Starting phenix.real_space_refine on Sat May 24 02:52:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zi1_60118/05_2025/8zi1_60118.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zi1_60118/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8zi1_60118/05_2025/8zi1_60118.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zi1_60118/05_2025/8zi1_60118.map" model { file = "/net/cci-nas-00/data/ceres_data/8zi1_60118/05_2025/8zi1_60118.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zi1_60118/05_2025/8zi1_60118.cif" } resolution = 2.92 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 14.58, per 1000 atoms: 0.58 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: 6.00 Conformation dependent library (CDL) restraints added in 3.1 seconds 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: 3.20 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: 9.44 Time building geometry restraints manager: 7.07 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: 2.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.070 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 55.420 Find NCS groups from input model: 1.270 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.360 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (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 TRP 0.006 0.001 TRP C 139 HIS 0.004 0.001 HIS e 38 PHE 0.020 0.001 PHE C 476 TYR 0.016 0.001 TYR e 16 ARG 0.003 0.000 ARG g 75 Details of bonding type rmsd hydrogen bonds : bond 0.19673 ( 1105) hydrogen bonds : angle 7.09221 ( 3162) covalent geometry : bond 0.00618 (25390) covalent geometry : angle 0.86389 (34412) *********************** 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 : 2.681 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: 1.6254 time to fit residues: 562.9822 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 : 2.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 272 optimal weight: 7.9990 chunk 244 optimal weight: 0.0970 chunk 135 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 chunk 165 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 253 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 153 optimal weight: 9.9990 chunk 188 optimal weight: 2.9990 chunk 293 optimal weight: 0.4980 overall best weight: 1.9184 ------------------------------------------------------------------------------- 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 E 164 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.109734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.077460 restraints weight = 49457.605| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.74 r_work: 0.3117 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1402 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= 0.181 Angle : 0.594 11.133 34412 Z= 0.314 Chirality : 0.045 0.175 3975 Planarity : 0.004 0.062 4484 Dihedral : 6.912 81.253 3683 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.87 % Allowed : 9.53 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.15), residues: 3260 helix: 1.41 (0.15), residues: 1289 sheet: 0.34 (0.21), residues: 561 loop : -0.96 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP g 206 HIS 0.007 0.001 HIS e 74 PHE 0.022 0.001 PHE D 405 TYR 0.023 0.001 TYR E 250 ARG 0.008 0.000 ARG g 33 Details of bonding type rmsd hydrogen bonds : bond 0.05709 ( 1105) hydrogen bonds : angle 5.26986 ( 3162) covalent geometry : bond 0.00424 (25390) covalent geometry : angle 0.59373 (34412) *********************** 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 226 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 177 time to evaluate : 2.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 7 ASP cc_start: 0.8541 (m-30) cc_final: 0.7923 (p0) REVERT: e 46 GLN cc_start: 0.8048 (mp10) cc_final: 0.7469 (pp30) REVERT: A 290 ASP cc_start: 0.7400 (t70) cc_final: 0.7039 (t0) REVERT: B 68 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8170 (mp0) REVERT: C 419 ARG cc_start: 0.7220 (mtm-85) cc_final: 0.6955 (mpp-170) REVERT: D 376 LYS cc_start: 0.8886 (pttt) cc_final: 0.8643 (mttt) REVERT: E 59 GLU cc_start: 0.7942 (pm20) cc_final: 0.7505 (pm20) REVERT: E 181 ARG cc_start: 0.7742 (OUTLIER) cc_final: 0.6825 (mtt90) REVERT: E 266 MET cc_start: 0.4310 (ptp) cc_final: 0.3372 (pmm) REVERT: E 450 MET cc_start: 0.9337 (mmm) cc_final: 0.9128 (mmm) REVERT: E 463 LYS cc_start: 0.8042 (ptmt) cc_final: 0.7774 (pttm) REVERT: F 55 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.8136 (mmm) REVERT: F 110 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.7264 (ptm160) REVERT: F 371 ARG cc_start: 0.9173 (OUTLIER) cc_final: 0.7963 (tpm170) REVERT: g 49 MET cc_start: 0.8759 (mmt) cc_final: 0.8080 (mmm) REVERT: g 156 MET cc_start: 0.8090 (tpt) cc_final: 0.7494 (tpt) REVERT: g 229 MET cc_start: 0.9286 (mmm) cc_final: 0.8978 (mmm) outliers start: 49 outliers final: 12 residues processed: 213 average time/residue: 1.5080 time to fit residues: 367.1943 Evaluate side-chains 177 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 160 time to evaluate : 2.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain B residue 68 GLU 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 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 37 THR Chi-restraints excluded: chain F residue 55 MET 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 67 optimal weight: 8.9990 chunk 141 optimal weight: 7.9990 chunk 133 optimal weight: 5.9990 chunk 225 optimal weight: 4.9990 chunk 318 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 284 optimal weight: 3.9990 chunk 6 optimal weight: 40.0000 chunk 220 optimal weight: 1.9990 chunk 143 optimal weight: 7.9990 chunk 176 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 74 HIS ** e 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 299 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.106385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.073887 restraints weight = 50071.560| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.76 r_work: 0.3049 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 25390 Z= 0.299 Angle : 0.666 12.130 34412 Z= 0.352 Chirality : 0.049 0.168 3975 Planarity : 0.005 0.054 4484 Dihedral : 7.062 80.418 3683 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.33 % Allowed : 11.48 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.14), residues: 3260 helix: 1.21 (0.15), residues: 1289 sheet: 0.05 (0.21), residues: 546 loop : -1.18 (0.15), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP C 139 HIS 0.008 0.001 HIS e 74 PHE 0.026 0.002 PHE B 341 TYR 0.031 0.002 TYR g 208 ARG 0.007 0.001 ARG D 5 Details of bonding type rmsd hydrogen bonds : bond 0.06449 ( 1105) hydrogen bonds : angle 5.30503 ( 3162) covalent geometry : bond 0.00736 (25390) covalent geometry : angle 0.66572 (34412) *********************** 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: 61 poor density : 162 time to evaluate : 2.759 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: e 7 ASP cc_start: 0.8538 (m-30) cc_final: 0.7905 (p0) REVERT: e 24 ILE cc_start: 0.8751 (mt) cc_final: 0.8549 (mt) REVERT: e 46 GLN cc_start: 0.8059 (mp10) cc_final: 0.7467 (pp30) REVERT: A 290 ASP cc_start: 0.7387 (t70) cc_final: 0.7112 (t0) REVERT: B 68 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8198 (mp0) REVERT: B 69 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.7454 (tp-100) REVERT: C 49 MET cc_start: 0.8668 (mtm) cc_final: 0.8455 (mtp) REVERT: D 5 ARG cc_start: 0.8245 (ttm110) cc_final: 0.7850 (tpp-160) REVERT: D 376 LYS cc_start: 0.8888 (pttt) cc_final: 0.8656 (mttt) REVERT: E 59 GLU cc_start: 0.7996 (pm20) cc_final: 0.7537 (pm20) REVERT: E 110 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7893 (mtp-110) REVERT: E 181 ARG cc_start: 0.7754 (OUTLIER) cc_final: 0.6869 (mtt90) REVERT: E 266 MET cc_start: 0.4299 (ptp) cc_final: 0.3646 (pmm) REVERT: E 450 MET cc_start: 0.9304 (mmm) cc_final: 0.9077 (mmm) REVERT: E 463 LYS cc_start: 0.8101 (ptmt) cc_final: 0.7740 (pttm) REVERT: F 371 ARG cc_start: 0.9166 (OUTLIER) cc_final: 0.8009 (tpm170) REVERT: g 49 MET cc_start: 0.8763 (mmt) cc_final: 0.8093 (mmm) REVERT: g 156 MET cc_start: 0.8018 (tpt) cc_final: 0.7563 (tpt) outliers start: 61 outliers final: 21 residues processed: 206 average time/residue: 1.5155 time to fit residues: 356.0294 Evaluate side-chains 173 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 147 time to evaluate : 2.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 32 LEU Chi-restraints excluded: chain e residue 74 HIS Chi-restraints excluded: chain A residue 174 THR 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 B residue 69 GLN Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 454 GLU 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 110 ARG Chi-restraints excluded: chain E residue 181 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 66 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 108 optimal weight: 3.9990 chunk 147 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 169 optimal weight: 1.9990 chunk 310 optimal weight: 20.0000 chunk 58 optimal weight: 7.9990 chunk 120 optimal weight: 3.9990 chunk 315 optimal weight: 10.0000 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.108488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.075795 restraints weight = 50580.256| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.82 r_work: 0.3097 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 25390 Z= 0.150 Angle : 0.551 11.855 34412 Z= 0.287 Chirality : 0.044 0.151 3975 Planarity : 0.004 0.055 4484 Dihedral : 6.544 85.115 3683 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.87 % Allowed : 13.42 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.15), residues: 3260 helix: 1.52 (0.15), residues: 1275 sheet: 0.14 (0.21), residues: 555 loop : -1.09 (0.15), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP g 206 HIS 0.015 0.001 HIS e 74 PHE 0.011 0.001 PHE B 341 TYR 0.016 0.001 TYR D 252 ARG 0.004 0.000 ARG D 5 Details of bonding type rmsd hydrogen bonds : bond 0.04983 ( 1105) hydrogen bonds : angle 4.96066 ( 3162) covalent geometry : bond 0.00354 (25390) covalent geometry : angle 0.55090 (34412) *********************** 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 208 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 159 time to evaluate : 2.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 46 GLN cc_start: 0.8067 (mp10) cc_final: 0.7523 (pp30) REVERT: A 290 ASP cc_start: 0.7348 (t70) cc_final: 0.7048 (t0) REVERT: B 68 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8208 (mp0) REVERT: D 104 GLU cc_start: 0.8202 (mp0) cc_final: 0.7918 (mp0) REVERT: D 376 LYS cc_start: 0.8868 (pttt) cc_final: 0.8662 (mttt) REVERT: D 451 VAL cc_start: 0.8359 (OUTLIER) cc_final: 0.8136 (t) REVERT: E 59 GLU cc_start: 0.8021 (pm20) cc_final: 0.7534 (pm20) REVERT: E 110 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7893 (mtp-110) REVERT: E 181 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.6741 (mtt90) REVERT: E 266 MET cc_start: 0.4272 (ptp) cc_final: 0.3596 (pmm) REVERT: E 450 MET cc_start: 0.9326 (mmm) cc_final: 0.9080 (mmm) REVERT: F 371 ARG cc_start: 0.9151 (OUTLIER) cc_final: 0.7971 (tpm170) REVERT: F 374 GLU cc_start: 0.8402 (mt-10) cc_final: 0.7993 (mt-10) REVERT: g 49 MET cc_start: 0.8753 (mmt) cc_final: 0.8103 (mmm) REVERT: g 156 MET cc_start: 0.8003 (tpt) cc_final: 0.7482 (tpt) REVERT: g 191 LEU cc_start: 0.8490 (pp) cc_final: 0.8263 (pt) outliers start: 49 outliers final: 24 residues processed: 198 average time/residue: 1.3914 time to fit residues: 317.4646 Evaluate side-chains 178 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 149 time to evaluate : 2.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain B residue 68 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 311 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 47 ASP Chi-restraints excluded: chain D residue 62 LYS Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain E residue 110 ARG Chi-restraints excluded: chain E residue 181 ARG 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 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 g residue 32 MET Chi-restraints excluded: chain g residue 100 VAL Chi-restraints excluded: chain g residue 115 PHE Chi-restraints excluded: chain g residue 134 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 89 optimal weight: 4.9990 chunk 231 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 250 optimal weight: 0.9980 chunk 261 optimal weight: 6.9990 chunk 259 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 chunk 203 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 184 optimal weight: 0.0970 chunk 33 optimal weight: 2.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.108756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.076514 restraints weight = 50294.934| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.78 r_work: 0.3087 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2112 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= 0.151 Angle : 0.544 10.974 34412 Z= 0.283 Chirality : 0.044 0.166 3975 Planarity : 0.004 0.060 4484 Dihedral : 6.304 89.187 3683 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.33 % Allowed : 13.81 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.15), residues: 3260 helix: 1.58 (0.15), residues: 1284 sheet: 0.20 (0.21), residues: 562 loop : -1.07 (0.16), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP g 206 HIS 0.002 0.001 HIS F 190 PHE 0.019 0.001 PHE E 415 TYR 0.016 0.001 TYR D 252 ARG 0.010 0.000 ARG D 5 Details of bonding type rmsd hydrogen bonds : bond 0.04836 ( 1105) hydrogen bonds : angle 4.85299 ( 3162) covalent geometry : bond 0.00359 (25390) covalent geometry : angle 0.54385 (34412) *********************** 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 224 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 163 time to evaluate : 3.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 46 GLN cc_start: 0.8089 (mp10) cc_final: 0.7555 (pp30) REVERT: A 290 ASP cc_start: 0.7342 (t70) cc_final: 0.7030 (t0) REVERT: B 68 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8204 (mp0) REVERT: B 214 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8305 (mt-10) REVERT: B 308 GLU cc_start: 0.8956 (OUTLIER) cc_final: 0.8563 (mp0) REVERT: C 311 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7403 (mp0) REVERT: D 5 ARG cc_start: 0.8202 (ttm110) cc_final: 0.7840 (tpp-160) REVERT: D 104 GLU cc_start: 0.8174 (mp0) cc_final: 0.7896 (mp0) REVERT: D 451 VAL cc_start: 0.8322 (OUTLIER) cc_final: 0.8117 (t) REVERT: E 59 GLU cc_start: 0.8017 (pm20) cc_final: 0.7556 (pm20) REVERT: E 110 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7913 (mtp-110) REVERT: E 181 ARG cc_start: 0.7675 (OUTLIER) cc_final: 0.7405 (mmt90) REVERT: E 266 MET cc_start: 0.4162 (ptp) cc_final: 0.3480 (pmm) REVERT: E 450 MET cc_start: 0.9285 (mmm) cc_final: 0.9071 (mmm) REVERT: F 371 ARG cc_start: 0.9146 (OUTLIER) cc_final: 0.7929 (tpm170) REVERT: F 374 GLU cc_start: 0.8400 (mt-10) cc_final: 0.7982 (mt-10) REVERT: g 49 MET cc_start: 0.8747 (mmt) cc_final: 0.8097 (mmm) REVERT: g 156 MET cc_start: 0.8012 (tpt) cc_final: 0.7471 (tpt) REVERT: g 191 LEU cc_start: 0.8483 (pp) cc_final: 0.8278 (pt) outliers start: 61 outliers final: 29 residues processed: 207 average time/residue: 1.4715 time to fit residues: 349.0638 Evaluate side-chains 189 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 152 time to evaluate : 2.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 34 ILE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 467 ASP 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 308 GLU 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 311 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 451 VAL Chi-restraints excluded: chain E residue 110 ARG Chi-restraints excluded: chain E residue 181 ARG Chi-restraints excluded: chain E residue 187 ASP Chi-restraints excluded: chain E residue 352 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 53 ILE 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 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 g residue 32 MET Chi-restraints excluded: chain g residue 100 VAL Chi-restraints excluded: chain g residue 134 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 57 optimal weight: 7.9990 chunk 43 optimal weight: 0.7980 chunk 312 optimal weight: 10.0000 chunk 266 optimal weight: 7.9990 chunk 177 optimal weight: 6.9990 chunk 102 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 281 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 chunk 86 optimal weight: 0.0010 overall best weight: 3.3592 ------------------------------------------------------------------------------- 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 74 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.105906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.073819 restraints weight = 50249.587| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.75 r_work: 0.3055 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 25390 Z= 0.266 Angle : 0.636 10.364 34412 Z= 0.333 Chirality : 0.047 0.167 3975 Planarity : 0.005 0.063 4484 Dihedral : 6.568 85.804 3683 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.90 % Allowed : 14.42 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.15), residues: 3260 helix: 1.38 (0.15), residues: 1270 sheet: -0.01 (0.21), residues: 562 loop : -1.21 (0.15), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP g 206 HIS 0.004 0.001 HIS F 190 PHE 0.016 0.002 PHE B 341 TYR 0.018 0.002 TYR E 250 ARG 0.006 0.000 ARG D 5 Details of bonding type rmsd hydrogen bonds : bond 0.05890 ( 1105) hydrogen bonds : angle 5.07907 ( 3162) covalent geometry : bond 0.00654 (25390) covalent geometry : angle 0.63604 (34412) *********************** 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 227 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 151 time to evaluate : 2.745 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: e 46 GLN cc_start: 0.8127 (mp10) cc_final: 0.7588 (pp30) REVERT: A 290 ASP cc_start: 0.7647 (t70) cc_final: 0.7402 (t0) REVERT: B 68 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.8429 (mp0) REVERT: B 403 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7928 (pt0) REVERT: C 49 MET cc_start: 0.8922 (mtm) cc_final: 0.8721 (mtp) REVERT: C 311 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7620 (mp0) REVERT: D 104 GLU cc_start: 0.8490 (mp0) cc_final: 0.8156 (mp0) REVERT: D 203 MET cc_start: 0.8611 (OUTLIER) cc_final: 0.8394 (mtm) REVERT: E 59 GLU cc_start: 0.8201 (pm20) cc_final: 0.7675 (pm20) REVERT: E 110 ARG cc_start: 0.8316 (OUTLIER) cc_final: 0.8049 (mtp-110) REVERT: E 181 ARG cc_start: 0.7705 (OUTLIER) cc_final: 0.7375 (mmt90) REVERT: E 266 MET cc_start: 0.4125 (ptp) cc_final: 0.3458 (pmm) REVERT: E 450 MET cc_start: 0.9258 (mmm) cc_final: 0.9057 (mmm) REVERT: F 371 ARG cc_start: 0.9168 (OUTLIER) cc_final: 0.8023 (tpm170) REVERT: g 49 MET cc_start: 0.8761 (mmt) cc_final: 0.8079 (mmm) REVERT: g 101 GLN cc_start: 0.7771 (OUTLIER) cc_final: 0.7284 (mp10) REVERT: g 156 MET cc_start: 0.8124 (tpt) cc_final: 0.7813 (tpp) outliers start: 76 outliers final: 37 residues processed: 208 average time/residue: 1.4254 time to fit residues: 340.9693 Evaluate side-chains 188 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 143 time to evaluate : 2.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 32 LEU Chi-restraints excluded: chain e residue 74 HIS Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 465 ILE 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 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 311 GLU Chi-restraints excluded: chain C residue 403 GLU 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 D residue 203 MET Chi-restraints excluded: chain E residue 110 ARG Chi-restraints excluded: chain E residue 181 ARG Chi-restraints excluded: chain E residue 187 ASP 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 53 ILE 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 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 133 VAL Chi-restraints excluded: chain g residue 134 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 76 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 140 optimal weight: 0.1980 chunk 199 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 179 optimal weight: 0.9990 chunk 274 optimal weight: 0.6980 chunk 67 optimal weight: 5.9990 chunk 47 optimal weight: 0.4980 chunk 20 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 319 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.109936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.077372 restraints weight = 50672.646| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.85 r_work: 0.3114 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.071 25390 Z= 0.112 Angle : 0.538 13.226 34412 Z= 0.276 Chirality : 0.043 0.155 3975 Planarity : 0.004 0.072 4484 Dihedral : 6.017 83.019 3683 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.91 % Allowed : 15.79 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.15), residues: 3260 helix: 1.72 (0.15), residues: 1265 sheet: 0.23 (0.21), residues: 560 loop : -1.06 (0.16), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP g 206 HIS 0.020 0.001 HIS e 74 PHE 0.010 0.001 PHE E 317 TYR 0.015 0.001 TYR D 252 ARG 0.010 0.000 ARG D 5 Details of bonding type rmsd hydrogen bonds : bond 0.04240 ( 1105) hydrogen bonds : angle 4.71329 ( 3162) covalent geometry : bond 0.00246 (25390) covalent geometry : angle 0.53832 (34412) *********************** 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 204 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 154 time to evaluate : 2.697 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: e 46 GLN cc_start: 0.8141 (mp10) cc_final: 0.7621 (pp30) REVERT: A 290 ASP cc_start: 0.7250 (t70) cc_final: 0.6931 (t0) REVERT: B 68 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8182 (mp0) REVERT: B 214 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8300 (mt-10) REVERT: C 297 ARG cc_start: 0.8877 (OUTLIER) cc_final: 0.8439 (ptt180) REVERT: C 311 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7352 (mp0) REVERT: D 5 ARG cc_start: 0.8196 (ttm110) cc_final: 0.7892 (tpp-160) REVERT: D 104 GLU cc_start: 0.8201 (mp0) cc_final: 0.7937 (mp0) REVERT: D 203 MET cc_start: 0.8343 (mtp) cc_final: 0.8105 (mtm) REVERT: E 59 GLU cc_start: 0.8011 (pm20) cc_final: 0.7538 (pm20) REVERT: E 263 LEU cc_start: -0.0724 (OUTLIER) cc_final: -0.1201 (pt) REVERT: E 266 MET cc_start: 0.4041 (ptp) cc_final: 0.3192 (pmm) REVERT: E 280 MET cc_start: 0.6648 (mmm) cc_final: 0.5988 (mmt) REVERT: E 450 MET cc_start: 0.9237 (mmm) cc_final: 0.9006 (mmm) REVERT: E 463 LYS cc_start: 0.8137 (ptmt) cc_final: 0.7881 (pttm) REVERT: g 49 MET cc_start: 0.8786 (mmt) cc_final: 0.8149 (mmm) REVERT: g 156 MET cc_start: 0.8248 (tpt) cc_final: 0.7735 (tpp) REVERT: g 187 GLN cc_start: 0.8180 (pp30) cc_final: 0.7969 (pp30) outliers start: 50 outliers final: 25 residues processed: 192 average time/residue: 1.4101 time to fit residues: 312.1388 Evaluate side-chains 175 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 145 time to evaluate : 2.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 34 ILE Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 465 ILE 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 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 297 ARG Chi-restraints excluded: chain C residue 311 GLU Chi-restraints excluded: chain C residue 332 GLU 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 E residue 181 ARG Chi-restraints excluded: chain E residue 263 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 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 375 LEU Chi-restraints excluded: chain g residue 32 MET Chi-restraints excluded: chain g residue 115 PHE Chi-restraints excluded: chain g residue 133 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 26 optimal weight: 5.9990 chunk 51 optimal weight: 20.0000 chunk 49 optimal weight: 2.9990 chunk 322 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 277 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 chunk 205 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 168 optimal weight: 1.9990 chunk 206 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 5 GLN ** e 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.108523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.075903 restraints weight = 50615.253| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 2.83 r_work: 0.3073 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 25390 Z= 0.172 Angle : 0.573 11.352 34412 Z= 0.294 Chirality : 0.044 0.158 3975 Planarity : 0.004 0.061 4484 Dihedral : 6.088 85.051 3683 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.91 % Allowed : 16.13 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.15), residues: 3260 helix: 1.64 (0.15), residues: 1271 sheet: 0.25 (0.22), residues: 558 loop : -1.12 (0.16), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP g 206 HIS 0.003 0.001 HIS F 190 PHE 0.028 0.001 PHE E 415 TYR 0.032 0.001 TYR g 231 ARG 0.008 0.000 ARG D 5 Details of bonding type rmsd hydrogen bonds : bond 0.04816 ( 1105) hydrogen bonds : angle 4.79049 ( 3162) covalent geometry : bond 0.00415 (25390) covalent geometry : angle 0.57287 (34412) *********************** 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 203 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 153 time to evaluate : 3.278 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: e 46 GLN cc_start: 0.8130 (mp10) cc_final: 0.7610 (pp30) REVERT: A 290 ASP cc_start: 0.7268 (t70) cc_final: 0.6958 (t0) REVERT: B 68 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8208 (mp0) REVERT: B 214 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8314 (mt-10) REVERT: B 263 ASP cc_start: 0.7283 (OUTLIER) cc_final: 0.7070 (m-30) REVERT: C 297 ARG cc_start: 0.8900 (OUTLIER) cc_final: 0.8468 (ptt180) REVERT: C 311 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7379 (mp0) REVERT: D 5 ARG cc_start: 0.8229 (ttm110) cc_final: 0.7957 (tpp-160) REVERT: D 104 GLU cc_start: 0.8242 (mp0) cc_final: 0.7947 (mp0) REVERT: D 203 MET cc_start: 0.8399 (mtp) cc_final: 0.8177 (mtm) REVERT: E 59 GLU cc_start: 0.8014 (pm20) cc_final: 0.7544 (pm20) REVERT: E 208 MET cc_start: 0.8900 (mpp) cc_final: 0.8105 (mpt) REVERT: E 266 MET cc_start: 0.3969 (ptp) cc_final: 0.3133 (pmm) REVERT: E 450 MET cc_start: 0.9213 (mmm) cc_final: 0.8981 (mmm) REVERT: E 463 LYS cc_start: 0.8143 (ptmt) cc_final: 0.7885 (pttm) REVERT: g 49 MET cc_start: 0.8772 (mmt) cc_final: 0.8157 (mmm) REVERT: g 101 GLN cc_start: 0.7599 (OUTLIER) cc_final: 0.7147 (mp10) REVERT: g 156 MET cc_start: 0.8295 (OUTLIER) cc_final: 0.7748 (tpp) REVERT: g 187 GLN cc_start: 0.8215 (pp30) cc_final: 0.8011 (pp30) outliers start: 50 outliers final: 30 residues processed: 192 average time/residue: 1.4544 time to fit residues: 321.1012 Evaluate side-chains 184 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 147 time to evaluate : 2.720 ------------------------------------------------------------------------------- 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 65 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 465 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 263 ASP 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 297 ARG Chi-restraints excluded: chain C residue 311 GLU Chi-restraints excluded: chain C residue 332 GLU Chi-restraints excluded: chain C residue 403 GLU Chi-restraints excluded: chain D residue 62 LYS 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 53 ILE 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 218 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 375 LEU Chi-restraints excluded: chain g residue 32 MET Chi-restraints excluded: chain g residue 101 GLN Chi-restraints excluded: chain g residue 115 PHE Chi-restraints excluded: chain g residue 133 VAL 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 129 optimal weight: 0.8980 chunk 290 optimal weight: 9.9990 chunk 174 optimal weight: 0.6980 chunk 94 optimal weight: 0.2980 chunk 72 optimal weight: 0.8980 chunk 136 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 146 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 47 optimal weight: 7.9990 chunk 160 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 319 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.109748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.077720 restraints weight = 49705.178| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.76 r_work: 0.3124 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 25390 Z= 0.108 Angle : 0.542 12.002 34412 Z= 0.276 Chirality : 0.043 0.219 3975 Planarity : 0.004 0.057 4484 Dihedral : 5.798 80.040 3683 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.33 % Allowed : 16.97 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.15), residues: 3260 helix: 1.78 (0.15), residues: 1266 sheet: 0.42 (0.22), residues: 553 loop : -1.01 (0.16), residues: 1441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP g 206 HIS 0.002 0.000 HIS E 319 PHE 0.016 0.001 PHE F 188 TYR 0.028 0.001 TYR g 231 ARG 0.008 0.000 ARG D 5 Details of bonding type rmsd hydrogen bonds : bond 0.03932 ( 1105) hydrogen bonds : angle 4.59997 ( 3162) covalent geometry : bond 0.00240 (25390) covalent geometry : angle 0.54197 (34412) *********************** 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 203 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 168 time to evaluate : 2.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 7 ASP cc_start: 0.8533 (m-30) cc_final: 0.8011 (p0) REVERT: e 46 GLN cc_start: 0.8147 (mp10) cc_final: 0.7659 (pp30) REVERT: A 290 ASP cc_start: 0.7239 (t70) cc_final: 0.6913 (t0) REVERT: B 214 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8285 (mt-10) REVERT: C 34 MET cc_start: 0.8160 (ttp) cc_final: 0.7837 (tmm) REVERT: C 297 ARG cc_start: 0.8854 (OUTLIER) cc_final: 0.8406 (ptt180) REVERT: C 311 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7323 (mp0) REVERT: D 5 ARG cc_start: 0.8131 (ttm110) cc_final: 0.7824 (tpp-160) REVERT: D 104 GLU cc_start: 0.8184 (mp0) cc_final: 0.7907 (mp0) REVERT: E 59 GLU cc_start: 0.8016 (pm20) cc_final: 0.7501 (pm20) REVERT: E 182 THR cc_start: 0.8424 (p) cc_final: 0.8131 (t) REVERT: E 266 MET cc_start: 0.4005 (ptp) cc_final: 0.3158 (pmm) REVERT: E 280 MET cc_start: 0.6625 (mmm) cc_final: 0.6004 (mmt) REVERT: E 450 MET cc_start: 0.9272 (mmm) cc_final: 0.9052 (mmm) REVERT: E 463 LYS cc_start: 0.8163 (ptmt) cc_final: 0.7905 (pttm) REVERT: F 371 ARG cc_start: 0.9159 (OUTLIER) cc_final: 0.7959 (tpm170) REVERT: F 374 GLU cc_start: 0.8332 (mt-10) cc_final: 0.7995 (mt-10) REVERT: g 49 MET cc_start: 0.8784 (mmt) cc_final: 0.8142 (mmm) REVERT: g 156 MET cc_start: 0.8238 (OUTLIER) cc_final: 0.7550 (tpp) REVERT: g 229 MET cc_start: 0.9140 (mmm) cc_final: 0.8413 (mmm) outliers start: 35 outliers final: 23 residues processed: 197 average time/residue: 1.4714 time to fit residues: 336.8292 Evaluate side-chains 178 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 150 time to evaluate : 3.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU 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 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 297 ARG Chi-restraints excluded: chain C residue 311 GLU Chi-restraints excluded: chain C residue 332 GLU Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 62 LYS 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 136 CYS Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 218 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 91 LEU Chi-restraints excluded: chain g residue 115 PHE Chi-restraints excluded: chain g residue 133 VAL 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 57 optimal weight: 2.9990 chunk 291 optimal weight: 2.9990 chunk 186 optimal weight: 7.9990 chunk 316 optimal weight: 1.9990 chunk 137 optimal weight: 4.9990 chunk 131 optimal weight: 6.9990 chunk 138 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 295 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 180 optimal weight: 0.0020 overall best weight: 1.3994 ------------------------------------------------------------------------------- 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 186 ASN E 319 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.108837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.076742 restraints weight = 49846.362| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.75 r_work: 0.3105 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.108 25390 Z= 0.140 Angle : 0.574 11.666 34412 Z= 0.293 Chirality : 0.044 0.230 3975 Planarity : 0.004 0.056 4484 Dihedral : 5.846 81.323 3683 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.30 % Allowed : 17.35 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.15), residues: 3260 helix: 1.75 (0.15), residues: 1267 sheet: 0.38 (0.22), residues: 559 loop : -1.02 (0.16), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP g 206 HIS 0.003 0.000 HIS E 319 PHE 0.030 0.001 PHE E 415 TYR 0.026 0.001 TYR g 231 ARG 0.008 0.000 ARG D 5 Details of bonding type rmsd hydrogen bonds : bond 0.04316 ( 1105) hydrogen bonds : angle 4.67067 ( 3162) covalent geometry : bond 0.00335 (25390) covalent geometry : angle 0.57385 (34412) ********************** 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 185 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 151 time to evaluate : 3.198 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: e 7 ASP cc_start: 0.8425 (m-30) cc_final: 0.7891 (p0) REVERT: e 46 GLN cc_start: 0.8138 (mp10) cc_final: 0.7645 (pp30) REVERT: A 290 ASP cc_start: 0.7241 (t70) cc_final: 0.6920 (t0) REVERT: B 214 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8292 (mt-10) REVERT: C 297 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.8425 (ptt180) REVERT: C 311 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7331 (mp0) REVERT: D 5 ARG cc_start: 0.8152 (ttm110) cc_final: 0.7898 (tpp-160) REVERT: D 104 GLU cc_start: 0.8197 (mp0) cc_final: 0.7909 (mp0) REVERT: E 59 GLU cc_start: 0.8016 (pm20) cc_final: 0.7503 (pm20) REVERT: E 263 LEU cc_start: -0.1339 (OUTLIER) cc_final: -0.1839 (pt) REVERT: E 266 MET cc_start: 0.3884 (ptp) cc_final: 0.3041 (pmm) REVERT: E 280 MET cc_start: 0.6777 (mmm) cc_final: 0.6189 (mmt) REVERT: E 450 MET cc_start: 0.9263 (mmm) cc_final: 0.9034 (mmm) REVERT: E 463 LYS cc_start: 0.8157 (ptmt) cc_final: 0.7908 (pttm) REVERT: F 371 ARG cc_start: 0.9164 (OUTLIER) cc_final: 0.7910 (tpm170) REVERT: g 49 MET cc_start: 0.8782 (mmt) cc_final: 0.8183 (mmm) REVERT: g 156 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.7678 (tpp) outliers start: 34 outliers final: 24 residues processed: 178 average time/residue: 1.4929 time to fit residues: 304.5815 Evaluate side-chains 177 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 147 time to evaluate : 2.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 465 ILE 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 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 297 ARG Chi-restraints excluded: chain C residue 311 GLU Chi-restraints excluded: chain C residue 332 GLU Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 62 LYS Chi-restraints excluded: chain E residue 181 ARG Chi-restraints excluded: chain E residue 263 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 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 115 PHE Chi-restraints excluded: chain g residue 133 VAL 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 287 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 256 optimal weight: 0.4980 chunk 240 optimal weight: 4.9990 chunk 312 optimal weight: 9.9990 chunk 140 optimal weight: 0.0070 chunk 192 optimal weight: 0.4980 chunk 170 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 223 optimal weight: 3.9990 overall best weight: 0.6000 ------------------------------------------------------------------------------- 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 186 ASN E 319 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.110448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.078412 restraints weight = 49347.699| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.75 r_work: 0.3139 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.089 25390 Z= 0.108 Angle : 0.556 11.560 34412 Z= 0.283 Chirality : 0.043 0.228 3975 Planarity : 0.004 0.060 4484 Dihedral : 5.672 78.823 3683 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.41 % Allowed : 17.20 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.15), residues: 3260 helix: 1.82 (0.15), residues: 1269 sheet: 0.52 (0.22), residues: 555 loop : -0.92 (0.16), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP g 206 HIS 0.002 0.000 HIS E 319 PHE 0.029 0.001 PHE F 188 TYR 0.024 0.001 TYR g 231 ARG 0.008 0.000 ARG D 5 Details of bonding type rmsd hydrogen bonds : bond 0.03767 ( 1105) hydrogen bonds : angle 4.54719 ( 3162) covalent geometry : bond 0.00243 (25390) covalent geometry : angle 0.55642 (34412) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15488.70 seconds wall clock time: 267 minutes 18.72 seconds (16038.72 seconds total)