) cc_final: 0.7664 (ptp-110) REVERT: B 68 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8184 (mp0) REVERT: C 34 MET cc_start: 0.8204 (ttp) cc_final: 0.7763 (tmm) REVERT: D 5 ARG cc_start: 0.8171 (ttm110) cc_final: 0.7822 (tpp-160) REVERT: D 104 GLU cc_start: 0.8169 (mp0) cc_final: 0.7892 (mp0) REVERT: E 59 GLU cc_start: 0.8025 (pm20) cc_final: 0.7557 (pm20) REVERT: E 110 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7933 (mtp-110) REVERT: E 266 MET cc_start: 0.3946 (ptp) cc_final: 0.3123 (pmm) REVERT: E 463 LYS cc_start: 0.8135 (ptmt) cc_final: 0.7874 (pttm) REVERT: F 371 ARG cc_start: 0.9155 (OUTLIER) cc_final: 0.7942 (tpm170) REVERT: g 49 MET cc_start: 0.8762 (mmt) cc_final: 0.8122 (mmm) REVERT: g 156 MET cc_start: 0.8010 (tpt) cc_final: 0.7584 (tpt) REVERT: g 229 MET cc_start: 0.9309 (mmm) cc_final: 0.9072 (mmm) outliers start: 55 outliers final: 21 residues processed: 202 average time/residue: 0.7319 time to fit residues: 169.1765 Evaluate side-chains 175 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 151 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 32 LEU Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 403 GLU Chi-restraints excluded: chain D residue 25 LYS Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 62 LYS Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain E residue 110 ARG Chi-restraints excluded: chain E residue 187 ASP Chi-restraints excluded: chain E residue 441 ASP Chi-restraints excluded: chain E residue 451 VAL Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 136 CYS Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 371 ARG Chi-restraints excluded: chain g residue 32 MET Chi-restraints excluded: chain g residue 100 VAL Chi-restraints excluded: chain g residue 115 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 117 optimal weight: 5.9990 chunk 277 optimal weight: 4.9990 chunk 238 optimal weight: 8.9990 chunk 47 optimal weight: 7.9990 chunk 33 optimal weight: 0.0980 chunk 150 optimal weight: 0.0570 chunk 125 optimal weight: 3.9990 chunk 167 optimal weight: 3.9990 chunk 202 optimal weight: 4.9990 chunk 44 optimal weight: 0.0980 chunk 292 optimal weight: 0.9990 overall best weight: 1.0502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.109612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.077454 restraints weight = 49582.308| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.76 r_work: 0.3117 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25390 Z= 0.116 Angle : 0.523 15.094 34412 Z= 0.268 Chirality : 0.043 0.160 3975 Planarity : 0.004 0.056 4484 Dihedral : 5.879 81.858 3683 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.60 % Allowed : 14.34 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.15), residues: 3260 helix: 1.79 (0.15), residues: 1279 sheet: 0.39 (0.21), residues: 560 loop : -0.90 (0.16), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 5 TYR 0.015 0.001 TYR D 252 PHE 0.010 0.001 PHE F 188 TRP 0.009 0.001 TRP g 206 HIS 0.002 0.000 HIS F 190 Details of bonding type rmsd covalent geometry : bond 0.00263 (25390) covalent geometry : angle 0.52274 (34412) hydrogen bonds : bond 0.04289 ( 1105) hydrogen bonds : angle 4.63829 ( 3162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 162 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: e 46 GLN cc_start: 0.8041 (mp10) cc_final: 0.7526 (pp30) REVERT: A 34 MET cc_start: 0.8088 (tmm) cc_final: 0.7812 (tmt) REVERT: A 290 ASP cc_start: 0.7185 (t70) cc_final: 0.6848 (t0) REVERT: A 377 ARG cc_start: 0.7993 (ptp-170) cc_final: 0.7662 (ptp-110) REVERT: B 68 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8170 (mp0) REVERT: C 34 MET cc_start: 0.8154 (ttp) cc_final: 0.7801 (tmm) REVERT: D 5 ARG cc_start: 0.8133 (ttm110) cc_final: 0.7803 (tpp-160) REVERT: D 104 GLU cc_start: 0.8163 (mp0) cc_final: 0.7901 (mp0) REVERT: E 59 GLU cc_start: 0.8021 (pm20) cc_final: 0.7552 (pm20) REVERT: E 266 MET cc_start: 0.3840 (ptp) cc_final: 0.3108 (pmm) REVERT: E 463 LYS cc_start: 0.8142 (ptmt) cc_final: 0.7885 (pttm) REVERT: F 371 ARG cc_start: 0.9153 (OUTLIER) cc_final: 0.7914 (tpm170) REVERT: F 374 GLU cc_start: 0.8352 (mt-10) cc_final: 0.7952 (mt-10) REVERT: g 49 MET cc_start: 0.8769 (mmt) cc_final: 0.8144 (mmm) REVERT: g 156 MET cc_start: 0.8032 (tpt) cc_final: 0.7479 (tpt) REVERT: g 229 MET cc_start: 0.9315 (mmm) cc_final: 0.9050 (mmm) outliers start: 42 outliers final: 22 residues processed: 192 average time/residue: 0.7537 time to fit residues: 165.6804 Evaluate side-chains 175 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 151 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 32 LEU Chi-restraints excluded: chain e residue 34 ILE Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 332 GLU Chi-restraints excluded: chain C residue 334 GLN Chi-restraints excluded: chain D residue 25 LYS Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 62 LYS Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 441 ASP Chi-restraints excluded: chain E residue 451 VAL Chi-restraints excluded: chain F residue 136 CYS Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 266 MET Chi-restraints excluded: chain F residue 371 ARG Chi-restraints excluded: chain F residue 375 LEU Chi-restraints excluded: chain g residue 32 MET Chi-restraints excluded: chain g residue 115 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 43 optimal weight: 3.9990 chunk 162 optimal weight: 9.9990 chunk 285 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 286 optimal weight: 1.9990 chunk 217 optimal weight: 10.0000 chunk 211 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 304 optimal weight: 4.9990 chunk 89 optimal weight: 0.3980 chunk 209 optimal weight: 4.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 366 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.107882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.075732 restraints weight = 49775.269| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.75 r_work: 0.3094 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 25390 Z= 0.180 Angle : 0.580 14.899 34412 Z= 0.298 Chirality : 0.044 0.152 3975 Planarity : 0.004 0.052 4484 Dihedral : 6.052 83.580 3683 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.10 % Allowed : 14.61 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.15), residues: 3260 helix: 1.71 (0.15), residues: 1279 sheet: 0.29 (0.21), residues: 564 loop : -0.99 (0.16), residues: 1417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 5 TYR 0.016 0.001 TYR D 252 PHE 0.027 0.001 PHE E 415 TRP 0.008 0.001 TRP g 206 HIS 0.003 0.001 HIS F 190 Details of bonding type rmsd covalent geometry : bond 0.00436 (25390) covalent geometry : angle 0.57990 (34412) hydrogen bonds : bond 0.04957 ( 1105) hydrogen bonds : angle 4.74962 ( 3162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 158 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: e 46 GLN cc_start: 0.8053 (mp10) cc_final: 0.7558 (pp30) REVERT: A 34 MET cc_start: 0.8085 (tmm) cc_final: 0.7826 (tmt) REVERT: A 290 ASP cc_start: 0.7287 (t70) cc_final: 0.6980 (t0) REVERT: A 377 ARG cc_start: 0.8072 (ptp-170) cc_final: 0.7733 (ptp-110) REVERT: B 68 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8197 (mp0) REVERT: D 104 GLU cc_start: 0.8170 (mp0) cc_final: 0.7913 (mp0) REVERT: E 59 GLU cc_start: 0.8036 (pm20) cc_final: 0.7554 (pm20) REVERT: E 181 ARG cc_start: 0.7684 (OUTLIER) cc_final: 0.6778 (mtt90) REVERT: E 266 MET cc_start: 0.3718 (ptp) cc_final: 0.3170 (pmm) REVERT: E 463 LYS cc_start: 0.8162 (ptmt) cc_final: 0.7794 (pttm) REVERT: F 371 ARG cc_start: 0.9164 (OUTLIER) cc_final: 0.7982 (tpm170) REVERT: g 49 MET cc_start: 0.8776 (mmt) cc_final: 0.8171 (mmm) REVERT: g 156 MET cc_start: 0.8238 (tpt) cc_final: 0.7686 (tpp) REVERT: g 229 MET cc_start: 0.9347 (mmm) cc_final: 0.9104 (mmm) outliers start: 55 outliers final: 31 residues processed: 199 average time/residue: 0.7794 time to fit residues: 177.4920 Evaluate side-chains 184 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 150 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 32 LEU Chi-restraints excluded: chain e residue 34 ILE Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 332 GLU Chi-restraints excluded: chain C residue 403 GLU Chi-restraints excluded: chain D residue 25 LYS Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 62 LYS Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 186 ASN Chi-restraints excluded: chain E residue 181 ARG Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 441 ASP Chi-restraints excluded: chain E residue 451 VAL Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 136 CYS Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 266 MET Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 371 ARG Chi-restraints excluded: chain F residue 375 LEU Chi-restraints excluded: chain g residue 32 MET Chi-restraints excluded: chain g residue 100 VAL Chi-restraints excluded: chain g residue 115 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 216 optimal weight: 0.9980 chunk 281 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 9 optimal weight: 20.0000 chunk 100 optimal weight: 7.9990 chunk 232 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 269 optimal weight: 1.9990 chunk 234 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 192 optimal weight: 0.5980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 366 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.109261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.077136 restraints weight = 49980.189| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.77 r_work: 0.3108 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25390 Z= 0.143 Angle : 0.560 15.173 34412 Z= 0.286 Chirality : 0.044 0.178 3975 Planarity : 0.004 0.065 4484 Dihedral : 5.954 81.290 3683 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.79 % Allowed : 15.37 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.15), residues: 3260 helix: 1.75 (0.15), residues: 1277 sheet: 0.33 (0.21), residues: 562 loop : -0.98 (0.16), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 5 TYR 0.016 0.001 TYR D 252 PHE 0.012 0.001 PHE E 317 TRP 0.008 0.001 TRP g 206 HIS 0.002 0.001 HIS F 190 Details of bonding type rmsd covalent geometry : bond 0.00341 (25390) covalent geometry : angle 0.55954 (34412) hydrogen bonds : bond 0.04519 ( 1105) hydrogen bonds : angle 4.66769 ( 3162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 159 time to evaluate : 1.179 Fit side-chains revert: symmetry clash REVERT: e 46 GLN cc_start: 0.8094 (mp10) cc_final: 0.7602 (pp30) REVERT: A 34 MET cc_start: 0.8048 (tmm) cc_final: 0.7782 (tmt) REVERT: A 290 ASP cc_start: 0.7279 (t70) cc_final: 0.6972 (t0) REVERT: A 377 ARG cc_start: 0.8106 (ptp-170) cc_final: 0.7740 (ptp-110) REVERT: A 430 GLU cc_start: 0.9190 (tp30) cc_final: 0.8527 (tm-30) REVERT: B 68 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8184 (mp0) REVERT: B 403 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7635 (pt0) REVERT: C 34 MET cc_start: 0.8178 (ttp) cc_final: 0.7842 (tmm) REVERT: C 49 MET cc_start: 0.8606 (mtm) cc_final: 0.8390 (mtp) REVERT: D 5 ARG cc_start: 0.8197 (ttm110) cc_final: 0.7911 (tpp-160) REVERT: D 104 GLU cc_start: 0.8169 (mp0) cc_final: 0.7922 (mp0) REVERT: D 203 MET cc_start: 0.8387 (mtp) cc_final: 0.8149 (mtm) REVERT: E 59 GLU cc_start: 0.8019 (pm20) cc_final: 0.7544 (pm20) REVERT: E 266 MET cc_start: 0.3620 (ptp) cc_final: 0.2903 (pmm) REVERT: E 280 MET cc_start: 0.6690 (mmm) cc_final: 0.6140 (mmt) REVERT: E 463 LYS cc_start: 0.8177 (ptmt) cc_final: 0.7819 (pttm) REVERT: F 371 ARG cc_start: 0.9162 (OUTLIER) cc_final: 0.7927 (tpm170) REVERT: F 374 GLU cc_start: 0.8381 (mt-10) cc_final: 0.7976 (mt-10) REVERT: g 49 MET cc_start: 0.8789 (mmt) cc_final: 0.8178 (mmm) REVERT: g 101 GLN cc_start: 0.7534 (OUTLIER) cc_final: 0.7094 (mp10) REVERT: g 156 MET cc_start: 0.8215 (OUTLIER) cc_final: 0.7597 (tpp) REVERT: g 226 ILE cc_start: 0.9449 (mm) cc_final: 0.9193 (pp) REVERT: g 229 MET cc_start: 0.9353 (mmm) cc_final: 0.9126 (mmm) outliers start: 47 outliers final: 29 residues processed: 197 average time/residue: 0.6921 time to fit residues: 156.6120 Evaluate side-chains 188 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 154 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 32 LEU Chi-restraints excluded: chain e residue 34 ILE Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 332 GLU Chi-restraints excluded: chain D residue 25 LYS Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 62 LYS Chi-restraints excluded: chain D residue 186 ASN Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 441 ASP Chi-restraints excluded: chain E residue 451 VAL Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 136 CYS Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 371 ARG Chi-restraints excluded: chain F residue 375 LEU Chi-restraints excluded: chain g residue 32 MET Chi-restraints excluded: chain g residue 100 VAL Chi-restraints excluded: chain g residue 101 GLN Chi-restraints excluded: chain g residue 115 PHE Chi-restraints excluded: chain g residue 156 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 94 optimal weight: 4.9990 chunk 171 optimal weight: 3.9990 chunk 310 optimal weight: 9.9990 chunk 135 optimal weight: 0.9980 chunk 201 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 208 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 319 HIS g 65 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.107881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.075406 restraints weight = 51006.152| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 2.95 r_work: 0.3020 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 25390 Z= 0.173 Angle : 0.584 15.231 34412 Z= 0.298 Chirality : 0.044 0.163 3975 Planarity : 0.004 0.061 4484 Dihedral : 6.048 82.003 3683 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.64 % Allowed : 15.71 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.15), residues: 3260 helix: 1.73 (0.15), residues: 1265 sheet: 0.29 (0.21), residues: 560 loop : -1.02 (0.16), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 5 TYR 0.016 0.001 TYR D 252 PHE 0.028 0.001 PHE E 415 TRP 0.008 0.001 TRP g 206 HIS 0.003 0.001 HIS F 190 Details of bonding type rmsd covalent geometry : bond 0.00418 (25390) covalent geometry : angle 0.58416 (34412) hydrogen bonds : bond 0.04794 ( 1105) hydrogen bonds : angle 4.73155 ( 3162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 154 time to evaluate : 0.763 Fit side-chains revert: symmetry clash REVERT: e 46 GLN cc_start: 0.8133 (mp10) cc_final: 0.7628 (pp30) REVERT: A 34 MET cc_start: 0.8090 (tmm) cc_final: 0.7659 (tmt) REVERT: A 290 ASP cc_start: 0.7247 (t70) cc_final: 0.6943 (t0) REVERT: A 377 ARG cc_start: 0.8147 (ptp-170) cc_final: 0.7737 (ptp-110) REVERT: A 430 GLU cc_start: 0.9183 (tp30) cc_final: 0.8495 (tm-30) REVERT: B 68 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8078 (mp0) REVERT: B 214 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8259 (mt-10) REVERT: B 403 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7536 (pt0) REVERT: C 34 MET cc_start: 0.8326 (ttp) cc_final: 0.7719 (tmm) REVERT: C 49 MET cc_start: 0.8541 (mtm) cc_final: 0.8315 (mtp) REVERT: D 5 ARG cc_start: 0.8110 (ttm110) cc_final: 0.7825 (tpp-160) REVERT: D 104 GLU cc_start: 0.8290 (mp0) cc_final: 0.7913 (mp0) REVERT: D 169 HIS cc_start: 0.7157 (OUTLIER) cc_final: 0.6931 (m-70) REVERT: D 203 MET cc_start: 0.8408 (mtp) cc_final: 0.8075 (mtm) REVERT: E 59 GLU cc_start: 0.8004 (pm20) cc_final: 0.7434 (pm20) REVERT: E 208 MET cc_start: 0.9013 (mpp) cc_final: 0.8751 (mmm) REVERT: E 266 MET cc_start: 0.3664 (ptp) cc_final: 0.2865 (pmm) REVERT: E 463 LYS cc_start: 0.8101 (ptmt) cc_final: 0.7763 (pttm) REVERT: F 371 ARG cc_start: 0.9086 (OUTLIER) cc_final: 0.7894 (tpm170) REVERT: g 49 MET cc_start: 0.8829 (mmt) cc_final: 0.8217 (mmm) REVERT: g 101 GLN cc_start: 0.7515 (OUTLIER) cc_final: 0.7108 (mp10) REVERT: g 156 MET cc_start: 0.8283 (OUTLIER) cc_final: 0.7755 (tpp) REVERT: g 226 ILE cc_start: 0.9506 (mm) cc_final: 0.9257 (pp) REVERT: g 229 MET cc_start: 0.9350 (mmm) cc_final: 0.9124 (mmm) outliers start: 43 outliers final: 31 residues processed: 187 average time/residue: 0.6809 time to fit residues: 147.0092 Evaluate side-chains 188 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 150 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 32 LEU Chi-restraints excluded: chain e residue 34 ILE Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 332 GLU Chi-restraints excluded: chain D residue 25 LYS Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 62 LYS Chi-restraints excluded: chain D residue 169 HIS Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 186 ASN Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 441 ASP Chi-restraints excluded: chain E residue 451 VAL Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 136 CYS Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 371 ARG Chi-restraints excluded: chain F residue 375 LEU Chi-restraints excluded: chain g residue 32 MET Chi-restraints excluded: chain g residue 100 VAL Chi-restraints excluded: chain g residue 101 GLN Chi-restraints excluded: chain g residue 115 PHE Chi-restraints excluded: chain g residue 156 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 11 optimal weight: 8.9990 chunk 6 optimal weight: 20.0000 chunk 242 optimal weight: 10.0000 chunk 129 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 73 optimal weight: 0.5980 chunk 301 optimal weight: 10.0000 chunk 244 optimal weight: 10.0000 chunk 135 optimal weight: 0.0980 chunk 304 optimal weight: 2.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 319 HIS E 366 GLN F 410 HIS g 65 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.105989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.073258 restraints weight = 51361.976| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.93 r_work: 0.2987 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 25390 Z= 0.250 Angle : 0.646 14.997 34412 Z= 0.333 Chirality : 0.047 0.159 3975 Planarity : 0.005 0.059 4484 Dihedral : 6.377 85.065 3683 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.68 % Allowed : 15.83 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.15), residues: 3260 helix: 1.52 (0.15), residues: 1261 sheet: 0.11 (0.21), residues: 559 loop : -1.17 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 5 TYR 0.017 0.001 TYR D 252 PHE 0.016 0.002 PHE B 341 TRP 0.008 0.002 TRP C 139 HIS 0.004 0.001 HIS g 65 Details of bonding type rmsd covalent geometry : bond 0.00612 (25390) covalent geometry : angle 0.64618 (34412) hydrogen bonds : bond 0.05619 ( 1105) hydrogen bonds : angle 4.95199 ( 3162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 149 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: e 46 GLN cc_start: 0.8150 (mp10) cc_final: 0.7626 (pp30) REVERT: A 34 MET cc_start: 0.8107 (tmm) cc_final: 0.7701 (tmt) REVERT: A 290 ASP cc_start: 0.7305 (t70) cc_final: 0.6795 (t0) REVERT: A 377 ARG cc_start: 0.8292 (ptp-170) cc_final: 0.7982 (ptp-110) REVERT: B 68 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8096 (mp0) REVERT: B 403 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7609 (pt0) REVERT: C 49 MET cc_start: 0.8678 (mtm) cc_final: 0.8445 (mtp) REVERT: C 284 ARG cc_start: 0.7768 (ttt180) cc_final: 0.6993 (ttm110) REVERT: D 5 ARG cc_start: 0.8200 (ttm110) cc_final: 0.7900 (tpp-160) REVERT: D 104 GLU cc_start: 0.8326 (mp0) cc_final: 0.7959 (mp0) REVERT: D 169 HIS cc_start: 0.7173 (OUTLIER) cc_final: 0.6958 (m-70) REVERT: D 203 MET cc_start: 0.8461 (mtp) cc_final: 0.8192 (mtm) REVERT: E 59 GLU cc_start: 0.8025 (pm20) cc_final: 0.7466 (pm20) REVERT: E 208 MET cc_start: 0.9104 (mpp) cc_final: 0.8691 (mmm) REVERT: E 266 MET cc_start: 0.3680 (ptp) cc_final: 0.2815 (pmm) REVERT: E 280 MET cc_start: 0.7027 (mmm) cc_final: 0.6414 (mmt) REVERT: E 463 LYS cc_start: 0.8088 (ptmt) cc_final: 0.7732 (pttm) REVERT: F 371 ARG cc_start: 0.9113 (OUTLIER) cc_final: 0.7944 (tpm170) REVERT: g 49 MET cc_start: 0.8812 (mmt) cc_final: 0.8216 (mmm) REVERT: g 101 GLN cc_start: 0.7537 (OUTLIER) cc_final: 0.7177 (mp10) REVERT: g 156 MET cc_start: 0.8273 (OUTLIER) cc_final: 0.7753 (tpp) REVERT: g 226 ILE cc_start: 0.9529 (mm) cc_final: 0.9283 (pp) outliers start: 44 outliers final: 27 residues processed: 185 average time/residue: 0.7554 time to fit residues: 160.4773 Evaluate side-chains 182 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 149 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 32 LEU Chi-restraints excluded: chain e residue 34 ILE Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 311 GLU Chi-restraints excluded: chain D residue 62 LYS Chi-restraints excluded: chain D residue 169 HIS Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 441 ASP Chi-restraints excluded: chain E residue 451 VAL Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 136 CYS Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 371 ARG Chi-restraints excluded: chain F residue 375 LEU Chi-restraints excluded: chain g residue 32 MET Chi-restraints excluded: chain g residue 100 VAL Chi-restraints excluded: chain g residue 101 GLN Chi-restraints excluded: chain g residue 115 PHE Chi-restraints excluded: chain g residue 156 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 259 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 301 optimal weight: 6.9990 chunk 143 optimal weight: 6.9990 chunk 322 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 210 optimal weight: 3.9990 chunk 265 optimal weight: 0.9990 chunk 239 optimal weight: 6.9990 chunk 218 optimal weight: 4.9990 chunk 185 optimal weight: 0.6980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 319 HIS F 410 HIS g 65 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.108149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.075433 restraints weight = 50764.927| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.94 r_work: 0.3036 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25390 Z= 0.134 Angle : 0.573 15.434 34412 Z= 0.291 Chirality : 0.044 0.158 3975 Planarity : 0.004 0.067 4484 Dihedral : 6.057 80.100 3683 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.37 % Allowed : 16.09 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.15), residues: 3260 helix: 1.69 (0.15), residues: 1264 sheet: 0.26 (0.21), residues: 555 loop : -1.07 (0.16), residues: 1441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 5 TYR 0.016 0.001 TYR D 252 PHE 0.032 0.001 PHE F 188 TRP 0.007 0.001 TRP g 206 HIS 0.003 0.000 HIS g 65 Details of bonding type rmsd covalent geometry : bond 0.00314 (25390) covalent geometry : angle 0.57308 (34412) hydrogen bonds : bond 0.04456 ( 1105) hydrogen bonds : angle 4.70836 ( 3162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7493.45 seconds wall clock time: 128 minutes 40.44 seconds (7720.44 seconds total)