Starting phenix.real_space_refine on Fri Feb 6 21:15:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o1c_70002/02_2026/9o1c_70002_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o1c_70002/02_2026/9o1c_70002.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9o1c_70002/02_2026/9o1c_70002.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o1c_70002/02_2026/9o1c_70002.map" model { file = "/net/cci-nas-00/data/ceres_data/9o1c_70002/02_2026/9o1c_70002_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o1c_70002/02_2026/9o1c_70002_neut.cif" } resolution = 2.05 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 15 5.49 5 Mg 5 5.21 5 S 94 5.16 5 C 17441 2.51 5 N 4825 2.21 5 O 5446 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 197 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27826 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 3872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3872 Classifications: {'peptide': 512} Link IDs: {'PTRANS': 17, 'TRANS': 494} Chain: "B" Number of atoms: 3846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 3846 Classifications: {'peptide': 509} Link IDs: {'PTRANS': 17, 'TRANS': 491} Chain: "C" Number of atoms: 3817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3817 Classifications: {'peptide': 505} Link IDs: {'PTRANS': 16, 'TRANS': 488} Chain: "D" Number of atoms: 3464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3464 Classifications: {'peptide': 456} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 435} Chain: "E" Number of atoms: 3464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3464 Classifications: {'peptide': 456} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 435} Chain: "F" Number of atoms: 3464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3464 Classifications: {'peptide': 456} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 435} Chain: "G" Number of atoms: 2074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2074 Classifications: {'peptide': 269} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 261} Chain breaks: 2 Chain: "H" Number of atoms: 916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 916 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain breaks: 1 Chain: "W" Number of atoms: 1345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1345 Classifications: {'peptide': 177} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 172} Chain: "X" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 710 Classifications: {'peptide': 95} Link IDs: {'TRANS': 94} Chain: "Y" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 675 Classifications: {'peptide': 90} Link IDs: {'TRANS': 89} 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" 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: 6.54, per 1000 atoms: 0.24 Number of scatterers: 27826 At special positions: 0 Unit cell: (131.14, 135.29, 175.96, 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 94 16.00 P 15 15.00 Mg 5 11.99 O 5446 8.00 N 4825 7.00 C 17441 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.45 Conformation dependent library (CDL) restraints added in 1.1 seconds 7244 Ramachandran restraints generated. 3622 Oldfield, 0 Emsley, 3622 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6620 Finding SS restraints... Secondary structure from input PDB file: 168 helices and 22 sheets defined 53.5% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 9 through 19 Processing helix chain 'A' and resid 57 through 59 No H-bonds generated for 'chain 'A' and resid 57 through 59' Processing helix chain 'A' and resid 101 through 105 Processing helix chain 'A' and resid 136 through 140 Processing helix chain 'A' and resid 151 through 158 Processing helix chain 'A' and resid 175 through 186 Processing helix chain 'A' and resid 202 through 216 Processing helix chain 'A' and resid 218 through 220 No H-bonds generated for 'chain 'A' and resid 218 through 220' Processing helix chain 'A' and resid 232 through 253 Proline residue: A 240 - end of helix removed outlier: 4.466A pdb=" N PHE A 250 " --> pdb=" O MET A 246 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG A 251 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG A 253 " --> pdb=" O TYR A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 278 Processing helix chain 'A' and resid 283 through 287 Processing helix chain 'A' and resid 290 through 300 removed outlier: 3.600A pdb=" N HIS A 295 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU A 298 " --> pdb=" O LEU A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 314 Processing helix chain 'A' and resid 340 through 350 Processing helix chain 'A' and resid 357 through 363 Processing helix chain 'A' and resid 378 through 383 removed outlier: 3.757A pdb=" N ALA A 381 " --> pdb=" O VAL A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 405 removed outlier: 3.851A pdb=" N GLY A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N GLY A 393 " --> pdb=" O LYS A 389 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 409 Processing helix chain 'A' and resid 410 through 414 removed outlier: 3.572A pdb=" N ASP A 413 " --> pdb=" O PHE A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 432 Processing helix chain 'A' and resid 441 through 455 removed outlier: 3.504A pdb=" N GLY A 455 " --> pdb=" O ALA A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 463 No H-bonds generated for 'chain 'A' and resid 461 through 463' Processing helix chain 'A' and resid 464 through 480 Processing helix chain 'A' and resid 480 through 491 removed outlier: 3.906A pdb=" N LEU A 484 " --> pdb=" O HIS A 480 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LYS A 490 " --> pdb=" O LYS A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 512 Processing helix chain 'B' and resid 7 through 19 removed outlier: 3.664A pdb=" N ARG B 16 " --> pdb=" O ILE B 12 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS B 19 " --> pdb=" O GLY B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 59 No H-bonds generated for 'chain 'B' and resid 57 through 59' Processing helix chain 'B' and resid 101 through 105 Processing helix chain 'B' and resid 136 through 140 removed outlier: 3.587A 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 Processing helix chain 'B' and resid 202 through 216 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 252 Proline residue: B 240 - end of helix removed outlier: 4.569A pdb=" N PHE B 250 " --> pdb=" O MET B 246 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG B 251 " --> pdb=" O GLY B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 278 Processing helix chain 'B' and resid 290 through 300 removed outlier: 3.743A pdb=" N HIS B 295 " --> pdb=" O VAL B 291 " (cutoff:3.500A) removed outlier: 3.657A 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: 3.620A pdb=" N SER B 348 " --> pdb=" O THR B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 363 Processing helix chain 'B' and resid 378 through 383 removed outlier: 3.508A pdb=" N ALA B 381 " --> pdb=" O VAL B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 392 Processing helix chain 'B' and resid 393 through 408 removed outlier: 3.592A pdb=" N GLU B 403 " --> pdb=" O ALA B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 432 removed outlier: 3.512A pdb=" N ARG B 427 " --> pdb=" O GLU B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 454 Processing helix chain 'B' and resid 455 through 460 removed outlier: 4.239A pdb=" N ASP B 459 " --> pdb=" O PHE 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 480 Processing helix chain 'B' and resid 480 through 488 Processing helix chain 'B' and resid 494 through 512 Processing helix chain 'C' and resid 10 through 19 Processing helix chain 'C' and resid 57 through 59 No H-bonds generated for 'chain 'C' and resid 57 through 59' Processing helix chain 'C' and resid 101 through 105 Processing helix chain 'C' and resid 136 through 140 removed outlier: 3.670A pdb=" N ARG C 140 " --> pdb=" O VAL C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 158 Processing helix chain 'C' and resid 175 through 187 removed outlier: 3.543A pdb=" N GLN C 187 " --> pdb=" O ALA C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 216 Processing helix chain 'C' and resid 218 through 220 No H-bonds generated for 'chain 'C' and resid 218 through 220' Processing helix chain 'C' and resid 232 through 253 Proline residue: C 240 - end of helix removed outlier: 4.346A pdb=" N PHE C 250 " --> pdb=" O MET C 246 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG C 251 " --> pdb=" O GLY C 247 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG C 253 " --> pdb=" O TYR C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 278 Processing helix chain 'C' and resid 283 through 287 Processing helix chain 'C' and resid 290 through 300 removed outlier: 3.697A pdb=" N HIS C 295 " --> pdb=" O VAL C 291 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU C 298 " --> pdb=" O LEU C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 314 Processing helix chain 'C' and resid 340 through 348 Processing helix chain 'C' and resid 357 through 363 Processing helix chain 'C' and resid 378 through 382 removed outlier: 3.598A pdb=" N ALA C 381 " --> pdb=" O VAL C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 403 removed outlier: 3.805A pdb=" N GLY C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N GLY C 393 " --> pdb=" O LYS C 389 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ILE C 394 " --> pdb=" O LEU C 390 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N THR C 396 " --> pdb=" O GLY C 392 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA C 397 " --> pdb=" O GLY C 393 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU C 403 " --> pdb=" O ALA C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 411 removed outlier: 4.445A pdb=" N GLN C 409 " --> pdb=" O ALA C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 432 Processing helix chain 'C' and resid 441 through 454 Processing helix chain 'C' and resid 461 through 463 No H-bonds generated for 'chain 'C' and resid 461 through 463' Processing helix chain 'C' and resid 464 through 480 Processing helix chain 'C' and resid 480 through 489 Processing helix chain 'C' and resid 494 through 512 Processing helix chain 'D' and resid 25 through 29 removed outlier: 4.029A pdb=" N VAL D 29 " --> pdb=" O ARG D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 89 Processing helix chain 'D' and resid 120 through 124 removed outlier: 3.694A pdb=" N GLN D 124 " --> pdb=" O TYR D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 142 Processing helix chain 'D' and resid 159 through 171 Processing helix chain 'D' and resid 187 through 201 Processing helix chain 'D' and resid 203 through 205 No H-bonds generated for 'chain 'D' and resid 203 through 205' Processing helix chain 'D' and resid 217 through 238 removed outlier: 5.228A pdb=" N ALA D 225 " --> pdb=" O ARG D 221 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N LEU D 226 " --> pdb=" O LEU D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 261 removed outlier: 3.815A pdb=" N THR D 253 " --> pdb=" O ILE D 249 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ALA D 261 " --> pdb=" O THR D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 272 Processing helix chain 'D' and resid 275 through 285 removed outlier: 3.611A 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: 3.508A 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 332 Processing helix chain 'D' and resid 355 through 383 removed outlier: 3.924A pdb=" N GLU D 374 " --> pdb=" O GLN D 370 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU D 375 " --> pdb=" O ARG D 371 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ASP D 377 " --> pdb=" O LYS D 373 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ILE D 378 " --> pdb=" O GLU D 374 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE D 381 " --> pdb=" O ASP D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 387 Processing helix chain 'D' and resid 388 through 405 removed outlier: 3.542A pdb=" N LEU D 393 " --> pdb=" O GLU D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 411 No H-bonds generated for 'chain 'D' and resid 409 through 411' Processing helix chain 'D' and resid 412 through 417 Processing helix chain 'D' and resid 424 through 438 Processing helix chain 'D' and resid 444 through 449 removed outlier: 3.617A pdb=" N PHE D 448 " --> pdb=" O GLU D 445 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR D 449 " --> pdb=" O GLN D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 461 removed outlier: 3.941A pdb=" N ALA D 457 " --> pdb=" O GLY D 453 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 89 Processing helix chain 'E' and resid 120 through 124 removed outlier: 3.628A pdb=" N GLN E 124 " --> pdb=" O TYR E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 142 Processing helix chain 'E' and resid 159 through 172 removed outlier: 3.631A pdb=" N ALA E 172 " --> pdb=" O ILE E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 201 removed outlier: 3.562A pdb=" N GLY E 191 " --> pdb=" O ARG E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 205 No H-bonds generated for 'chain 'E' and resid 203 through 205' Processing helix chain 'E' and resid 217 through 238 removed outlier: 3.505A pdb=" N ARG E 221 " --> pdb=" O PRO E 217 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ALA E 225 " --> pdb=" O ARG E 221 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N LEU E 226 " --> pdb=" O LEU E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 261 removed outlier: 3.861A pdb=" N THR E 253 " --> pdb=" O ILE E 249 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL E 259 " --> pdb=" O ALA E 255 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ALA E 261 " --> pdb=" O THR E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 272 Processing helix chain 'E' and resid 275 through 285 removed outlier: 3.636A pdb=" N LEU E 283 " --> pdb=" O GLU E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 304 through 307 Processing helix chain 'E' and resid 310 through 317 Processing helix chain 'E' and resid 318 through 320 No H-bonds generated for 'chain 'E' and resid 318 through 320' Processing helix chain 'E' and resid 327 through 333 removed outlier: 3.585A pdb=" N LEU E 333 " --> pdb=" O ASP E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 355 Processing helix chain 'E' and resid 355 through 383 removed outlier: 3.533A pdb=" N LEU E 375 " --> pdb=" O ARG E 371 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS E 376 " --> pdb=" O TYR E 372 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ASP E 377 " --> pdb=" O LYS E 373 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N ILE E 378 " --> pdb=" O GLU E 374 " (cutoff:3.500A) Processing helix chain 'E' and resid 384 through 387 Processing helix chain 'E' and resid 388 through 405 removed outlier: 3.517A pdb=" N LEU E 393 " --> pdb=" O GLU E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 412 through 417 removed outlier: 3.673A pdb=" N THR E 416 " --> pdb=" O ALA E 412 " (cutoff:3.500A) Processing helix chain 'E' and resid 424 through 438 Processing helix chain 'E' and resid 444 through 449 removed outlier: 3.616A pdb=" N PHE E 448 " --> pdb=" O GLU E 445 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR E 449 " --> pdb=" O GLN E 446 " (cutoff:3.500A) Processing helix chain 'E' and resid 453 through 461 removed outlier: 3.904A pdb=" N ALA E 457 " --> pdb=" O GLY E 453 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL E 458 " --> pdb=" O ILE E 454 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 89 Processing helix chain 'F' and resid 120 through 124 removed outlier: 3.770A pdb=" N GLN F 124 " --> pdb=" O TYR F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 142 Processing helix chain 'F' and resid 159 through 176 removed outlier: 3.644A pdb=" N ALA F 172 " --> pdb=" O ILE F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 201 Processing helix chain 'F' and resid 203 through 205 No H-bonds generated for 'chain 'F' and resid 203 through 205' Processing helix chain 'F' and resid 217 through 238 removed outlier: 3.589A pdb=" N ARG F 221 " --> pdb=" O PRO F 217 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N ALA F 225 " --> pdb=" O ARG F 221 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N LEU F 226 " --> pdb=" O LEU F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 263 removed outlier: 3.732A pdb=" N TYR F 252 " --> pdb=" O ASN F 248 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 272 Processing helix chain 'F' and resid 275 through 285 removed outlier: 3.596A pdb=" N LEU F 283 " --> pdb=" O GLU F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 307 removed outlier: 3.504A pdb=" N ASP F 306 " --> pdb=" O VAL F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 318 removed outlier: 3.766A pdb=" N ALA F 318 " --> pdb=" O ALA F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 333 Processing helix chain 'F' and resid 350 through 355 Processing helix chain 'F' and resid 355 through 380 removed outlier: 3.627A pdb=" N ASP F 377 " --> pdb=" O LYS F 373 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 387 Processing helix chain 'F' and resid 388 through 405 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 448 Processing helix chain 'F' and resid 453 through 461 removed outlier: 3.760A pdb=" N ALA F 457 " --> pdb=" O GLY F 453 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 42 removed outlier: 3.747A pdb=" N ILE G 20 " --> pdb=" O SER G 16 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS G 26 " --> pdb=" O ASN G 22 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY G 42 " --> pdb=" O ARG G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 59 removed outlier: 3.985A pdb=" N ALA G 46 " --> pdb=" O GLY G 42 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N HIS G 55 " --> pdb=" O GLN G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 69 removed outlier: 3.763A pdb=" N VAL G 69 " --> pdb=" O PRO G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 109 removed outlier: 3.789A pdb=" N LYS G 101 " --> pdb=" O LYS G 97 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASP G 102 " --> pdb=" O SER G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 129 Processing helix chain 'G' and resid 145 through 148 Processing helix chain 'G' and resid 149 through 162 removed outlier: 3.574A pdb=" N MET G 156 " --> pdb=" O SER G 152 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR G 160 " --> pdb=" O MET G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 210 through 286 removed outlier: 3.660A pdb=" N VAL G 220 " --> pdb=" O ASP G 216 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA G 285 " --> pdb=" O GLY G 281 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 106 removed outlier: 3.811A pdb=" N ALA H 95 " --> pdb=" O ASP H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 129 removed outlier: 4.610A pdb=" N ALA H 117 " --> pdb=" O PHE H 113 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA H 127 " --> pdb=" O ALA H 123 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN H 128 " --> pdb=" O GLU H 124 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU H 129 " --> pdb=" O ALA H 125 " (cutoff:3.500A) Processing helix chain 'W' and resid 3 through 22 Proline residue: W 10 - end of helix Processing helix chain 'W' and resid 24 through 40 removed outlier: 3.566A pdb=" N GLN W 40 " --> pdb=" O ALA W 36 " (cutoff:3.500A) Processing helix chain 'W' and resid 41 through 50 removed outlier: 3.674A pdb=" N GLN W 46 " --> pdb=" O ASP W 42 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS W 49 " --> pdb=" O ARG W 45 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU W 50 " --> pdb=" O GLN W 46 " (cutoff:3.500A) Processing helix chain 'W' and resid 54 through 67 Processing helix chain 'W' and resid 68 through 70 No H-bonds generated for 'chain 'W' and resid 68 through 70' Processing helix chain 'W' and resid 71 through 84 Processing helix chain 'W' and resid 86 through 88 No H-bonds generated for 'chain 'W' and resid 86 through 88' Processing helix chain 'W' and resid 89 through 105 Processing helix chain 'W' and resid 119 through 135 Processing helix chain 'W' and resid 164 through 178 removed outlier: 3.607A pdb=" N LYS W 168 " --> pdb=" O SER W 164 " (cutoff:3.500A) Processing helix chain 'X' and resid 62 through 137 removed outlier: 3.783A pdb=" N GLN X 85 " --> pdb=" O LYS X 81 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N ASN X 114 " --> pdb=" O GLU X 110 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N SER X 115 " --> pdb=" O GLN X 111 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL X 116 " --> pdb=" O GLU X 112 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA X 119 " --> pdb=" O SER X 115 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA X 122 " --> pdb=" O ASP X 118 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N GLY X 125 " --> pdb=" O ARG X 121 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ALA X 126 " --> pdb=" O ALA X 122 " (cutoff:3.500A) Processing helix chain 'X' and resid 140 through 143 Processing helix chain 'X' and resid 144 through 152 removed outlier: 3.573A pdb=" N SER X 150 " --> pdb=" O GLU X 146 " (cutoff:3.500A) Processing helix chain 'X' and resid 153 through 155 No H-bonds generated for 'chain 'X' and resid 153 through 155' Processing helix chain 'Y' and resid 67 through 97 Processing helix chain 'Y' and resid 98 through 102 Processing helix chain 'Y' and resid 106 through 140 removed outlier: 3.607A pdb=" N GLN Y 123 " --> pdb=" O ALA Y 119 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA Y 126 " --> pdb=" O ALA Y 122 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA Y 138 " --> pdb=" O LYS Y 134 " (cutoff:3.500A) Processing helix chain 'Y' and resid 141 through 146 removed outlier: 3.881A pdb=" N HIS Y 145 " --> pdb=" O ASP Y 141 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLU Y 146 " --> pdb=" O ALA Y 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 141 through 146' Processing helix chain 'Y' and resid 148 through 153 Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 67 removed outlier: 4.493A pdb=" N GLU A 52 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N MET A 53 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ARG A 41 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N VAL A 35 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE A 39 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL A 75 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ALA A 64 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ALA F 35 " --> pdb=" O THR F 76 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N GLU F 34 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ARG F 57 " --> pdb=" O GLN F 48 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N GLN F 50 " --> pdb=" O VAL F 55 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N VAL F 55 " --> pdb=" O GLN F 50 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N VAL F 19 " --> pdb=" O ILE F 15 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ILE F 15 " --> pdb=" O VAL F 19 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ASP F 21 " --> pdb=" O VAL F 13 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 100 removed outlier: 4.118A pdb=" N ALA A 126 " --> pdb=" O VAL A 100 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 108 through 110 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 108 through 110 current: chain 'A' and resid 222 through 227 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 222 through 227 current: chain 'A' and resid 323 through 332 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 323 through 332 current: chain 'A' and resid 375 through 376 No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 25 through 35 removed outlier: 6.684A pdb=" N ARG B 41 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N VAL B 35 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ILE B 39 " --> pdb=" O VAL B 35 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 39 through 43 current: chain 'B' and resid 61 through 67 removed outlier: 5.729A pdb=" N ALA B 64 " --> pdb=" O VAL B 75 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL B 75 " --> pdb=" O ALA B 64 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 72 through 76 current: chain 'D' and resid 19 through 23 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 19 through 23 current: chain 'D' and resid 44 through 52 removed outlier: 6.897A pdb=" N ARG D 57 " --> pdb=" O GLN D 48 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N GLN D 50 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N VAL D 55 " --> pdb=" O GLN D 50 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 55 through 60 current: chain 'W' and resid 137 through 144 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 137 through 144 current: chain 'W' and resid 159 through 162 Processing sheet with id=AA5, first strand: chain 'B' and resid 97 through 99 Processing sheet with id=AA6, first strand: chain 'B' and resid 108 through 110 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 108 through 110 current: chain 'B' and resid 222 through 227 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 222 through 227 current: chain 'B' and resid 323 through 332 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 323 through 332 current: chain 'B' and resid 375 through 376 No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 61 through 67 removed outlier: 4.428A pdb=" N GLU C 52 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N MET C 53 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ARG C 41 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N VAL C 35 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ILE C 39 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VAL C 75 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N ALA C 64 " --> pdb=" O VAL C 75 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ALA E 35 " --> pdb=" O THR E 76 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLU E 34 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ARG E 57 " --> pdb=" O GLN E 48 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N GLN E 50 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N VAL E 55 " --> pdb=" O GLN E 50 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N VAL E 19 " --> pdb=" O ILE E 15 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ILE E 15 " --> pdb=" O VAL E 19 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ASP E 21 " --> pdb=" O VAL E 13 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 97 through 100 removed outlier: 3.983A pdb=" N ALA C 126 " --> pdb=" O VAL C 100 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 108 through 109 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 108 through 109 current: chain 'C' and resid 222 through 228 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 222 through 228 current: chain 'C' and resid 323 through 332 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 323 through 332 current: chain 'C' and resid 375 through 376 No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 146 through 147 removed outlier: 4.428A pdb=" N VAL C 160 " --> pdb=" O VAL C 147 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 81 through 83 Processing sheet with id=AB3, first strand: chain 'D' and resid 92 through 93 removed outlier: 6.205A pdb=" N MET D 93 " --> pdb=" O TYR D 211 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N SER D 179 " --> pdb=" O ALA D 208 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N VAL D 210 " --> pdb=" O SER D 179 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N PHE D 181 " --> pdb=" O VAL D 210 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N GLY D 212 " --> pdb=" O PHE D 181 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N GLY D 183 " --> pdb=" O GLY D 212 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N TYR D 178 " --> pdb=" O ASP D 241 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL D 242 " --> pdb=" O THR D 296 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N ILE D 298 " --> pdb=" O VAL D 242 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU D 244 " --> pdb=" O ILE D 298 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N ALA D 300 " --> pdb=" O LEU D 244 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ILE D 246 " --> pdb=" O ALA D 300 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N TYR D 302 " --> pdb=" O ILE D 246 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LYS D 149 " --> pdb=" O ALA D 322 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N VAL D 324 " --> pdb=" O LYS D 149 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLY D 151 " --> pdb=" O VAL D 324 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 130 through 131 removed outlier: 4.169A pdb=" N PHE D 144 " --> pdb=" O LEU D 131 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 81 through 84 removed outlier: 4.914A pdb=" N GLU E 110 " --> pdb=" O VAL E 84 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 92 through 93 removed outlier: 6.625A pdb=" N MET E 93 " --> pdb=" O TYR E 211 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL E 150 " --> pdb=" O GLN E 299 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N VAL E 301 " --> pdb=" O VAL E 150 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU E 152 " --> pdb=" O VAL E 301 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LYS E 149 " --> pdb=" O ALA E 322 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N VAL E 324 " --> pdb=" O LYS E 149 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLY E 151 " --> pdb=" O VAL E 324 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 130 through 131 removed outlier: 4.189A pdb=" N PHE E 144 " --> pdb=" O LEU E 131 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 81 through 83 Processing sheet with id=AB9, first strand: chain 'F' and resid 92 through 93 removed outlier: 6.303A pdb=" N MET F 93 " --> pdb=" O TYR F 211 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N GLN F 213 " --> pdb=" O MET F 93 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N TYR F 178 " --> pdb=" O ASP F 241 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N VAL F 242 " --> pdb=" O THR F 296 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N ILE F 298 " --> pdb=" O VAL F 242 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LEU F 244 " --> pdb=" O ILE F 298 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N ALA F 300 " --> pdb=" O LEU F 244 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N ILE F 246 " --> pdb=" O ALA F 300 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL F 150 " --> pdb=" O GLN F 299 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 130 through 131 removed outlier: 4.664A pdb=" N PHE F 144 " --> pdb=" O LEU F 131 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 133 through 137 removed outlier: 7.482A pdb=" N LEU G 115 " --> pdb=" O VAL G 134 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ALA G 136 " --> pdb=" O LEU G 115 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N VAL G 117 " --> pdb=" O ALA G 136 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ILE G 79 " --> pdb=" O VAL G 171 " (cutoff:3.500A) removed outlier: 8.666A pdb=" N ASN G 173 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 8.996A pdb=" N VAL G 81 " --> pdb=" O ASN G 173 " (cutoff:3.500A) removed outlier: 12.163A pdb=" N PHE G 175 " --> pdb=" O VAL G 81 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N THR G 180 " --> pdb=" O VAL G 176 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 15 through 21 removed outlier: 6.392A pdb=" N ILE H 9 " --> pdb=" O ILE H 16 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N SER H 18 " --> pdb=" O CYS H 7 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N CYS H 7 " --> pdb=" O SER H 18 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LEU H 20 " --> pdb=" O VAL H 5 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N VAL H 5 " --> pdb=" O LEU H 20 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 31 through 35 removed outlier: 3.520A pdb=" N MET H 23 " --> pdb=" O VAL H 54 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N HIS H 27 " --> pdb=" O PRO H 50 " (cutoff:3.500A) 1384 hydrogen bonds defined for protein. 3945 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: 5.60 Time building geometry restraints manager: 3.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5724 1.32 - 1.45: 5815 1.45 - 1.57: 16486 1.57 - 1.70: 19 1.70 - 1.83: 171 Bond restraints: 28215 Sorted by residual: bond pdb=" C4 ADP F 501 " pdb=" C5 ADP F 501 " ideal model delta sigma weight residual 1.490 1.351 0.139 2.00e-02 2.50e+03 4.85e+01 bond pdb=" C4 ADP E 501 " pdb=" C5 ADP E 501 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.11e+01 bond pdb=" C4 ADP D 501 " pdb=" C5 ADP D 501 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.05e+01 bond pdb=" CZ ARG B 284 " pdb=" NH1 ARG B 284 " ideal model delta sigma weight residual 1.323 1.249 0.074 1.40e-02 5.10e+03 2.76e+01 bond pdb=" C5 ADP F 501 " pdb=" C6 ADP F 501 " ideal model delta sigma weight residual 1.490 1.389 0.101 2.00e-02 2.50e+03 2.56e+01 ... (remaining 28210 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.91: 36642 3.91 - 7.83: 1480 7.83 - 11.74: 37 11.74 - 15.66: 4 15.66 - 19.57: 2 Bond angle restraints: 38165 Sorted by residual: angle pdb=" PB ATP B 600 " pdb=" O3B ATP B 600 " pdb=" PG ATP B 600 " ideal model delta sigma weight residual 139.87 123.97 15.90 1.00e+00 1.00e+00 2.53e+02 angle pdb=" PA ATP B 600 " pdb=" O3A ATP B 600 " pdb=" PB ATP B 600 " ideal model delta sigma weight residual 136.83 123.07 13.76 1.00e+00 1.00e+00 1.89e+02 angle pdb=" PB ATP C 600 " pdb=" O3B ATP C 600 " pdb=" PG ATP C 600 " ideal model delta sigma weight residual 139.87 131.25 8.62 1.00e+00 1.00e+00 7.44e+01 angle pdb=" CA ALA C 183 " pdb=" C ALA C 183 " pdb=" O ALA C 183 " ideal model delta sigma weight residual 120.80 112.51 8.29 1.05e+00 9.07e-01 6.23e+01 angle pdb=" O GLN C 434 " pdb=" C GLN C 434 " pdb=" N LYS C 435 " ideal model delta sigma weight residual 123.24 113.71 9.53 1.23e+00 6.61e-01 6.01e+01 ... (remaining 38160 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.14: 16880 35.14 - 70.28: 321 70.28 - 105.41: 21 105.41 - 140.55: 4 140.55 - 175.69: 2 Dihedral angle restraints: 17228 sinusoidal: 6854 harmonic: 10374 Sorted by residual: dihedral pdb=" O1B ADP D 501 " pdb=" O3A ADP D 501 " pdb=" PB ADP D 501 " pdb=" PA ADP D 501 " ideal model delta sinusoidal sigma weight residual -60.00 115.69 -175.69 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O2A ADP F 501 " pdb=" O3A ADP F 501 " pdb=" PA ADP F 501 " pdb=" PB ADP F 501 " ideal model delta sinusoidal sigma weight residual -60.00 98.96 -158.96 1 2.00e+01 2.50e-03 4.64e+01 dihedral pdb=" C VAL E 270 " pdb=" N VAL E 270 " pdb=" CA VAL E 270 " pdb=" CB VAL E 270 " ideal model delta harmonic sigma weight residual -122.00 -138.37 16.37 0 2.50e+00 1.60e-01 4.29e+01 ... (remaining 17225 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 3059 0.100 - 0.200: 1156 0.200 - 0.300: 130 0.300 - 0.401: 21 0.401 - 0.501: 9 Chirality restraints: 4375 Sorted by residual: chirality pdb=" CA LEU G 87 " pdb=" N LEU G 87 " pdb=" C LEU G 87 " pdb=" CB LEU G 87 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.27e+00 chirality pdb=" CA ARG B 279 " pdb=" N ARG B 279 " pdb=" C ARG B 279 " pdb=" CB ARG B 279 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.27e+00 chirality pdb=" CA VAL E 270 " pdb=" N VAL E 270 " pdb=" C VAL E 270 " pdb=" CB VAL E 270 " both_signs ideal model delta sigma weight residual False 2.44 1.96 0.48 2.00e-01 2.50e+01 5.75e+00 ... (remaining 4372 not shown) Planarity restraints: 4984 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 475 " 0.134 2.00e-02 2.50e+03 7.99e-02 1.28e+02 pdb=" CG TYR C 475 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR C 475 " -0.053 2.00e-02 2.50e+03 pdb=" CD2 TYR C 475 " -0.059 2.00e-02 2.50e+03 pdb=" CE1 TYR C 475 " -0.062 2.00e-02 2.50e+03 pdb=" CE2 TYR C 475 " -0.054 2.00e-02 2.50e+03 pdb=" CZ TYR C 475 " -0.019 2.00e-02 2.50e+03 pdb=" OH TYR C 475 " 0.139 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 121 " -0.128 2.00e-02 2.50e+03 6.94e-02 9.64e+01 pdb=" CG TYR F 121 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR F 121 " 0.049 2.00e-02 2.50e+03 pdb=" CD2 TYR F 121 " 0.061 2.00e-02 2.50e+03 pdb=" CE1 TYR F 121 " 0.042 2.00e-02 2.50e+03 pdb=" CE2 TYR F 121 " 0.033 2.00e-02 2.50e+03 pdb=" CZ TYR F 121 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR F 121 " -0.105 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 434 " -0.051 2.00e-02 2.50e+03 9.68e-02 9.36e+01 pdb=" C GLN C 434 " 0.167 2.00e-02 2.50e+03 pdb=" O GLN C 434 " -0.062 2.00e-02 2.50e+03 pdb=" N LYS C 435 " -0.055 2.00e-02 2.50e+03 ... (remaining 4981 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 23 2.46 - 3.07: 16703 3.07 - 3.68: 40331 3.68 - 4.29: 62744 4.29 - 4.90: 103197 Nonbonded interactions: 222998 Sorted by model distance: nonbonded pdb=" OG1 THR A 177 " pdb="MG MG A 601 " model vdw 1.849 2.170 nonbonded pdb=" O2G ATP C 600 " pdb="MG MG C 601 " model vdw 1.870 2.170 nonbonded pdb=" OG SER B 24 " pdb=" OE1 GLU Y 155 " model vdw 1.880 3.040 nonbonded pdb=" O2G ATP B 600 " pdb="MG MG B 601 " model vdw 1.902 2.170 nonbonded pdb=" O1G ATP A 600 " pdb="MG MG A 601 " model vdw 1.927 2.170 ... (remaining 222993 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 8 through 601) selection = (chain 'B' and resid 8 through 601) selection = chain 'C' } ncs_group { reference = (chain 'D' and resid 8 through 501) selection = (chain 'E' and resid 8 through 501) selection = chain 'F' } ncs_group { reference = (chain 'X' and resid 66 through 155) selection = chain 'Y' } 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: 3.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 26.390 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.050 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:6.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6766 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 : 0.013 0.139 28215 Z= 0.796 Angle : 1.867 19.572 38165 Z= 1.262 Chirality : 0.099 0.501 4375 Planarity : 0.016 0.262 4984 Dihedral : 13.413 175.690 10608 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 1.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.95 % Favored : 96.99 % Rotamer: Outliers : 0.17 % Allowed : 3.32 % Favored : 96.51 % Cbeta Deviations : 0.66 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.13), residues: 3622 helix: -0.37 (0.11), residues: 1629 sheet: -0.00 (0.20), residues: 515 loop : -0.40 (0.16), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.040 0.002 ARG C 251 TYR 0.139 0.017 TYR C 475 PHE 0.078 0.013 PHE C 407 TRP 0.052 0.018 TRP B 139 HIS 0.012 0.003 HIS E 175 Details of bonding type rmsd covalent geometry : bond 0.01272 (28215) covalent geometry : angle 1.86722 (38165) hydrogen bonds : bond 0.20191 ( 1384) hydrogen bonds : angle 7.06034 ( 3945) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7244 Ramachandran restraints generated. 3622 Oldfield, 0 Emsley, 3622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7244 Ramachandran restraints generated. 3622 Oldfield, 0 Emsley, 3622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 455 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 445 MET cc_start: 0.8696 (mtm) cc_final: 0.8388 (mtp) REVERT: A 464 LYS cc_start: 0.8045 (mttt) cc_final: 0.7845 (tttt) outliers start: 5 outliers final: 1 residues processed: 459 average time/residue: 0.8920 time to fit residues: 459.8454 Evaluate side-chains 240 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 239 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 5.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 315 ASN A 424 HIS A 458 GLN A 512 GLN B 458 GLN C 295 HIS C 424 HIS E 128 ASN E 248 ASN E 402 GLN E 437 ASN F 358 HIS G 226 GLN H 128 GLN W 20 GLN X 78 GLN X 93 GLN X 147 GLN Y 93 GLN Y 114 ASN Y 123 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.148539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.109491 restraints weight = 37488.589| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 1.31 r_work: 0.3507 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3427 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 28215 Z= 0.181 Angle : 0.646 7.867 38165 Z= 0.347 Chirality : 0.046 0.205 4375 Planarity : 0.005 0.062 4984 Dihedral : 8.021 161.164 4086 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.35 % Favored : 98.59 % Rotamer: Outliers : 2.11 % Allowed : 8.69 % Favored : 89.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.14), residues: 3622 helix: 1.46 (0.12), residues: 1652 sheet: 0.42 (0.20), residues: 554 loop : 0.23 (0.17), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG X 91 TYR 0.019 0.002 TYR F 449 PHE 0.016 0.002 PHE G 125 TRP 0.014 0.003 TRP W 28 HIS 0.008 0.001 HIS C 424 Details of bonding type rmsd covalent geometry : bond 0.00375 (28215) covalent geometry : angle 0.64599 (38165) hydrogen bonds : bond 0.05390 ( 1384) hydrogen bonds : angle 4.76204 ( 3945) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7244 Ramachandran restraints generated. 3622 Oldfield, 0 Emsley, 3622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7244 Ramachandran restraints generated. 3622 Oldfield, 0 Emsley, 3622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 296 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 ASP cc_start: 0.8831 (m-30) cc_final: 0.8624 (m-30) REVERT: A 409 GLN cc_start: 0.7763 (mm-40) cc_final: 0.7211 (tt0) REVERT: A 419 ARG cc_start: 0.7595 (OUTLIER) cc_final: 0.6804 (tpp-160) REVERT: A 464 LYS cc_start: 0.8218 (mttt) cc_final: 0.7359 (tttt) REVERT: A 478 ARG cc_start: 0.7736 (OUTLIER) cc_final: 0.6337 (ttp80) REVERT: B 459 ASP cc_start: 0.6414 (p0) cc_final: 0.6137 (p0) REVERT: B 507 LYS cc_start: 0.7618 (mtpt) cc_final: 0.7264 (mmmt) REVERT: C 29 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7144 (mp0) REVERT: D 108 GLU cc_start: 0.5424 (OUTLIER) cc_final: 0.4896 (tm-30) REVERT: D 131 LEU cc_start: 0.7561 (tp) cc_final: 0.7350 (tt) REVERT: D 363 ARG cc_start: 0.6520 (mmt180) cc_final: 0.6140 (mmm160) REVERT: D 371 ARG cc_start: 0.6988 (tpp80) cc_final: 0.6465 (tpt-90) REVERT: D 376 LYS cc_start: 0.7046 (ttmt) cc_final: 0.6765 (ptpt) REVERT: D 382 LEU cc_start: 0.7064 (mt) cc_final: 0.6734 (mp) REVERT: D 427 ASP cc_start: 0.5911 (t0) cc_final: 0.5692 (t0) REVERT: E 129 GLU cc_start: 0.7760 (tt0) cc_final: 0.7313 (pm20) REVERT: E 357 ASP cc_start: 0.8205 (t0) cc_final: 0.8004 (t70) REVERT: E 459 GLU cc_start: 0.7052 (mm-30) cc_final: 0.6467 (mt-10) REVERT: G 32 MET cc_start: 0.8511 (ttp) cc_final: 0.8158 (ttt) REVERT: G 143 GLU cc_start: 0.6457 (pm20) cc_final: 0.6079 (mm-30) REVERT: G 174 LYS cc_start: 0.7795 (mttt) cc_final: 0.7557 (mmtm) REVERT: G 251 ASP cc_start: 0.8185 (m-30) cc_final: 0.7945 (m-30) REVERT: H 9 ILE cc_start: 0.4401 (mt) cc_final: 0.4158 (tt) REVERT: H 128 GLN cc_start: 0.6578 (mt0) cc_final: 0.6242 (mm-40) REVERT: X 123 GLN cc_start: 0.5348 (mm110) cc_final: 0.4774 (mm-40) REVERT: X 147 GLN cc_start: 0.5588 (tp40) cc_final: 0.4934 (mt0) outliers start: 61 outliers final: 15 residues processed: 338 average time/residue: 0.8272 time to fit residues: 317.1906 Evaluate side-chains 230 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 211 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 ARG Chi-restraints excluded: chain A residue 478 ARG Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 453 GLU Chi-restraints excluded: chain D residue 108 GLU Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain E residue 292 LYS Chi-restraints excluded: chain F residue 108 GLU Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 201 SER Chi-restraints excluded: chain F residue 384 MET Chi-restraints excluded: chain F residue 425 LEU Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 275 GLU Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain W residue 138 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 357 optimal weight: 4.9990 chunk 211 optimal weight: 5.9990 chunk 332 optimal weight: 3.9990 chunk 137 optimal weight: 0.9980 chunk 172 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 chunk 259 optimal weight: 4.9990 chunk 325 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 chunk 129 optimal weight: 4.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 470 GLN D 348 GLN G 229 GLN W 22 HIS ** X 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 78 GLN X 104 GLN Y 123 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.135944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.094176 restraints weight = 35584.202| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.29 r_work: 0.3258 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.5146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 28215 Z= 0.172 Angle : 0.633 8.812 38165 Z= 0.339 Chirality : 0.045 0.169 4375 Planarity : 0.005 0.063 4984 Dihedral : 8.352 168.259 4084 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.77 % Favored : 98.18 % Rotamer: Outliers : 1.83 % Allowed : 9.52 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.14), residues: 3622 helix: 1.92 (0.13), residues: 1644 sheet: 0.38 (0.20), residues: 571 loop : 0.26 (0.17), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 251 TYR 0.020 0.002 TYR C 293 PHE 0.022 0.002 PHE C 250 TRP 0.014 0.001 TRP W 28 HIS 0.006 0.002 HIS E 196 Details of bonding type rmsd covalent geometry : bond 0.00347 (28215) covalent geometry : angle 0.63260 (38165) hydrogen bonds : bond 0.06367 ( 1384) hydrogen bonds : angle 4.75225 ( 3945) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7244 Ramachandran restraints generated. 3622 Oldfield, 0 Emsley, 3622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7244 Ramachandran restraints generated. 3622 Oldfield, 0 Emsley, 3622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 242 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3 GLN cc_start: 0.7917 (pt0) cc_final: 0.7141 (tm-30) REVERT: A 464 LYS cc_start: 0.8196 (mttt) cc_final: 0.7370 (ttpt) REVERT: A 478 ARG cc_start: 0.7743 (OUTLIER) cc_final: 0.6228 (ttp80) REVERT: B 507 LYS cc_start: 0.7789 (mtpt) cc_final: 0.7425 (mmmt) REVERT: C 29 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8466 (tp30) REVERT: C 440 MET cc_start: 0.8707 (mtp) cc_final: 0.8408 (mtp) REVERT: D 374 GLU cc_start: 0.6531 (OUTLIER) cc_final: 0.6187 (mt-10) REVERT: D 382 LEU cc_start: 0.7170 (mt) cc_final: 0.6877 (mp) REVERT: D 427 ASP cc_start: 0.6207 (t0) cc_final: 0.5909 (t0) REVERT: E 130 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8558 (tm) REVERT: E 164 MET cc_start: 0.9223 (ttm) cc_final: 0.9003 (ttm) REVERT: E 248 ASN cc_start: 0.7661 (t0) cc_final: 0.7355 (t0) REVERT: E 292 LYS cc_start: 0.8784 (OUTLIER) cc_final: 0.8568 (mtpp) REVERT: E 373 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8264 (ttpp) REVERT: E 459 GLU cc_start: 0.7667 (mm-30) cc_final: 0.7294 (tm-30) REVERT: G 32 MET cc_start: 0.8423 (ttp) cc_final: 0.8103 (ttt) REVERT: G 174 LYS cc_start: 0.7784 (mttt) cc_final: 0.7501 (mmtm) REVERT: G 251 ASP cc_start: 0.8213 (m-30) cc_final: 0.7998 (m-30) REVERT: H 76 MET cc_start: 0.4971 (tpp) cc_final: 0.4319 (ptt) outliers start: 53 outliers final: 16 residues processed: 283 average time/residue: 0.7817 time to fit residues: 252.8574 Evaluate side-chains 229 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 207 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 478 ARG Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 237 TYR Chi-restraints excluded: chain C residue 453 GLU Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 374 GLU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 292 LYS Chi-restraints excluded: chain E residue 373 LYS Chi-restraints excluded: chain F residue 108 GLU Chi-restraints excluded: chain F residue 142 CYS Chi-restraints excluded: chain F residue 371 ARG Chi-restraints excluded: chain F residue 425 LEU Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 275 GLU Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain W residue 110 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 226 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 342 optimal weight: 3.9990 chunk 278 optimal weight: 9.9990 chunk 132 optimal weight: 7.9990 chunk 221 optimal weight: 0.8980 chunk 229 optimal weight: 0.9990 chunk 180 optimal weight: 2.9990 chunk 203 optimal weight: 8.9990 chunk 269 optimal weight: 0.9980 chunk 300 optimal weight: 6.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 221 ASN C 426 GLN ** F 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 437 ASN F 442 HIS W 22 HIS W 24 GLN ** X 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 104 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.137540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.096507 restraints weight = 36467.042| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.28 r_work: 0.3300 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.5388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 28215 Z= 0.112 Angle : 0.512 7.464 38165 Z= 0.270 Chirality : 0.042 0.193 4375 Planarity : 0.003 0.048 4984 Dihedral : 7.905 178.482 4084 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.35 % Favored : 98.59 % Rotamer: Outliers : 1.49 % Allowed : 10.48 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.14), residues: 3622 helix: 2.22 (0.13), residues: 1643 sheet: 0.48 (0.20), residues: 570 loop : 0.31 (0.17), residues: 1409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 371 TYR 0.018 0.001 TYR D 252 PHE 0.021 0.001 PHE F 194 TRP 0.007 0.001 TRP C 139 HIS 0.003 0.001 HIS H 6 Details of bonding type rmsd covalent geometry : bond 0.00224 (28215) covalent geometry : angle 0.51209 (38165) hydrogen bonds : bond 0.04800 ( 1384) hydrogen bonds : angle 4.42082 ( 3945) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7244 Ramachandran restraints generated. 3622 Oldfield, 0 Emsley, 3622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7244 Ramachandran restraints generated. 3622 Oldfield, 0 Emsley, 3622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 218 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLN cc_start: 0.8203 (pt0) cc_final: 0.7479 (tm-30) REVERT: A 95 ILE cc_start: 0.8753 (OUTLIER) cc_final: 0.8495 (pp) REVERT: A 246 MET cc_start: 0.9138 (mtt) cc_final: 0.8874 (mtt) REVERT: A 409 GLN cc_start: 0.7647 (mm-40) cc_final: 0.7127 (tt0) REVERT: A 464 LYS cc_start: 0.8277 (mttt) cc_final: 0.7408 (tttt) REVERT: A 478 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.6324 (ttp80) REVERT: A 507 LYS cc_start: 0.7834 (ttmm) cc_final: 0.7514 (mmmt) REVERT: B 507 LYS cc_start: 0.7873 (mtpt) cc_final: 0.7571 (tttp) REVERT: D 108 GLU cc_start: 0.5726 (OUTLIER) cc_final: 0.5014 (tm-30) REVERT: D 131 LEU cc_start: 0.7860 (tp) cc_final: 0.7583 (tt) REVERT: D 374 GLU cc_start: 0.6474 (OUTLIER) cc_final: 0.6129 (mt-10) REVERT: D 427 ASP cc_start: 0.6220 (t0) cc_final: 0.5965 (t0) REVERT: E 130 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8651 (tm) REVERT: E 248 ASN cc_start: 0.7608 (t0) cc_final: 0.7370 (t0) REVERT: E 459 GLU cc_start: 0.7666 (mm-30) cc_final: 0.7429 (tm-30) REVERT: G 32 MET cc_start: 0.8546 (ttp) cc_final: 0.8183 (ttt) REVERT: G 167 ARG cc_start: 0.5702 (mtt90) cc_final: 0.5280 (pmt-80) REVERT: G 174 LYS cc_start: 0.7872 (mttt) cc_final: 0.7640 (mmtm) outliers start: 43 outliers final: 17 residues processed: 248 average time/residue: 0.8299 time to fit residues: 234.7462 Evaluate side-chains 220 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 198 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 478 ARG Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 366 ARG Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 237 TYR Chi-restraints excluded: chain C residue 453 GLU Chi-restraints excluded: chain D residue 108 GLU Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 374 GLU Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain F residue 108 GLU Chi-restraints excluded: chain F residue 371 ARG Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 275 GLU Chi-restraints excluded: chain G residue 276 ILE Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 84 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 39 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 172 optimal weight: 0.8980 chunk 3 optimal weight: 7.9990 chunk 191 optimal weight: 8.9990 chunk 34 optimal weight: 3.9990 chunk 251 optimal weight: 2.9990 chunk 162 optimal weight: 6.9990 chunk 59 optimal weight: 8.9990 chunk 344 optimal weight: 5.9990 chunk 241 optimal weight: 3.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 295 HIS C 470 GLN D 248 ASN ** D 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 128 ASN F 370 GLN F 437 ASN F 442 HIS H 6 HIS W 24 GLN W 99 GLN ** X 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.131897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.090443 restraints weight = 35193.294| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 1.27 r_work: 0.3221 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.5742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 28215 Z= 0.191 Angle : 0.646 9.882 38165 Z= 0.344 Chirality : 0.046 0.183 4375 Planarity : 0.005 0.052 4984 Dihedral : 8.552 172.726 4084 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.99 % Favored : 97.98 % Rotamer: Outliers : 1.90 % Allowed : 9.62 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.14), residues: 3622 helix: 1.93 (0.13), residues: 1656 sheet: 0.31 (0.20), residues: 565 loop : 0.24 (0.17), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 251 TYR 0.018 0.002 TYR D 252 PHE 0.015 0.002 PHE F 194 TRP 0.011 0.001 TRP C 139 HIS 0.007 0.001 HIS E 196 Details of bonding type rmsd covalent geometry : bond 0.00432 (28215) covalent geometry : angle 0.64640 (38165) hydrogen bonds : bond 0.06496 ( 1384) hydrogen bonds : angle 4.72259 ( 3945) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7244 Ramachandran restraints generated. 3622 Oldfield, 0 Emsley, 3622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7244 Ramachandran restraints generated. 3622 Oldfield, 0 Emsley, 3622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 221 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 GLN cc_start: 0.7203 (OUTLIER) cc_final: 0.6783 (tt0) REVERT: A 3 GLN cc_start: 0.8340 (pt0) cc_final: 0.7684 (tm-30) REVERT: A 464 LYS cc_start: 0.8295 (mttt) cc_final: 0.7425 (tttt) REVERT: A 478 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.6552 (ttp80) REVERT: A 507 LYS cc_start: 0.7934 (ttmm) cc_final: 0.7610 (mmmt) REVERT: B 366 ARG cc_start: 0.6410 (OUTLIER) cc_final: 0.5729 (mmt180) REVERT: B 432 MET cc_start: 0.8327 (mmt) cc_final: 0.8031 (mmt) REVERT: D 108 GLU cc_start: 0.5964 (OUTLIER) cc_final: 0.5098 (tm-30) REVERT: D 374 GLU cc_start: 0.6696 (OUTLIER) cc_final: 0.6289 (mt-10) REVERT: D 427 ASP cc_start: 0.6313 (t0) cc_final: 0.6061 (t0) REVERT: E 130 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8727 (tm) REVERT: E 248 ASN cc_start: 0.7669 (t0) cc_final: 0.7376 (t0) REVERT: E 373 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8477 (ttpp) REVERT: E 389 GLU cc_start: 0.7381 (tp30) cc_final: 0.7152 (tp30) REVERT: G 32 MET cc_start: 0.8576 (ttp) cc_final: 0.8192 (ttt) REVERT: G 148 ASP cc_start: 0.7529 (m-30) cc_final: 0.7302 (m-30) REVERT: G 167 ARG cc_start: 0.5771 (mtt90) cc_final: 0.5373 (pmt-80) REVERT: W 41 ASP cc_start: 0.8783 (t70) cc_final: 0.8565 (t70) REVERT: X 63 GLN cc_start: 0.4536 (OUTLIER) cc_final: 0.4112 (mp-120) outliers start: 55 outliers final: 23 residues processed: 261 average time/residue: 0.8459 time to fit residues: 251.2290 Evaluate side-chains 226 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 195 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLN Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 478 ARG Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 366 ARG Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 237 TYR Chi-restraints excluded: chain C residue 453 GLU Chi-restraints excluded: chain C residue 474 SER Chi-restraints excluded: chain D residue 108 GLU Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 374 GLU Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 373 LYS Chi-restraints excluded: chain F residue 108 GLU Chi-restraints excluded: chain F residue 142 CYS Chi-restraints excluded: chain F residue 169 ARG Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 371 ARG Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 275 GLU Chi-restraints excluded: chain G residue 276 ILE Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain W residue 108 VAL Chi-restraints excluded: chain W residue 110 VAL Chi-restraints excluded: chain X residue 63 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 1 optimal weight: 6.9990 chunk 301 optimal weight: 10.0000 chunk 329 optimal weight: 8.9990 chunk 40 optimal weight: 3.9990 chunk 121 optimal weight: 0.9980 chunk 189 optimal weight: 9.9990 chunk 210 optimal weight: 10.0000 chunk 145 optimal weight: 7.9990 chunk 39 optimal weight: 10.0000 chunk 51 optimal weight: 0.0980 chunk 125 optimal weight: 10.0000 overall best weight: 4.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 470 GLN D 248 ASN ** D 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 437 ASN F 442 HIS W 24 GLN ** X 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.129778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.087288 restraints weight = 35122.700| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.27 r_work: 0.3132 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.6040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 28215 Z= 0.214 Angle : 0.679 11.121 38165 Z= 0.361 Chirality : 0.048 0.186 4375 Planarity : 0.005 0.058 4984 Dihedral : 8.197 173.140 4084 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.68 % Favored : 98.29 % Rotamer: Outliers : 1.97 % Allowed : 10.07 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.14), residues: 3622 helix: 1.78 (0.13), residues: 1655 sheet: 0.25 (0.20), residues: 565 loop : 0.19 (0.17), residues: 1402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 140 TYR 0.018 0.002 TYR D 252 PHE 0.015 0.002 PHE F 194 TRP 0.013 0.002 TRP C 139 HIS 0.007 0.002 HIS E 196 Details of bonding type rmsd covalent geometry : bond 0.00495 (28215) covalent geometry : angle 0.67924 (38165) hydrogen bonds : bond 0.06692 ( 1384) hydrogen bonds : angle 4.80402 ( 3945) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7244 Ramachandran restraints generated. 3622 Oldfield, 0 Emsley, 3622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7244 Ramachandran restraints generated. 3622 Oldfield, 0 Emsley, 3622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 214 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 GLN cc_start: 0.7254 (OUTLIER) cc_final: 0.6875 (tt0) REVERT: A 3 GLN cc_start: 0.8284 (pt0) cc_final: 0.8076 (pt0) REVERT: A 246 MET cc_start: 0.9222 (mtt) cc_final: 0.8971 (mtt) REVERT: A 464 LYS cc_start: 0.8268 (mttt) cc_final: 0.7368 (tttt) REVERT: A 478 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.6748 (ttp80) REVERT: B 366 ARG cc_start: 0.6413 (OUTLIER) cc_final: 0.5855 (mmt180) REVERT: B 432 MET cc_start: 0.8342 (mmt) cc_final: 0.8109 (mmt) REVERT: D 108 GLU cc_start: 0.6127 (OUTLIER) cc_final: 0.5141 (tm-30) REVERT: D 130 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8425 (tm) REVERT: D 374 GLU cc_start: 0.6628 (OUTLIER) cc_final: 0.6318 (mt-10) REVERT: D 427 ASP cc_start: 0.6249 (t0) cc_final: 0.5982 (t0) REVERT: E 130 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8719 (tm) REVERT: E 248 ASN cc_start: 0.7759 (t0) cc_final: 0.7435 (t0) REVERT: E 373 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8383 (ttpp) REVERT: E 389 GLU cc_start: 0.7596 (tp30) cc_final: 0.7364 (tp30) REVERT: G 32 MET cc_start: 0.8527 (ttp) cc_final: 0.8121 (ttt) REVERT: G 167 ARG cc_start: 0.5688 (mtt90) cc_final: 0.5286 (pmt-80) REVERT: H 23 MET cc_start: 0.3850 (tpp) cc_final: 0.3182 (tmt) REVERT: H 124 GLU cc_start: 0.6878 (tt0) cc_final: 0.6508 (tm-30) REVERT: W 41 ASP cc_start: 0.8736 (t70) cc_final: 0.8462 (t70) REVERT: X 63 GLN cc_start: 0.4660 (OUTLIER) cc_final: 0.4264 (mp-120) outliers start: 57 outliers final: 26 residues processed: 259 average time/residue: 0.8209 time to fit residues: 241.1214 Evaluate side-chains 228 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 193 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLN Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 478 ARG Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 366 ARG Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 237 TYR Chi-restraints excluded: chain C residue 453 GLU Chi-restraints excluded: chain C residue 474 SER Chi-restraints excluded: chain D residue 108 GLU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 374 GLU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 373 LYS Chi-restraints excluded: chain F residue 108 GLU Chi-restraints excluded: chain F residue 142 CYS Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 371 ARG Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 275 GLU Chi-restraints excluded: chain G residue 276 ILE Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain W residue 108 VAL Chi-restraints excluded: chain W residue 110 VAL Chi-restraints excluded: chain X residue 63 GLN Chi-restraints excluded: chain Y residue 145 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 139 optimal weight: 6.9990 chunk 207 optimal weight: 3.9990 chunk 280 optimal weight: 8.9990 chunk 221 optimal weight: 0.8980 chunk 186 optimal weight: 9.9990 chunk 67 optimal weight: 5.9990 chunk 211 optimal weight: 5.9990 chunk 330 optimal weight: 1.9990 chunk 194 optimal weight: 0.1980 chunk 123 optimal weight: 0.7980 chunk 212 optimal weight: 5.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 248 ASN F 128 ASN F 437 ASN F 442 HIS W 24 GLN ** X 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.131554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.089301 restraints weight = 35206.795| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.28 r_work: 0.3168 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.6117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 28215 Z= 0.129 Angle : 0.551 9.256 38165 Z= 0.291 Chirality : 0.043 0.163 4375 Planarity : 0.004 0.051 4984 Dihedral : 7.627 168.437 4084 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.77 % Favored : 98.21 % Rotamer: Outliers : 1.59 % Allowed : 11.14 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.14), residues: 3622 helix: 2.11 (0.13), residues: 1650 sheet: 0.32 (0.20), residues: 561 loop : 0.24 (0.17), residues: 1411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 64 TYR 0.018 0.001 TYR D 252 PHE 0.022 0.001 PHE F 194 TRP 0.008 0.001 TRP C 139 HIS 0.005 0.001 HIS E 196 Details of bonding type rmsd covalent geometry : bond 0.00274 (28215) covalent geometry : angle 0.55087 (38165) hydrogen bonds : bond 0.05375 ( 1384) hydrogen bonds : angle 4.54948 ( 3945) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7244 Ramachandran restraints generated. 3622 Oldfield, 0 Emsley, 3622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7244 Ramachandran restraints generated. 3622 Oldfield, 0 Emsley, 3622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 205 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 GLN cc_start: 0.7257 (mt0) cc_final: 0.6912 (tt0) REVERT: A 3 GLN cc_start: 0.8277 (pt0) cc_final: 0.8069 (pt0) REVERT: A 95 ILE cc_start: 0.8877 (OUTLIER) cc_final: 0.8625 (pp) REVERT: A 246 MET cc_start: 0.9202 (mtt) cc_final: 0.8989 (mtt) REVERT: A 464 LYS cc_start: 0.8253 (mttt) cc_final: 0.7346 (tttt) REVERT: A 478 ARG cc_start: 0.7825 (OUTLIER) cc_final: 0.6390 (ttp80) REVERT: B 47 ASP cc_start: 0.8365 (OUTLIER) cc_final: 0.8115 (t70) REVERT: B 95 ILE cc_start: 0.8993 (OUTLIER) cc_final: 0.8776 (pp) REVERT: B 366 ARG cc_start: 0.6344 (OUTLIER) cc_final: 0.5948 (mmt180) REVERT: B 432 MET cc_start: 0.8325 (mmt) cc_final: 0.8016 (mmt) REVERT: D 108 GLU cc_start: 0.5966 (OUTLIER) cc_final: 0.4991 (tm-30) REVERT: D 374 GLU cc_start: 0.6602 (OUTLIER) cc_final: 0.6292 (mt-10) REVERT: D 427 ASP cc_start: 0.6212 (t0) cc_final: 0.5958 (t0) REVERT: E 130 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8704 (tm) REVERT: E 248 ASN cc_start: 0.7640 (t0) cc_final: 0.7331 (t0) REVERT: E 373 LYS cc_start: 0.8625 (OUTLIER) cc_final: 0.8374 (ttpp) REVERT: E 389 GLU cc_start: 0.7531 (tp30) cc_final: 0.7313 (tp30) REVERT: G 32 MET cc_start: 0.8515 (ttp) cc_final: 0.8065 (ttt) REVERT: G 69 VAL cc_start: 0.5883 (OUTLIER) cc_final: 0.5520 (t) REVERT: G 167 ARG cc_start: 0.5720 (mtt90) cc_final: 0.5314 (pmt-80) REVERT: H 23 MET cc_start: 0.4155 (tpp) cc_final: 0.3472 (tmt) REVERT: H 124 GLU cc_start: 0.6825 (tt0) cc_final: 0.6461 (tm-30) REVERT: W 41 ASP cc_start: 0.8709 (t70) cc_final: 0.8441 (t70) outliers start: 46 outliers final: 21 residues processed: 242 average time/residue: 0.8804 time to fit residues: 240.4340 Evaluate side-chains 230 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 199 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 478 ARG Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 366 ARG Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 237 TYR Chi-restraints excluded: chain C residue 474 SER Chi-restraints excluded: chain D residue 108 GLU Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 374 GLU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 373 LYS Chi-restraints excluded: chain F residue 108 GLU Chi-restraints excluded: chain F residue 142 CYS Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 169 ARG Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 371 ARG Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 275 GLU Chi-restraints excluded: chain G residue 276 ILE Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain W residue 108 VAL Chi-restraints excluded: chain W residue 110 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 229 optimal weight: 3.9990 chunk 154 optimal weight: 0.0570 chunk 236 optimal weight: 0.9980 chunk 132 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 286 optimal weight: 0.3980 chunk 37 optimal weight: 0.2980 chunk 39 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 chunk 170 optimal weight: 7.9990 chunk 209 optimal weight: 5.9990 overall best weight: 1.1500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 248 ASN F 437 ASN F 442 HIS G 252 ASN X 64 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.132324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.090246 restraints weight = 35457.631| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 1.29 r_work: 0.3185 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.6172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 28215 Z= 0.115 Angle : 0.527 9.091 38165 Z= 0.275 Chirality : 0.042 0.160 4375 Planarity : 0.004 0.053 4984 Dihedral : 7.244 163.778 4084 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.42 % Allowed : 11.38 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.14), residues: 3622 helix: 2.29 (0.13), residues: 1643 sheet: 0.39 (0.20), residues: 559 loop : 0.27 (0.17), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 64 TYR 0.018 0.001 TYR D 252 PHE 0.023 0.001 PHE F 194 TRP 0.007 0.001 TRP C 139 HIS 0.004 0.001 HIS E 196 Details of bonding type rmsd covalent geometry : bond 0.00238 (28215) covalent geometry : angle 0.52657 (38165) hydrogen bonds : bond 0.04923 ( 1384) hydrogen bonds : angle 4.42837 ( 3945) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7244 Ramachandran restraints generated. 3622 Oldfield, 0 Emsley, 3622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7244 Ramachandran restraints generated. 3622 Oldfield, 0 Emsley, 3622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 203 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 GLN cc_start: 0.7264 (OUTLIER) cc_final: 0.6970 (tt0) REVERT: A 95 ILE cc_start: 0.8876 (OUTLIER) cc_final: 0.8615 (pp) REVERT: A 464 LYS cc_start: 0.8237 (mttt) cc_final: 0.7327 (tttt) REVERT: A 478 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.6343 (ttp80) REVERT: B 47 ASP cc_start: 0.8362 (OUTLIER) cc_final: 0.8113 (t70) REVERT: B 95 ILE cc_start: 0.8974 (OUTLIER) cc_final: 0.8751 (pp) REVERT: D 374 GLU cc_start: 0.6523 (OUTLIER) cc_final: 0.6231 (mt-10) REVERT: D 384 MET cc_start: 0.7394 (tpt) cc_final: 0.7184 (mmm) REVERT: D 427 ASP cc_start: 0.6221 (t0) cc_final: 0.5949 (t0) REVERT: D 456 GLU cc_start: 0.6872 (mt-10) cc_final: 0.6672 (mt-10) REVERT: E 130 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8696 (tm) REVERT: E 174 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7344 (pm20) REVERT: E 248 ASN cc_start: 0.7587 (t0) cc_final: 0.7268 (t0) REVERT: E 389 GLU cc_start: 0.7485 (tp30) cc_final: 0.7274 (tp30) REVERT: G 32 MET cc_start: 0.8479 (ttp) cc_final: 0.8104 (ttt) REVERT: G 69 VAL cc_start: 0.5880 (OUTLIER) cc_final: 0.5542 (t) REVERT: G 167 ARG cc_start: 0.5750 (mtt90) cc_final: 0.5307 (pmt-80) REVERT: G 174 LYS cc_start: 0.7810 (mttt) cc_final: 0.7603 (mmtm) REVERT: W 41 ASP cc_start: 0.8656 (t70) cc_final: 0.8372 (t70) REVERT: Y 100 ARG cc_start: 0.6002 (mpp80) cc_final: 0.5495 (mtt90) outliers start: 41 outliers final: 16 residues processed: 235 average time/residue: 0.8282 time to fit residues: 219.7867 Evaluate side-chains 218 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 194 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLN Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 478 ARG Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 474 SER Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 374 GLU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain F residue 108 GLU Chi-restraints excluded: chain F residue 142 CYS Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 275 GLU Chi-restraints excluded: chain G residue 276 ILE Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain W residue 108 VAL Chi-restraints excluded: chain W residue 110 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 353 optimal weight: 10.0000 chunk 12 optimal weight: 0.5980 chunk 212 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 166 optimal weight: 9.9990 chunk 193 optimal weight: 2.9990 chunk 260 optimal weight: 0.9980 chunk 198 optimal weight: 4.9990 chunk 244 optimal weight: 5.9990 chunk 277 optimal weight: 2.9990 chunk 144 optimal weight: 7.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 248 ASN F 437 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.131313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.089141 restraints weight = 35322.396| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.28 r_work: 0.3165 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.6204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 28215 Z= 0.131 Angle : 0.555 8.493 38165 Z= 0.291 Chirality : 0.043 0.161 4375 Planarity : 0.004 0.052 4984 Dihedral : 7.349 165.389 4084 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.21 % Allowed : 11.90 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.14), residues: 3622 helix: 2.22 (0.13), residues: 1652 sheet: 0.37 (0.20), residues: 561 loop : 0.26 (0.17), residues: 1409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 64 TYR 0.018 0.001 TYR D 252 PHE 0.020 0.001 PHE F 194 TRP 0.008 0.001 TRP C 139 HIS 0.005 0.001 HIS E 196 Details of bonding type rmsd covalent geometry : bond 0.00281 (28215) covalent geometry : angle 0.55515 (38165) hydrogen bonds : bond 0.05308 ( 1384) hydrogen bonds : angle 4.47773 ( 3945) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7244 Ramachandran restraints generated. 3622 Oldfield, 0 Emsley, 3622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7244 Ramachandran restraints generated. 3622 Oldfield, 0 Emsley, 3622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 199 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 GLN cc_start: 0.7292 (OUTLIER) cc_final: 0.6993 (tt0) REVERT: A 95 ILE cc_start: 0.8899 (OUTLIER) cc_final: 0.8638 (pp) REVERT: A 464 LYS cc_start: 0.8257 (mttt) cc_final: 0.7372 (ttpt) REVERT: A 478 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.6354 (ttp80) REVERT: B 47 ASP cc_start: 0.8381 (OUTLIER) cc_final: 0.8136 (t70) REVERT: B 95 ILE cc_start: 0.8992 (OUTLIER) cc_final: 0.8748 (pp) REVERT: D 374 GLU cc_start: 0.6540 (OUTLIER) cc_final: 0.6246 (mt-10) REVERT: D 427 ASP cc_start: 0.6216 (t0) cc_final: 0.5942 (t0) REVERT: E 130 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8710 (tm) REVERT: E 248 ASN cc_start: 0.7615 (t0) cc_final: 0.7288 (t0) REVERT: E 373 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8393 (ttpp) REVERT: E 389 GLU cc_start: 0.7470 (tp30) cc_final: 0.7249 (tp30) REVERT: F 109 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7813 (pm20) REVERT: F 426 LYS cc_start: 0.8424 (ptmm) cc_final: 0.7930 (pttp) REVERT: G 32 MET cc_start: 0.8471 (ttp) cc_final: 0.8117 (ttt) REVERT: G 69 VAL cc_start: 0.5907 (OUTLIER) cc_final: 0.5559 (t) REVERT: G 167 ARG cc_start: 0.5717 (mtt90) cc_final: 0.5256 (pmt-80) REVERT: G 174 LYS cc_start: 0.7770 (mttt) cc_final: 0.7558 (mmtm) REVERT: H 23 MET cc_start: 0.3925 (tpp) cc_final: 0.3131 (tmt) REVERT: W 41 ASP cc_start: 0.8636 (t70) cc_final: 0.8363 (t70) REVERT: Y 100 ARG cc_start: 0.5958 (mpp80) cc_final: 0.5471 (mtt90) outliers start: 35 outliers final: 20 residues processed: 227 average time/residue: 0.8828 time to fit residues: 225.9404 Evaluate side-chains 225 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 195 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLN Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 478 ARG Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 263 ASP Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 474 SER Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 374 GLU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 373 LYS Chi-restraints excluded: chain F residue 108 GLU Chi-restraints excluded: chain F residue 109 GLU Chi-restraints excluded: chain F residue 142 CYS Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 371 ARG Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 275 GLU Chi-restraints excluded: chain G residue 276 ILE Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain W residue 42 ASP Chi-restraints excluded: chain W residue 108 VAL Chi-restraints excluded: chain W residue 110 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 24 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 285 optimal weight: 0.8980 chunk 126 optimal weight: 0.6980 chunk 279 optimal weight: 6.9990 chunk 188 optimal weight: 7.9990 chunk 61 optimal weight: 0.7980 chunk 264 optimal weight: 2.9990 chunk 167 optimal weight: 10.0000 chunk 111 optimal weight: 0.8980 chunk 225 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN D 248 ASN F 370 GLN F 437 ASN G 252 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.132856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.091095 restraints weight = 35470.095| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 1.31 r_work: 0.3196 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.6266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 28215 Z= 0.106 Angle : 0.515 9.135 38165 Z= 0.267 Chirality : 0.041 0.158 4375 Planarity : 0.003 0.051 4984 Dihedral : 6.941 160.602 4084 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.00 % Allowed : 12.25 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.14), residues: 3622 helix: 2.40 (0.13), residues: 1642 sheet: 0.49 (0.20), residues: 565 loop : 0.31 (0.17), residues: 1415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 64 TYR 0.018 0.001 TYR D 252 PHE 0.025 0.001 PHE F 194 TRP 0.005 0.001 TRP C 139 HIS 0.010 0.001 HIS H 6 Details of bonding type rmsd covalent geometry : bond 0.00216 (28215) covalent geometry : angle 0.51495 (38165) hydrogen bonds : bond 0.04553 ( 1384) hydrogen bonds : angle 4.33738 ( 3945) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7244 Ramachandran restraints generated. 3622 Oldfield, 0 Emsley, 3622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7244 Ramachandran restraints generated. 3622 Oldfield, 0 Emsley, 3622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 200 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 GLN cc_start: 0.7266 (OUTLIER) cc_final: 0.6964 (tt0) REVERT: A 95 ILE cc_start: 0.8816 (OUTLIER) cc_final: 0.8569 (pp) REVERT: A 464 LYS cc_start: 0.8166 (mttt) cc_final: 0.7282 (ttpt) REVERT: B 47 ASP cc_start: 0.8358 (OUTLIER) cc_final: 0.8075 (t70) REVERT: B 95 ILE cc_start: 0.8925 (OUTLIER) cc_final: 0.8661 (pp) REVERT: D 374 GLU cc_start: 0.6446 (OUTLIER) cc_final: 0.6206 (mt-10) REVERT: D 382 LEU cc_start: 0.6996 (mt) cc_final: 0.6698 (mp) REVERT: D 427 ASP cc_start: 0.6102 (t0) cc_final: 0.5850 (t0) REVERT: E 130 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8661 (tm) REVERT: E 174 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7276 (pm20) REVERT: E 248 ASN cc_start: 0.7696 (t0) cc_final: 0.7358 (t0) REVERT: E 389 GLU cc_start: 0.7414 (tp30) cc_final: 0.7190 (tp30) REVERT: F 426 LYS cc_start: 0.8388 (ptmm) cc_final: 0.7868 (pttp) REVERT: G 32 MET cc_start: 0.8378 (ttp) cc_final: 0.8051 (ttt) REVERT: G 69 VAL cc_start: 0.5922 (OUTLIER) cc_final: 0.5588 (t) REVERT: G 167 ARG cc_start: 0.5708 (mtt90) cc_final: 0.5264 (pmt-80) REVERT: G 174 LYS cc_start: 0.7757 (mttt) cc_final: 0.7523 (mmtm) REVERT: H 23 MET cc_start: 0.3941 (tpp) cc_final: 0.3159 (tmt) REVERT: W 41 ASP cc_start: 0.8631 (t70) cc_final: 0.8327 (t70) REVERT: Y 100 ARG cc_start: 0.5965 (mpp80) cc_final: 0.5458 (mtt90) outliers start: 29 outliers final: 17 residues processed: 224 average time/residue: 0.9237 time to fit residues: 233.3408 Evaluate side-chains 217 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 193 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLN Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 263 ASP Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 474 SER Chi-restraints excluded: chain D residue 374 GLU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain F residue 108 GLU Chi-restraints excluded: chain F residue 142 CYS Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 371 ARG Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 275 GLU Chi-restraints excluded: chain G residue 276 ILE Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain W residue 108 VAL Chi-restraints excluded: chain W residue 110 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 230 optimal weight: 0.9980 chunk 115 optimal weight: 0.0670 chunk 328 optimal weight: 5.9990 chunk 198 optimal weight: 4.9990 chunk 125 optimal weight: 9.9990 chunk 191 optimal weight: 2.9990 chunk 177 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 chunk 19 optimal weight: 7.9990 chunk 2 optimal weight: 9.9990 chunk 100 optimal weight: 9.9990 overall best weight: 2.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 248 ASN ** F 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 437 ASN G 252 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.130446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.088196 restraints weight = 34944.851| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.30 r_work: 0.3142 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.6265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 28215 Z= 0.167 Angle : 0.606 9.176 38165 Z= 0.319 Chirality : 0.044 0.166 4375 Planarity : 0.004 0.051 4984 Dihedral : 7.519 169.543 4084 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.21 % Allowed : 12.04 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.14), residues: 3622 helix: 2.15 (0.13), residues: 1655 sheet: 0.37 (0.20), residues: 561 loop : 0.25 (0.17), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 64 TYR 0.019 0.002 TYR D 252 PHE 0.016 0.002 PHE F 194 TRP 0.011 0.001 TRP C 139 HIS 0.006 0.001 HIS E 196 Details of bonding type rmsd covalent geometry : bond 0.00374 (28215) covalent geometry : angle 0.60589 (38165) hydrogen bonds : bond 0.05899 ( 1384) hydrogen bonds : angle 4.57997 ( 3945) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16537.30 seconds wall clock time: 280 minutes 19.41 seconds (16819.41 seconds total)