Starting phenix.real_space_refine on Sat Feb 7 22:14:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o1f_70005/02_2026/9o1f_70005_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o1f_70005/02_2026/9o1f_70005.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9o1f_70005/02_2026/9o1f_70005.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o1f_70005/02_2026/9o1f_70005.map" model { file = "/net/cci-nas-00/data/ceres_data/9o1f_70005/02_2026/9o1f_70005_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o1f_70005/02_2026/9o1f_70005_neut.cif" } resolution = 2.76 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= 0.012 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 15 5.49 5 Mg 5 5.21 5 S 159 5.16 5 C 23557 2.51 5 N 6274 2.21 5 O 6994 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 215 residue(s): 0.04s 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: 37005 Number of models: 1 Model: "" Number of chains: 29 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: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 933 Classifications: {'peptide': 128} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 121} Chain: "I" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 594 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain: "J" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 594 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain: "L" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 594 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain: "M" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 594 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain: "N" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 594 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain: "O" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 594 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain: "P" Number of atoms: 591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 591 Classifications: {'peptide': 83} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "Q" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 594 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain: "R" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 594 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain: "S" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 594 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} 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: 1183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1183 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "Y" Number of atoms: 1183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1183 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "a" Number of atoms: 2243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2243 Classifications: {'peptide': 286} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 275} 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} Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.92, per 1000 atoms: 0.24 Number of scatterers: 37005 At special positions: 0 Unit cell: (131.14, 135.29, 239.87, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 159 16.00 P 15 15.00 Mg 5 11.99 O 6994 8.00 N 6274 7.00 C 23557 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: 2.81 Conformation dependent library (CDL) restraints added in 1.4 seconds 9692 Ramachandran restraints generated. 4846 Oldfield, 0 Emsley, 4846 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8790 Finding SS restraints... Secondary structure from input PDB file: 215 helices and 23 sheets defined 62.7% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 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: 3.560A pdb=" N ALA A 381 " --> pdb=" O VAL A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 405 removed outlier: 4.207A pdb=" N GLY A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N GLY A 393 " --> pdb=" O LYS A 389 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ILE A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 414 removed outlier: 4.225A pdb=" N GLN A 409 " --> pdb=" O ALA A 406 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA A 411 " --> pdb=" O ALA A 408 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N SER A 412 " --> pdb=" O GLN A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 432 removed outlier: 3.719A pdb=" N GLN A 421 " --> pdb=" O ALA A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 454 removed outlier: 3.568A pdb=" N SER A 448 " --> pdb=" O GLU A 444 " (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 removed outlier: 3.525A pdb=" N ARG A 478 " --> pdb=" O SER A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 489 Processing helix chain 'A' and resid 494 through 510 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 151 through 158 Processing helix chain 'C' and resid 175 through 186 Processing helix chain 'C' and resid 187 through 189 No H-bonds generated for 'chain 'C' and resid 187 through 189' 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: 3.587A pdb=" N LEU E 167 " --> pdb=" O ASN E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 201 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 Processing helix chain 'E' and resid 412 through 417 removed outlier: 3.708A 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: 3.857A pdb=" N ILE G 7 " --> pdb=" O GLY G 3 " (cutoff:3.500A) 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: 3.583A pdb=" N HIS G 55 " --> pdb=" O GLN G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 69 removed outlier: 3.592A pdb=" N VAL G 69 " --> pdb=" O PRO G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 109 removed outlier: 3.780A 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 130 removed outlier: 3.572A pdb=" N ALA G 123 " --> pdb=" O GLY G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 148 Processing helix chain 'G' and resid 149 through 162 removed outlier: 3.597A 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: 3.775A 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 102 removed outlier: 3.818A pdb=" N ALA H 95 " --> pdb=" O ASP H 91 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA H 102 " --> pdb=" O ALA H 98 " (cutoff:3.500A) Processing helix chain 'H' and resid 114 through 129 removed outlier: 3.790A pdb=" N ARG H 121 " --> pdb=" O ALA H 117 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU H 129 " --> pdb=" O ALA H 125 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 41 removed outlier: 3.536A pdb=" N THR I 8 " --> pdb=" O VAL I 4 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE I 10 " --> pdb=" O GLY I 6 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY I 19 " --> pdb=" O LEU I 15 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS I 33 " --> pdb=" O LEU I 29 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU I 36 " --> pdb=" O GLY I 32 " (cutoff:3.500A) Processing helix chain 'I' and resid 44 through 76 removed outlier: 3.663A pdb=" N GLY I 57 " --> pdb=" O PHE I 53 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU I 58 " --> pdb=" O ILE I 54 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA I 61 " --> pdb=" O GLY I 57 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N VAL I 62 " --> pdb=" O LEU I 58 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N THR I 63 " --> pdb=" O LEU I 59 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 83 Processing helix chain 'J' and resid 2 through 41 removed outlier: 3.677A pdb=" N ALA J 11 " --> pdb=" O LEU J 7 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY J 19 " --> pdb=" O LEU J 15 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS J 33 " --> pdb=" O LEU J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 44 through 60 removed outlier: 3.580A pdb=" N VAL J 50 " --> pdb=" O PRO J 46 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU J 58 " --> pdb=" O ILE J 54 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 76 removed outlier: 3.547A pdb=" N ILE J 65 " --> pdb=" O ALA J 61 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU J 71 " --> pdb=" O VAL J 67 " (cutoff:3.500A) Processing helix chain 'J' and resid 79 through 83 Processing helix chain 'L' and resid 2 through 41 removed outlier: 3.520A pdb=" N ALA L 9 " --> pdb=" O VAL L 5 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE L 10 " --> pdb=" O GLY L 6 " (cutoff:3.500A) Processing helix chain 'L' and resid 44 through 76 removed outlier: 3.693A pdb=" N VAL L 50 " --> pdb=" O PRO L 46 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU L 58 " --> pdb=" O ILE L 54 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N VAL L 62 " --> pdb=" O LEU L 58 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N THR L 63 " --> pdb=" O LEU L 59 " (cutoff:3.500A) Processing helix chain 'L' and resid 77 through 83 removed outlier: 4.005A pdb=" N GLY L 81 " --> pdb=" O ASN L 77 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 41 removed outlier: 4.248A pdb=" N GLY M 19 " --> pdb=" O LEU M 15 " (cutoff:3.500A) Processing helix chain 'M' and resid 44 through 76 removed outlier: 3.545A pdb=" N VAL M 50 " --> pdb=" O PRO M 46 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU M 58 " --> pdb=" O ILE M 54 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N VAL M 62 " --> pdb=" O LEU M 58 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N THR M 63 " --> pdb=" O LEU M 59 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 83 removed outlier: 3.751A pdb=" N ILE M 83 " --> pdb=" O VAL M 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 41 removed outlier: 3.898A pdb=" N GLY N 19 " --> pdb=" O LEU N 15 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA N 24 " --> pdb=" O ALA N 20 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 60 removed outlier: 3.764A pdb=" N LEU N 58 " --> pdb=" O ILE N 54 " (cutoff:3.500A) Processing helix chain 'N' and resid 60 through 75 removed outlier: 3.572A pdb=" N MET N 64 " --> pdb=" O ASP N 60 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N PHE N 75 " --> pdb=" O LEU N 71 " (cutoff:3.500A) Processing helix chain 'N' and resid 77 through 82 removed outlier: 4.120A pdb=" N GLY N 81 " --> pdb=" O ASN N 77 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLN N 82 " --> pdb=" O PRO N 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 77 through 82' Processing helix chain 'O' and resid 2 through 41 removed outlier: 3.601A pdb=" N ILE O 10 " --> pdb=" O GLY O 6 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY O 19 " --> pdb=" O LEU O 15 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS O 33 " --> pdb=" O LEU O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 44 through 75 removed outlier: 3.575A pdb=" N VAL O 50 " --> pdb=" O PRO O 46 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU O 58 " --> pdb=" O ILE O 54 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N VAL O 62 " --> pdb=" O LEU O 58 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N THR O 63 " --> pdb=" O LEU O 59 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU O 71 " --> pdb=" O VAL O 67 " (cutoff:3.500A) Processing helix chain 'O' and resid 77 through 83 removed outlier: 4.474A pdb=" N GLY O 81 " --> pdb=" O ASN O 77 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLN O 82 " --> pdb=" O PRO O 78 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE O 83 " --> pdb=" O PHE O 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 77 through 83' Processing helix chain 'P' and resid 2 through 41 removed outlier: 3.511A pdb=" N ILE P 10 " --> pdb=" O GLY P 6 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLY P 19 " --> pdb=" O LEU P 15 " (cutoff:3.500A) Processing helix chain 'P' and resid 44 through 60 removed outlier: 3.586A pdb=" N VAL P 50 " --> pdb=" O PRO P 46 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU P 58 " --> pdb=" O ILE P 54 " (cutoff:3.500A) Processing helix chain 'P' and resid 60 through 76 Processing helix chain 'Q' and resid 2 through 41 removed outlier: 3.531A pdb=" N ILE Q 10 " --> pdb=" O GLY Q 6 " (cutoff:3.500A) Processing helix chain 'Q' and resid 44 through 60 removed outlier: 3.603A pdb=" N VAL Q 50 " --> pdb=" O PRO Q 46 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU Q 58 " --> pdb=" O ILE Q 54 " (cutoff:3.500A) Processing helix chain 'Q' and resid 60 through 76 Processing helix chain 'Q' and resid 79 through 83 removed outlier: 3.793A pdb=" N ILE Q 83 " --> pdb=" O VAL Q 80 " (cutoff:3.500A) Processing helix chain 'R' and resid 2 through 41 removed outlier: 3.637A pdb=" N ILE R 10 " --> pdb=" O GLY R 6 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY R 19 " --> pdb=" O LEU R 15 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS R 33 " --> pdb=" O LEU R 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 44 through 60 removed outlier: 3.830A pdb=" N VAL R 50 " --> pdb=" O PRO R 46 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU R 58 " --> pdb=" O ILE R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 76 removed outlier: 3.668A pdb=" N ILE R 65 " --> pdb=" O ALA R 61 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 41 removed outlier: 3.710A pdb=" N ILE S 10 " --> pdb=" O GLY S 6 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS S 33 " --> pdb=" O LEU S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 44 through 76 removed outlier: 3.646A pdb=" N VAL S 50 " --> pdb=" O PRO S 46 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU S 58 " --> pdb=" O ILE S 54 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N VAL S 62 " --> pdb=" O LEU S 58 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N THR S 63 " --> pdb=" O LEU S 59 " (cutoff:3.500A) Processing helix chain 'S' and resid 79 through 83 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 5 through 25 removed outlier: 3.522A pdb=" N SER X 11 " --> pdb=" O LEU X 7 " (cutoff:3.500A) Processing helix chain 'X' and resid 25 through 137 removed outlier: 3.816A pdb=" N VAL X 29 " --> pdb=" O VAL X 25 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA X 32 " --> pdb=" O PRO X 28 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU X 33 " --> pdb=" O VAL X 29 " (cutoff:3.500A) 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 2 through 25 removed outlier: 3.611A pdb=" N LEU Y 7 " --> pdb=" O ILE Y 3 " (cutoff:3.500A) Processing helix chain 'Y' and resid 26 through 97 Processing helix chain 'Y' and resid 99 through 104 Processing helix chain 'Y' and resid 105 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 helix chain 'a' and resid 5 through 14 removed outlier: 3.546A pdb=" N LEU a 14 " --> pdb=" O ILE a 10 " (cutoff:3.500A) Processing helix chain 'a' and resid 32 through 38 Processing helix chain 'a' and resid 47 through 66 removed outlier: 3.629A pdb=" N VAL a 53 " --> pdb=" O LEU a 49 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU a 54 " --> pdb=" O GLY a 50 " (cutoff:3.500A) Processing helix chain 'a' and resid 76 through 95 removed outlier: 3.802A pdb=" N PHE a 81 " --> pdb=" O GLY a 77 " (cutoff:3.500A) Processing helix chain 'a' and resid 103 through 121 removed outlier: 3.679A pdb=" N ILE a 121 " --> pdb=" O LEU a 117 " (cutoff:3.500A) Processing helix chain 'a' and resid 122 through 124 No H-bonds generated for 'chain 'a' and resid 122 through 124' Processing helix chain 'a' and resid 127 through 138 Processing helix chain 'a' and resid 147 through 150 Processing helix chain 'a' and resid 151 through 186 removed outlier: 3.766A pdb=" N VAL a 162 " --> pdb=" O LEU a 158 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ILE a 176 " --> pdb=" O LYS a 172 " (cutoff:3.500A) removed outlier: 8.869A pdb=" N GLY a 177 " --> pdb=" O VAL a 173 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N HIS a 186 " --> pdb=" O GLU a 182 " (cutoff:3.500A) Processing helix chain 'a' and resid 192 through 197 removed outlier: 3.680A pdb=" N ILE a 197 " --> pdb=" O ILE a 193 " (cutoff:3.500A) Processing helix chain 'a' and resid 199 through 242 removed outlier: 3.638A pdb=" N LYS a 214 " --> pdb=" O THR a 210 " (cutoff:3.500A) Proline residue: a 215 - end of helix removed outlier: 3.770A pdb=" N LEU a 222 " --> pdb=" O LEU a 218 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N MET a 239 " --> pdb=" O LEU a 235 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N PHE a 240 " --> pdb=" O ILE a 236 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY a 241 " --> pdb=" O ALA a 237 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER a 242 " --> pdb=" O VAL a 238 " (cutoff:3.500A) Processing helix chain 'a' and resid 244 through 283 removed outlier: 3.993A pdb=" N LEU a 250 " --> pdb=" O LEU a 246 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL a 252 " --> pdb=" O SER a 248 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LEU a 264 " --> pdb=" O VAL a 260 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA a 270 " --> pdb=" O ILE a 266 " (cutoff:3.500A) 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: 7.163A pdb=" N ALA F 35 " --> pdb=" O THR F 76 " (cutoff:3.500A) removed outlier: 4.398A 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: 6.759A pdb=" N LYS E 149 " --> pdb=" O ALA E 322 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N VAL E 324 " --> pdb=" O LYS E 149 " (cutoff:3.500A) removed outlier: 6.316A 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: 7.054A pdb=" N LEU G 115 " --> pdb=" O ALA G 135 " (cutoff:3.500A) removed outlier: 8.912A pdb=" N ILE G 137 " --> pdb=" O LEU G 115 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N VAL G 117 " --> pdb=" O ILE G 137 " (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: 6.409A pdb=" N ILE H 9 " --> pdb=" O ILE H 16 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N SER H 18 " --> pdb=" O CYS H 7 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N CYS H 7 " --> pdb=" O SER H 18 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LEU H 20 " --> pdb=" O VAL H 5 " (cutoff:3.500A) removed outlier: 6.092A 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: 5.158A pdb=" N HIS H 27 " --> pdb=" O PRO H 50 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU H 59 " --> pdb=" O LYS H 55 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'a' and resid 18 through 19 removed outlier: 4.272A pdb=" N PHE a 44 " --> pdb=" O PHE a 19 " (cutoff:3.500A) 2232 hydrogen bonds defined for protein. 6465 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.22 Time building geometry restraints manager: 3.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 6349 1.27 - 1.41: 8327 1.41 - 1.55: 22184 1.55 - 1.69: 408 1.69 - 1.83: 299 Bond restraints: 37567 Sorted by residual: bond pdb=" C GLY R 81 " pdb=" O GLY R 81 " ideal model delta sigma weight residual 1.235 1.131 0.104 1.15e-02 7.56e+03 8.22e+01 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 1.355 0.135 2.00e-02 2.50e+03 4.58e+01 bond pdb=" C4 ADP D 501 " pdb=" C5 ADP D 501 " ideal model delta sigma weight residual 1.490 1.378 0.112 2.00e-02 2.50e+03 3.13e+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 ... (remaining 37562 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.52: 50819 9.52 - 19.04: 17 19.04 - 28.56: 2 28.56 - 38.08: 2 38.08 - 47.60: 2 Bond angle restraints: 50842 Sorted by residual: angle pdb=" CA ASN X 2 " pdb=" C ASN X 2 " pdb=" N ILE X 3 " ideal model delta sigma weight residual 117.04 164.64 -47.60 1.24e+00 6.50e-01 1.47e+03 angle pdb=" O ASN X 2 " pdb=" C ASN X 2 " pdb=" N ILE X 3 " ideal model delta sigma weight residual 122.11 77.83 44.28 1.16e+00 7.43e-01 1.46e+03 angle pdb=" CA ASN X 2 " pdb=" C ASN X 2 " pdb=" O ASN X 2 " ideal model delta sigma weight residual 120.80 86.81 33.99 1.05e+00 9.07e-01 1.05e+03 angle pdb=" O ALA a 284 " pdb=" C ALA a 284 " pdb=" N HIS a 285 " ideal model delta sigma weight residual 122.34 89.61 32.73 1.25e+00 6.40e-01 6.85e+02 angle pdb=" PB ATP C 600 " pdb=" O3B ATP C 600 " pdb=" PG ATP C 600 " ideal model delta sigma weight residual 139.87 122.87 17.00 1.00e+00 1.00e+00 2.89e+02 ... (remaining 50837 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.79: 22067 31.79 - 63.58: 501 63.58 - 95.38: 46 95.38 - 127.17: 0 127.17 - 158.96: 5 Dihedral angle restraints: 22619 sinusoidal: 8836 harmonic: 13783 Sorted by residual: 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=" 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 85.86 -145.87 1 2.00e+01 2.50e-03 4.39e+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 22616 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.141: 5152 0.141 - 0.282: 729 0.282 - 0.423: 38 0.423 - 0.564: 9 0.564 - 0.705: 1 Chirality restraints: 5929 Sorted by residual: chirality pdb=" CA ASN X 4 " pdb=" N ASN X 4 " pdb=" C ASN X 4 " pdb=" CB ASN X 4 " both_signs ideal model delta sigma weight residual False 2.51 1.81 0.70 2.00e-01 2.50e+01 1.24e+01 chirality pdb=" CA ASN X 2 " pdb=" N ASN X 2 " pdb=" C ASN X 2 " pdb=" CB ASN X 2 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 6.93e+00 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 ... (remaining 5926 not shown) Planarity restraints: 6560 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA a 284 " -0.114 2.00e-02 2.50e+03 1.87e-01 3.48e+02 pdb=" C ALA a 284 " 0.323 2.00e-02 2.50e+03 pdb=" O ALA a 284 " -0.111 2.00e-02 2.50e+03 pdb=" N HIS a 285 " -0.098 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY R 81 " 0.069 2.00e-02 2.50e+03 1.29e-01 1.66e+02 pdb=" C GLY R 81 " -0.223 2.00e-02 2.50e+03 pdb=" O GLY R 81 " 0.084 2.00e-02 2.50e+03 pdb=" N GLN R 82 " 0.070 2.00e-02 2.50e+03 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 ... (remaining 6557 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 20 2.46 - 3.07: 22006 3.07 - 3.68: 54126 3.68 - 4.29: 83434 4.29 - 4.90: 138017 Nonbonded interactions: 297603 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 1.869 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=" O1B ADP E 501 " pdb="MG MG E 502 " model vdw 1.905 2.170 ... (remaining 297598 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 'I' and (resid 1 through 82 or (resid 83 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'J' and (resid 1 through 82 or (resid 83 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'L' and (resid 1 through 82 or (resid 83 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'M' and (resid 1 through 82 or (resid 83 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'N' and (resid 1 through 82 or (resid 83 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'O' and (resid 1 through 82 or (resid 83 and (name N or name CA or name C \ or name O or name CB )))) selection = chain 'P' selection = (chain 'Q' and (resid 1 through 82 or (resid 83 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'R' and (resid 1 through 82 or (resid 83 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'S' and (resid 1 through 82 or (resid 83 and (name N or name CA or name C \ or name O or name CB )))) } ncs_group { reference = chain 'X' 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: 3.920 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: 0.550 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 34.050 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 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 37567 Z= 0.776 Angle : 1.907 47.598 50842 Z= 1.303 Chirality : 0.098 0.705 5929 Planarity : 0.016 0.262 6560 Dihedral : 13.218 158.961 13829 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 0.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.52 % Favored : 97.44 % Rotamer: Outliers : 0.26 % Allowed : 3.96 % Favored : 95.78 % Cbeta Deviations : 0.75 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.02 % 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: -0.97 (0.11), residues: 4846 helix: -0.61 (0.09), residues: 2662 sheet: -0.05 (0.20), residues: 517 loop : -0.57 (0.15), residues: 1667 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 0.012 PHE a 41 TRP 0.115 0.021 TRP G 203 HIS 0.012 0.003 HIS E 175 Details of bonding type rmsd covalent geometry : bond 0.01258 (37567) covalent geometry : angle 1.90651 (50842) hydrogen bonds : bond 0.22022 ( 2232) hydrogen bonds : angle 7.33618 ( 6465) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9692 Ramachandran restraints generated. 4846 Oldfield, 0 Emsley, 4846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9692 Ramachandran restraints generated. 4846 Oldfield, 0 Emsley, 4846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 3818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 503 time to evaluate : 1.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 53 MET cc_start: 0.8425 (mtp) cc_final: 0.8103 (mtp) outliers start: 10 outliers final: 6 residues processed: 508 average time/residue: 0.8189 time to fit residues: 487.5287 Evaluate side-chains 323 residues out of total 3818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 317 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain H residue 45 ASP Chi-restraints excluded: chain H residue 115 TYR Chi-restraints excluded: chain M residue 60 ASP Chi-restraints excluded: chain S residue 23 THR Chi-restraints excluded: chain Y residue 58 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 432 optimal weight: 6.9990 chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 2.9990 chunk 455 optimal weight: 5.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 2.9990 chunk 470 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 409 GLN C 295 HIS C 400 GLN C 470 GLN E 437 ASN F 358 HIS H 73 GLN N 82 GLN P 82 GLN Q 77 ASN Q 82 GLN R 82 GLN S 82 GLN ** X 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 114 ASN a 31 HIS a 196 GLN a 225 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.107940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.078418 restraints weight = 81657.739| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.13 r_work: 0.3199 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 37567 Z= 0.167 Angle : 0.651 8.201 50842 Z= 0.346 Chirality : 0.044 0.191 5929 Planarity : 0.004 0.047 6560 Dihedral : 7.773 162.956 5357 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.26 % Favored : 98.70 % Rotamer: Outliers : 1.76 % Allowed : 9.46 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 1.06 (0.12), residues: 4846 helix: 1.34 (0.10), residues: 2689 sheet: 0.22 (0.20), residues: 552 loop : -0.05 (0.16), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 454 TYR 0.020 0.002 TYR D 252 PHE 0.027 0.002 PHE a 41 TRP 0.011 0.002 TRP F 112 HIS 0.011 0.001 HIS a 141 Details of bonding type rmsd covalent geometry : bond 0.00350 (37567) covalent geometry : angle 0.65123 (50842) hydrogen bonds : bond 0.06366 ( 2232) hydrogen bonds : angle 4.78656 ( 6465) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9692 Ramachandran restraints generated. 4846 Oldfield, 0 Emsley, 4846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9692 Ramachandran restraints generated. 4846 Oldfield, 0 Emsley, 4846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 3818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 356 time to evaluate : 1.588 Fit side-chains revert: symmetry clash REVERT: C 445 MET cc_start: 0.7426 (mtm) cc_final: 0.7226 (mtm) REVERT: D 347 ARG cc_start: 0.8027 (ttp80) cc_final: 0.7776 (ttp80) REVERT: E 214 MET cc_start: 0.8833 (mtt) cc_final: 0.8518 (mtp) REVERT: E 402 GLN cc_start: 0.8392 (tt0) cc_final: 0.8142 (mt0) REVERT: E 446 GLN cc_start: 0.7994 (tm-30) cc_final: 0.7496 (tm-30) REVERT: F 371 ARG cc_start: 0.7252 (OUTLIER) cc_final: 0.6453 (tmt-80) REVERT: F 389 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8172 (mp0) REVERT: H 45 ASP cc_start: 0.8407 (t70) cc_final: 0.8143 (t0) REVERT: I 36 GLU cc_start: 0.7347 (mm-30) cc_final: 0.7139 (mm-30) REVERT: J 41 GLN cc_start: 0.7213 (mp10) cc_final: 0.6417 (mt0) REVERT: J 44 MET cc_start: 0.7183 (mtt) cc_final: 0.6826 (mtt) REVERT: L 1 MET cc_start: 0.7243 (mmp) cc_final: 0.6975 (mmp) REVERT: M 41 GLN cc_start: 0.8038 (mm-40) cc_final: 0.7805 (mm-40) REVERT: O 1 MET cc_start: 0.8654 (tpt) cc_final: 0.8347 (tpp) REVERT: Q 43 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7978 (pm20) REVERT: Q 82 GLN cc_start: 0.7130 (OUTLIER) cc_final: 0.6558 (tp-100) REVERT: R 40 ARG cc_start: 0.7988 (OUTLIER) cc_final: 0.7502 (ttm110) REVERT: R 54 ILE cc_start: 0.8931 (OUTLIER) cc_final: 0.8721 (mp) REVERT: S 41 GLN cc_start: 0.7137 (mt0) cc_final: 0.6913 (mt0) REVERT: S 44 MET cc_start: 0.7470 (OUTLIER) cc_final: 0.7164 (mtp) REVERT: X 95 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.7448 (mtp180) REVERT: X 100 ARG cc_start: 0.7743 (ttp-170) cc_final: 0.7460 (ttp-110) REVERT: X 133 GLU cc_start: 0.7426 (tt0) cc_final: 0.6962 (mm-30) REVERT: Y 102 LYS cc_start: 0.6659 (OUTLIER) cc_final: 0.6346 (pmtt) REVERT: a 127 ASP cc_start: 0.6327 (OUTLIER) cc_final: 0.6065 (t0) outliers start: 67 outliers final: 19 residues processed: 395 average time/residue: 0.7779 time to fit residues: 364.8648 Evaluate side-chains 320 residues out of total 3818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 291 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain C residue 475 TYR Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 297 SER Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain F residue 371 ARG Chi-restraints excluded: chain F residue 389 GLU Chi-restraints excluded: chain G residue 106 TYR Chi-restraints excluded: chain G residue 243 MET Chi-restraints excluded: chain H residue 115 TYR Chi-restraints excluded: chain M residue 3 THR Chi-restraints excluded: chain M residue 44 MET Chi-restraints excluded: chain M residue 60 ASP Chi-restraints excluded: chain M residue 72 PHE Chi-restraints excluded: chain Q residue 43 GLU Chi-restraints excluded: chain Q residue 64 MET Chi-restraints excluded: chain Q residue 82 GLN Chi-restraints excluded: chain R residue 40 ARG Chi-restraints excluded: chain R residue 54 ILE Chi-restraints excluded: chain S residue 44 MET Chi-restraints excluded: chain X residue 22 MET Chi-restraints excluded: chain X residue 40 ILE Chi-restraints excluded: chain X residue 60 LYS Chi-restraints excluded: chain X residue 95 ARG Chi-restraints excluded: chain Y residue 29 VAL Chi-restraints excluded: chain Y residue 58 HIS Chi-restraints excluded: chain Y residue 102 LYS Chi-restraints excluded: chain a residue 24 ASN Chi-restraints excluded: chain a residue 127 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 239 optimal weight: 10.0000 chunk 279 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 92 optimal weight: 7.9990 chunk 350 optimal weight: 0.6980 chunk 432 optimal weight: 7.9990 chunk 338 optimal weight: 7.9990 chunk 152 optimal weight: 6.9990 chunk 357 optimal weight: 10.0000 chunk 107 optimal weight: 2.9990 chunk 402 optimal weight: 6.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 HIS B 295 HIS E 437 ASN I 41 GLN N 41 GLN P 82 GLN ** a 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 289 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.103409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.071756 restraints weight = 81019.077| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.11 r_work: 0.3090 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 37567 Z= 0.239 Angle : 0.689 9.659 50842 Z= 0.358 Chirality : 0.046 0.194 5929 Planarity : 0.005 0.047 6560 Dihedral : 7.688 157.721 5351 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.06 % Favored : 97.92 % Rotamer: Outliers : 3.07 % Allowed : 10.24 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 1.17 (0.12), residues: 4846 helix: 1.53 (0.10), residues: 2704 sheet: 0.11 (0.21), residues: 542 loop : -0.17 (0.16), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG X 82 TYR 0.021 0.002 TYR D 252 PHE 0.026 0.002 PHE Y 20 TRP 0.010 0.002 TRP X 26 HIS 0.010 0.002 HIS a 141 Details of bonding type rmsd covalent geometry : bond 0.00579 (37567) covalent geometry : angle 0.68901 (50842) hydrogen bonds : bond 0.06548 ( 2232) hydrogen bonds : angle 4.61745 ( 6465) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9692 Ramachandran restraints generated. 4846 Oldfield, 0 Emsley, 4846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9692 Ramachandran restraints generated. 4846 Oldfield, 0 Emsley, 4846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 3818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 309 time to evaluate : 1.471 Fit side-chains revert: symmetry clash REVERT: B 25 GLN cc_start: 0.8142 (mt0) cc_final: 0.7934 (mt0) REVERT: B 409 GLN cc_start: 0.7523 (tp-100) cc_final: 0.7268 (tp-100) REVERT: B 489 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7158 (pm20) REVERT: B 502 LYS cc_start: 0.8899 (tttt) cc_final: 0.8579 (ttpp) REVERT: C 321 LYS cc_start: 0.8071 (OUTLIER) cc_final: 0.7801 (mtmm) REVERT: C 391 SER cc_start: 0.7800 (p) cc_final: 0.7593 (m) REVERT: D 402 GLN cc_start: 0.7560 (tt0) cc_final: 0.7285 (mt0) REVERT: E 347 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.8073 (ttm170) REVERT: E 402 GLN cc_start: 0.8622 (tt0) cc_final: 0.8333 (mt0) REVERT: E 446 GLN cc_start: 0.8288 (tm-30) cc_final: 0.7945 (tm-30) REVERT: F 371 ARG cc_start: 0.7362 (OUTLIER) cc_final: 0.6838 (tmt-80) REVERT: F 389 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8183 (mp0) REVERT: H 45 ASP cc_start: 0.8591 (t70) cc_final: 0.8344 (t0) REVERT: H 91 ASP cc_start: 0.8257 (t0) cc_final: 0.7979 (t70) REVERT: H 106 LEU cc_start: 0.6158 (OUTLIER) cc_final: 0.5905 (mm) REVERT: H 113 PHE cc_start: 0.7570 (t80) cc_final: 0.7363 (t80) REVERT: H 128 GLN cc_start: 0.6129 (mm-40) cc_final: 0.5650 (mm-40) REVERT: J 41 GLN cc_start: 0.7549 (mp10) cc_final: 0.6899 (mt0) REVERT: L 1 MET cc_start: 0.7042 (mmp) cc_final: 0.6608 (mmp) REVERT: P 82 GLN cc_start: 0.6857 (OUTLIER) cc_final: 0.5549 (mp-120) REVERT: Q 43 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7982 (pm20) REVERT: Q 44 MET cc_start: 0.7941 (mtp) cc_final: 0.7343 (mmm) REVERT: Q 82 GLN cc_start: 0.7003 (mm-40) cc_final: 0.6728 (tp-100) REVERT: R 40 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7661 (ttm110) REVERT: S 41 GLN cc_start: 0.7525 (mt0) cc_final: 0.7283 (mt0) REVERT: S 44 MET cc_start: 0.7509 (OUTLIER) cc_final: 0.7198 (mtp) REVERT: X 81 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7736 (mtpt) REVERT: X 95 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7529 (mtp180) REVERT: X 100 ARG cc_start: 0.7857 (ttp-170) cc_final: 0.7566 (ttp-110) REVERT: Y 95 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7855 (ttt-90) REVERT: a 127 ASP cc_start: 0.6582 (OUTLIER) cc_final: 0.6376 (t0) REVERT: a 206 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7550 (mt) outliers start: 117 outliers final: 38 residues processed: 394 average time/residue: 0.7549 time to fit residues: 356.0112 Evaluate side-chains 337 residues out of total 3818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 284 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 489 GLU Chi-restraints excluded: chain C residue 237 TYR Chi-restraints excluded: chain C residue 321 LYS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 297 SER Chi-restraints excluded: chain E residue 347 ARG Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain F residue 371 ARG Chi-restraints excluded: chain F residue 389 GLU Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain G residue 186 GLU Chi-restraints excluded: chain G residue 276 ILE Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 115 TYR Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain M residue 3 THR Chi-restraints excluded: chain M residue 49 GLN Chi-restraints excluded: chain M residue 65 ILE Chi-restraints excluded: chain M residue 83 ILE Chi-restraints excluded: chain N residue 23 THR Chi-restraints excluded: chain N residue 69 ILE Chi-restraints excluded: chain O residue 49 GLN Chi-restraints excluded: chain P residue 82 GLN Chi-restraints excluded: chain Q residue 43 GLU Chi-restraints excluded: chain Q residue 64 MET Chi-restraints excluded: chain Q residue 83 ILE Chi-restraints excluded: chain R residue 14 LEU Chi-restraints excluded: chain R residue 40 ARG Chi-restraints excluded: chain R residue 52 MET Chi-restraints excluded: chain S residue 23 THR Chi-restraints excluded: chain S residue 44 MET Chi-restraints excluded: chain W residue 114 SER Chi-restraints excluded: chain X residue 22 MET Chi-restraints excluded: chain X residue 60 LYS Chi-restraints excluded: chain X residue 81 LYS Chi-restraints excluded: chain X residue 95 ARG Chi-restraints excluded: chain X residue 109 ILE Chi-restraints excluded: chain Y residue 29 VAL Chi-restraints excluded: chain Y residue 30 ILE Chi-restraints excluded: chain Y residue 95 ARG Chi-restraints excluded: chain Y residue 96 THR Chi-restraints excluded: chain Y residue 116 VAL Chi-restraints excluded: chain Y residue 129 VAL Chi-restraints excluded: chain a residue 127 ASP Chi-restraints excluded: chain a residue 206 LEU Chi-restraints excluded: chain a residue 287 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 444 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 294 optimal weight: 1.9990 chunk 466 optimal weight: 4.9990 chunk 186 optimal weight: 5.9990 chunk 332 optimal weight: 10.0000 chunk 51 optimal weight: 0.5980 chunk 469 optimal weight: 20.0000 chunk 393 optimal weight: 1.9990 chunk 213 optimal weight: 2.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 437 ASN a 35 GLN ** a 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.104341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.072848 restraints weight = 80924.354| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.11 r_work: 0.3116 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 37567 Z= 0.153 Angle : 0.573 10.206 50842 Z= 0.298 Chirality : 0.042 0.221 5929 Planarity : 0.004 0.050 6560 Dihedral : 7.307 158.500 5347 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.38 % Favored : 98.60 % Rotamer: Outliers : 2.36 % Allowed : 11.71 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 1.44 (0.12), residues: 4846 helix: 1.81 (0.10), residues: 2711 sheet: 0.17 (0.21), residues: 538 loop : -0.17 (0.16), residues: 1597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG X 82 TYR 0.021 0.001 TYR C 475 PHE 0.018 0.001 PHE I 72 TRP 0.007 0.001 TRP a 42 HIS 0.008 0.001 HIS a 141 Details of bonding type rmsd covalent geometry : bond 0.00347 (37567) covalent geometry : angle 0.57272 (50842) hydrogen bonds : bond 0.05501 ( 2232) hydrogen bonds : angle 4.38390 ( 6465) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9692 Ramachandran restraints generated. 4846 Oldfield, 0 Emsley, 4846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9692 Ramachandran restraints generated. 4846 Oldfield, 0 Emsley, 4846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 3818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 297 time to evaluate : 1.551 Fit side-chains revert: symmetry clash REVERT: B 409 GLN cc_start: 0.7427 (tp-100) cc_final: 0.7199 (tp-100) REVERT: B 489 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7191 (pm20) REVERT: B 502 LYS cc_start: 0.8846 (tttt) cc_final: 0.8518 (ttpp) REVERT: C 391 SER cc_start: 0.7836 (p) cc_final: 0.7630 (m) REVERT: C 445 MET cc_start: 0.7685 (mtm) cc_final: 0.7447 (mtm) REVERT: D 128 ASN cc_start: 0.7581 (p0) cc_final: 0.7063 (m-40) REVERT: D 402 GLN cc_start: 0.7587 (tt0) cc_final: 0.7358 (mt0) REVERT: E 402 GLN cc_start: 0.8585 (tt0) cc_final: 0.8184 (mt0) REVERT: E 446 GLN cc_start: 0.8335 (tm-30) cc_final: 0.7987 (tm-30) REVERT: F 149 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.7091 (mtmt) REVERT: F 371 ARG cc_start: 0.7320 (OUTLIER) cc_final: 0.6872 (tmt-80) REVERT: H 45 ASP cc_start: 0.8517 (t70) cc_final: 0.8310 (t0) REVERT: H 91 ASP cc_start: 0.8301 (OUTLIER) cc_final: 0.8077 (t70) REVERT: H 106 LEU cc_start: 0.6141 (OUTLIER) cc_final: 0.5929 (mm) REVERT: H 113 PHE cc_start: 0.7545 (t80) cc_final: 0.7241 (t80) REVERT: H 128 GLN cc_start: 0.6107 (mm-40) cc_final: 0.5891 (mm-40) REVERT: J 41 GLN cc_start: 0.7297 (mp10) cc_final: 0.6749 (mt0) REVERT: J 43 GLU cc_start: 0.8285 (pm20) cc_final: 0.8025 (pm20) REVERT: J 44 MET cc_start: 0.7180 (mtt) cc_final: 0.6720 (mtt) REVERT: L 1 MET cc_start: 0.7026 (mmp) cc_final: 0.6598 (mmp) REVERT: M 49 GLN cc_start: 0.8094 (OUTLIER) cc_final: 0.7846 (mt0) REVERT: Q 43 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7994 (pm20) REVERT: Q 82 GLN cc_start: 0.7191 (mm-40) cc_final: 0.6844 (tp-100) REVERT: R 40 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7653 (ttm110) REVERT: S 44 MET cc_start: 0.7354 (OUTLIER) cc_final: 0.7096 (mtp) REVERT: X 81 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7714 (mtpt) REVERT: X 95 ARG cc_start: 0.8143 (OUTLIER) cc_final: 0.7908 (mtm180) REVERT: X 100 ARG cc_start: 0.7865 (ttp-170) cc_final: 0.7605 (ttp-110) REVERT: Y 22 MET cc_start: 0.5578 (tpp) cc_final: 0.5272 (tpt) REVERT: Y 95 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7811 (ttt-90) REVERT: a 127 ASP cc_start: 0.6533 (OUTLIER) cc_final: 0.6310 (t0) REVERT: a 206 LEU cc_start: 0.7868 (OUTLIER) cc_final: 0.7588 (mt) outliers start: 90 outliers final: 27 residues processed: 357 average time/residue: 0.7905 time to fit residues: 335.8576 Evaluate side-chains 325 residues out of total 3818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 284 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 489 GLU Chi-restraints excluded: chain C residue 237 TYR Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 297 SER Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain F residue 149 LYS Chi-restraints excluded: chain F residue 371 ARG Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain G residue 106 TYR Chi-restraints excluded: chain G residue 186 GLU Chi-restraints excluded: chain G residue 243 MET Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain H residue 91 ASP Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain M residue 3 THR Chi-restraints excluded: chain M residue 44 MET Chi-restraints excluded: chain M residue 49 GLN Chi-restraints excluded: chain N residue 23 THR Chi-restraints excluded: chain N residue 69 ILE Chi-restraints excluded: chain P residue 59 LEU Chi-restraints excluded: chain Q residue 43 GLU Chi-restraints excluded: chain Q residue 47 MET Chi-restraints excluded: chain R residue 40 ARG Chi-restraints excluded: chain R residue 83 ILE Chi-restraints excluded: chain S residue 44 MET Chi-restraints excluded: chain X residue 22 MET Chi-restraints excluded: chain X residue 40 ILE Chi-restraints excluded: chain X residue 81 LYS Chi-restraints excluded: chain X residue 95 ARG Chi-restraints excluded: chain Y residue 95 ARG Chi-restraints excluded: chain Y residue 116 VAL Chi-restraints excluded: chain a residue 127 ASP Chi-restraints excluded: chain a residue 149 THR Chi-restraints excluded: chain a residue 206 LEU Chi-restraints excluded: chain a residue 287 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 354 optimal weight: 7.9990 chunk 236 optimal weight: 0.0270 chunk 138 optimal weight: 5.9990 chunk 358 optimal weight: 8.9990 chunk 173 optimal weight: 5.9990 chunk 215 optimal weight: 9.9990 chunk 400 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 119 optimal weight: 6.9990 chunk 121 optimal weight: 2.9990 chunk 261 optimal weight: 2.9990 overall best weight: 2.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 437 ASN ** a 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 288 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.104570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.073716 restraints weight = 81040.168| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.19 r_work: 0.3120 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 37567 Z= 0.142 Angle : 0.549 10.174 50842 Z= 0.285 Chirality : 0.041 0.213 5929 Planarity : 0.004 0.051 6560 Dihedral : 7.055 164.296 5345 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.67 % Favored : 98.31 % Rotamer: Outliers : 2.67 % Allowed : 11.97 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 (0.12), residues: 4846 helix: 2.03 (0.10), residues: 2714 sheet: 0.20 (0.21), residues: 538 loop : -0.12 (0.16), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG X 82 TYR 0.026 0.001 TYR H 115 PHE 0.016 0.001 PHE I 72 TRP 0.006 0.001 TRP a 256 HIS 0.007 0.001 HIS a 141 Details of bonding type rmsd covalent geometry : bond 0.00321 (37567) covalent geometry : angle 0.54930 (50842) hydrogen bonds : bond 0.05153 ( 2232) hydrogen bonds : angle 4.24751 ( 6465) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9692 Ramachandran restraints generated. 4846 Oldfield, 0 Emsley, 4846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9692 Ramachandran restraints generated. 4846 Oldfield, 0 Emsley, 4846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 3818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 309 time to evaluate : 1.496 Fit side-chains REVERT: B 409 GLN cc_start: 0.7466 (tp-100) cc_final: 0.7260 (tp40) REVERT: B 426 GLN cc_start: 0.7414 (mt0) cc_final: 0.7204 (mt0) REVERT: B 489 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7074 (pm20) REVERT: B 502 LYS cc_start: 0.8760 (tttt) cc_final: 0.8415 (ttpp) REVERT: C 391 SER cc_start: 0.7762 (p) cc_final: 0.7548 (m) REVERT: C 456 PHE cc_start: 0.7295 (m-80) cc_final: 0.7039 (m-80) REVERT: D 384 MET cc_start: 0.6582 (tmm) cc_final: 0.6110 (tpt) REVERT: E 402 GLN cc_start: 0.8432 (tt0) cc_final: 0.8107 (mt0) REVERT: E 446 GLN cc_start: 0.8288 (tm-30) cc_final: 0.7917 (tm-30) REVERT: F 149 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.6824 (mtmt) REVERT: H 45 ASP cc_start: 0.8475 (t70) cc_final: 0.8251 (t0) REVERT: H 60 GLN cc_start: 0.6900 (OUTLIER) cc_final: 0.6217 (mp-120) REVERT: H 91 ASP cc_start: 0.8178 (OUTLIER) cc_final: 0.7875 (t70) REVERT: H 96 GLN cc_start: 0.7976 (mm-40) cc_final: 0.7609 (mm-40) REVERT: H 106 LEU cc_start: 0.6306 (OUTLIER) cc_final: 0.6045 (mm) REVERT: H 122 LEU cc_start: 0.6796 (OUTLIER) cc_final: 0.6507 (mm) REVERT: J 41 GLN cc_start: 0.7094 (mp10) cc_final: 0.6537 (mt0) REVERT: J 43 GLU cc_start: 0.8176 (pm20) cc_final: 0.7914 (pm20) REVERT: J 44 MET cc_start: 0.7093 (mtt) cc_final: 0.6617 (mtt) REVERT: L 1 MET cc_start: 0.6836 (mmp) cc_final: 0.6485 (mmp) REVERT: M 49 GLN cc_start: 0.7911 (OUTLIER) cc_final: 0.7706 (mt0) REVERT: Q 43 GLU cc_start: 0.8391 (pm20) cc_final: 0.8007 (pm20) REVERT: Q 82 GLN cc_start: 0.7171 (mm-40) cc_final: 0.6756 (tp-100) REVERT: R 83 ILE cc_start: 0.6353 (OUTLIER) cc_final: 0.5781 (mt) REVERT: X 16 ILE cc_start: 0.7354 (OUTLIER) cc_final: 0.7124 (mp) REVERT: X 81 LYS cc_start: 0.8092 (OUTLIER) cc_final: 0.7550 (mtpt) REVERT: X 95 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.7804 (mtm180) REVERT: X 100 ARG cc_start: 0.7762 (ttp-170) cc_final: 0.7499 (ttp-110) REVERT: Y 22 MET cc_start: 0.5347 (tpp) cc_final: 0.5070 (tpt) REVERT: a 62 ILE cc_start: 0.6787 (OUTLIER) cc_final: 0.6470 (mt) REVERT: a 206 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7424 (mt) REVERT: a 286 GLU cc_start: 0.7865 (pm20) cc_final: 0.7457 (mp0) outliers start: 102 outliers final: 37 residues processed: 379 average time/residue: 0.7849 time to fit residues: 354.4268 Evaluate side-chains 338 residues out of total 3818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 288 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain B residue 25 GLN Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 489 GLU Chi-restraints excluded: chain C residue 237 TYR Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 297 SER Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain F residue 142 CYS Chi-restraints excluded: chain F residue 149 LYS Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 106 TYR Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 186 GLU Chi-restraints excluded: chain G residue 276 ILE Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain H residue 60 GLN Chi-restraints excluded: chain H residue 91 ASP Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain M residue 3 THR Chi-restraints excluded: chain M residue 44 MET Chi-restraints excluded: chain M residue 49 GLN Chi-restraints excluded: chain N residue 23 THR Chi-restraints excluded: chain N residue 69 ILE Chi-restraints excluded: chain O residue 49 GLN Chi-restraints excluded: chain P residue 59 LEU Chi-restraints excluded: chain Q residue 10 ILE Chi-restraints excluded: chain R residue 47 MET Chi-restraints excluded: chain R residue 52 MET Chi-restraints excluded: chain R residue 83 ILE Chi-restraints excluded: chain S residue 23 THR Chi-restraints excluded: chain X residue 16 ILE Chi-restraints excluded: chain X residue 22 MET Chi-restraints excluded: chain X residue 40 ILE Chi-restraints excluded: chain X residue 81 LYS Chi-restraints excluded: chain X residue 95 ARG Chi-restraints excluded: chain X residue 109 ILE Chi-restraints excluded: chain Y residue 116 VAL Chi-restraints excluded: chain a residue 62 ILE Chi-restraints excluded: chain a residue 149 THR Chi-restraints excluded: chain a residue 206 LEU Chi-restraints excluded: chain a residue 231 LEU Chi-restraints excluded: chain a residue 244 MET Chi-restraints excluded: chain a residue 287 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 419 optimal weight: 6.9990 chunk 182 optimal weight: 4.9990 chunk 176 optimal weight: 3.9990 chunk 222 optimal weight: 1.9990 chunk 227 optimal weight: 0.6980 chunk 34 optimal weight: 7.9990 chunk 361 optimal weight: 8.9990 chunk 366 optimal weight: 5.9990 chunk 252 optimal weight: 0.0870 chunk 57 optimal weight: 0.9980 chunk 358 optimal weight: 5.9990 overall best weight: 1.5562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 424 HIS D 402 GLN E 437 ASN N 49 GLN ** a 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 45 HIS ** a 285 HIS ** 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 = 0.3817 r_free = 0.3817 target = 0.105155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.074361 restraints weight = 81162.803| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.19 r_work: 0.3136 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 37567 Z= 0.126 Angle : 0.532 9.538 50842 Z= 0.276 Chirality : 0.041 0.158 5929 Planarity : 0.004 0.050 6560 Dihedral : 6.893 174.475 5345 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.44 % Favored : 98.53 % Rotamer: Outliers : 2.15 % Allowed : 12.94 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 1.86 (0.12), residues: 4846 helix: 2.20 (0.10), residues: 2710 sheet: 0.29 (0.21), residues: 526 loop : -0.06 (0.16), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG X 121 TYR 0.023 0.001 TYR C 475 PHE 0.015 0.001 PHE I 72 TRP 0.006 0.001 TRP a 256 HIS 0.006 0.001 HIS a 141 Details of bonding type rmsd covalent geometry : bond 0.00276 (37567) covalent geometry : angle 0.53238 (50842) hydrogen bonds : bond 0.04844 ( 2232) hydrogen bonds : angle 4.15938 ( 6465) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9692 Ramachandran restraints generated. 4846 Oldfield, 0 Emsley, 4846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9692 Ramachandran restraints generated. 4846 Oldfield, 0 Emsley, 4846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 3818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 306 time to evaluate : 1.438 Fit side-chains REVERT: A 61 TYR cc_start: 0.8603 (m-80) cc_final: 0.8349 (m-80) REVERT: B 426 GLN cc_start: 0.7378 (mt0) cc_final: 0.7156 (mt0) REVERT: B 489 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7058 (pm20) REVERT: B 502 LYS cc_start: 0.8746 (tttt) cc_final: 0.8413 (ttpp) REVERT: C 391 SER cc_start: 0.7787 (p) cc_final: 0.7564 (m) REVERT: C 456 PHE cc_start: 0.7282 (m-80) cc_final: 0.7053 (m-80) REVERT: D 128 ASN cc_start: 0.7764 (p0) cc_final: 0.7072 (m-40) REVERT: D 384 MET cc_start: 0.6506 (mmm) cc_final: 0.6052 (tpt) REVERT: E 402 GLN cc_start: 0.8393 (tt0) cc_final: 0.8076 (mt0) REVERT: E 446 GLN cc_start: 0.8278 (tm-30) cc_final: 0.7907 (tm-30) REVERT: H 45 ASP cc_start: 0.8400 (t70) cc_final: 0.8178 (t0) REVERT: H 60 GLN cc_start: 0.6948 (OUTLIER) cc_final: 0.6295 (mp-120) REVERT: H 91 ASP cc_start: 0.8165 (OUTLIER) cc_final: 0.7858 (t70) REVERT: H 96 GLN cc_start: 0.8007 (mm-40) cc_final: 0.7663 (mm-40) REVERT: H 106 LEU cc_start: 0.6298 (OUTLIER) cc_final: 0.6074 (mm) REVERT: H 122 LEU cc_start: 0.6781 (OUTLIER) cc_final: 0.6553 (mm) REVERT: H 128 GLN cc_start: 0.6037 (mm-40) cc_final: 0.5766 (mm-40) REVERT: H 129 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7436 (tp) REVERT: J 41 GLN cc_start: 0.7019 (mp10) cc_final: 0.6481 (mt0) REVERT: J 43 GLU cc_start: 0.8173 (pm20) cc_final: 0.7910 (pm20) REVERT: J 44 MET cc_start: 0.7037 (mtt) cc_final: 0.6626 (mtt) REVERT: J 54 ILE cc_start: 0.7776 (mt) cc_final: 0.7572 (mt) REVERT: L 1 MET cc_start: 0.6844 (mmp) cc_final: 0.6561 (mmp) REVERT: N 1 MET cc_start: 0.6877 (ttp) cc_final: 0.6550 (tmt) REVERT: O 47 MET cc_start: 0.7827 (ptm) cc_final: 0.7602 (tmm) REVERT: Q 43 GLU cc_start: 0.8390 (pm20) cc_final: 0.7977 (pm20) REVERT: Q 82 GLN cc_start: 0.7155 (mm-40) cc_final: 0.6711 (tp-100) REVERT: R 43 GLU cc_start: 0.8101 (pm20) cc_final: 0.7831 (pp20) REVERT: R 83 ILE cc_start: 0.6358 (OUTLIER) cc_final: 0.5811 (mt) REVERT: S 44 MET cc_start: 0.7279 (mtp) cc_final: 0.7017 (mtp) REVERT: X 16 ILE cc_start: 0.7359 (OUTLIER) cc_final: 0.7148 (mp) REVERT: X 81 LYS cc_start: 0.8086 (OUTLIER) cc_final: 0.7552 (mtpt) REVERT: X 100 ARG cc_start: 0.7734 (ttp-170) cc_final: 0.7467 (ttp-110) REVERT: Y 22 MET cc_start: 0.5375 (tpp) cc_final: 0.5079 (tpt) REVERT: a 62 ILE cc_start: 0.6804 (OUTLIER) cc_final: 0.6479 (mt) REVERT: a 206 LEU cc_start: 0.7801 (OUTLIER) cc_final: 0.7480 (mt) REVERT: a 239 MET cc_start: 0.6716 (ptp) cc_final: 0.6361 (ppp) outliers start: 82 outliers final: 32 residues processed: 362 average time/residue: 0.7717 time to fit residues: 334.0513 Evaluate side-chains 328 residues out of total 3818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 285 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 GLN Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 489 GLU Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 237 TYR Chi-restraints excluded: chain D residue 297 SER Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain F residue 142 CYS Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 106 TYR Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 186 GLU Chi-restraints excluded: chain H residue 60 GLN Chi-restraints excluded: chain H residue 91 ASP Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 115 TYR Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain I residue 36 GLU Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain M residue 3 THR Chi-restraints excluded: chain N residue 23 THR Chi-restraints excluded: chain N residue 69 ILE Chi-restraints excluded: chain Q residue 10 ILE Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain R residue 47 MET Chi-restraints excluded: chain R residue 83 ILE Chi-restraints excluded: chain S residue 23 THR Chi-restraints excluded: chain W residue 114 SER Chi-restraints excluded: chain X residue 16 ILE Chi-restraints excluded: chain X residue 22 MET Chi-restraints excluded: chain X residue 40 ILE Chi-restraints excluded: chain X residue 81 LYS Chi-restraints excluded: chain Y residue 116 VAL Chi-restraints excluded: chain Y residue 140 ILE Chi-restraints excluded: chain a residue 62 ILE Chi-restraints excluded: chain a residue 149 THR Chi-restraints excluded: chain a residue 206 LEU Chi-restraints excluded: chain a residue 231 LEU Chi-restraints excluded: chain a residue 244 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 264 optimal weight: 10.0000 chunk 291 optimal weight: 0.8980 chunk 339 optimal weight: 0.0670 chunk 115 optimal weight: 5.9990 chunk 391 optimal weight: 2.9990 chunk 221 optimal weight: 0.9980 chunk 223 optimal weight: 0.9980 chunk 18 optimal weight: 10.0000 chunk 396 optimal weight: 6.9990 chunk 431 optimal weight: 10.0000 chunk 179 optimal weight: 10.0000 overall best weight: 1.1920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 402 GLN E 49 GLN E 437 ASN O 49 GLN a 35 GLN ** a 285 HIS ** 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 = 0.3822 r_free = 0.3822 target = 0.105464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.075149 restraints weight = 81289.061| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.15 r_work: 0.3143 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 37567 Z= 0.117 Angle : 0.524 9.429 50842 Z= 0.271 Chirality : 0.040 0.182 5929 Planarity : 0.004 0.049 6560 Dihedral : 6.747 176.966 5345 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.53 % Favored : 98.45 % Rotamer: Outliers : 2.02 % Allowed : 13.26 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 1.98 (0.12), residues: 4846 helix: 2.31 (0.10), residues: 2708 sheet: 0.33 (0.21), residues: 535 loop : -0.03 (0.16), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG X 121 TYR 0.038 0.001 TYR H 115 PHE 0.017 0.001 PHE C 468 TRP 0.006 0.001 TRP a 256 HIS 0.005 0.001 HIS a 141 Details of bonding type rmsd covalent geometry : bond 0.00247 (37567) covalent geometry : angle 0.52431 (50842) hydrogen bonds : bond 0.04649 ( 2232) hydrogen bonds : angle 4.08091 ( 6465) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9692 Ramachandran restraints generated. 4846 Oldfield, 0 Emsley, 4846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9692 Ramachandran restraints generated. 4846 Oldfield, 0 Emsley, 4846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 3818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 313 time to evaluate : 1.346 Fit side-chains revert: symmetry clash REVERT: A 445 MET cc_start: 0.7934 (mtp) cc_final: 0.7733 (mtp) REVERT: B 426 GLN cc_start: 0.7437 (mt0) cc_final: 0.7215 (mt0) REVERT: B 489 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7088 (pm20) REVERT: C 391 SER cc_start: 0.7758 (p) cc_final: 0.7528 (m) REVERT: C 407 PHE cc_start: 0.4828 (OUTLIER) cc_final: 0.4388 (t80) REVERT: C 415 ASP cc_start: 0.6356 (p0) cc_final: 0.5977 (p0) REVERT: C 456 PHE cc_start: 0.7314 (m-80) cc_final: 0.7026 (m-80) REVERT: C 469 GLU cc_start: 0.6741 (OUTLIER) cc_final: 0.6410 (pp20) REVERT: C 470 GLN cc_start: 0.7618 (tp40) cc_final: 0.7382 (mm-40) REVERT: D 371 ARG cc_start: 0.7987 (tpt-90) cc_final: 0.7776 (tpt-90) REVERT: D 384 MET cc_start: 0.6577 (mmm) cc_final: 0.6137 (tpt) REVERT: E 402 GLN cc_start: 0.8408 (tt0) cc_final: 0.8110 (mt0) REVERT: E 446 GLN cc_start: 0.8288 (tm-30) cc_final: 0.7926 (tm-30) REVERT: F 392 LYS cc_start: 0.7241 (mttt) cc_final: 0.7011 (mptt) REVERT: H 45 ASP cc_start: 0.8379 (t70) cc_final: 0.8162 (t0) REVERT: H 60 GLN cc_start: 0.7004 (OUTLIER) cc_final: 0.6361 (mp-120) REVERT: H 91 ASP cc_start: 0.8184 (OUTLIER) cc_final: 0.7855 (t70) REVERT: H 96 GLN cc_start: 0.8031 (mm-40) cc_final: 0.7667 (mm-40) REVERT: H 106 LEU cc_start: 0.6310 (OUTLIER) cc_final: 0.6090 (mm) REVERT: H 122 LEU cc_start: 0.6816 (OUTLIER) cc_final: 0.6607 (mm) REVERT: H 128 GLN cc_start: 0.5956 (mm-40) cc_final: 0.5631 (mm-40) REVERT: H 129 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7431 (tp) REVERT: J 41 GLN cc_start: 0.6998 (mp10) cc_final: 0.6469 (mt0) REVERT: J 43 GLU cc_start: 0.8167 (pm20) cc_final: 0.7888 (pm20) REVERT: J 44 MET cc_start: 0.7064 (mtt) cc_final: 0.6591 (mtt) REVERT: J 54 ILE cc_start: 0.7811 (mt) cc_final: 0.7577 (mt) REVERT: L 1 MET cc_start: 0.6852 (mmp) cc_final: 0.6590 (mmp) REVERT: M 3 THR cc_start: 0.7731 (OUTLIER) cc_final: 0.7482 (t) REVERT: N 1 MET cc_start: 0.6784 (ttp) cc_final: 0.6374 (tmt) REVERT: O 47 MET cc_start: 0.7846 (ptm) cc_final: 0.7602 (tmm) REVERT: Q 43 GLU cc_start: 0.8406 (pm20) cc_final: 0.7998 (pm20) REVERT: Q 82 GLN cc_start: 0.7155 (mm-40) cc_final: 0.6742 (tp-100) REVERT: R 43 GLU cc_start: 0.8035 (pm20) cc_final: 0.7822 (pp20) REVERT: R 83 ILE cc_start: 0.6320 (OUTLIER) cc_final: 0.5820 (mt) REVERT: S 43 GLU cc_start: 0.7928 (mp0) cc_final: 0.7676 (mp0) REVERT: S 44 MET cc_start: 0.7312 (OUTLIER) cc_final: 0.7090 (mtp) REVERT: X 16 ILE cc_start: 0.7370 (OUTLIER) cc_final: 0.7156 (mp) REVERT: X 20 PHE cc_start: 0.5914 (t80) cc_final: 0.5517 (t80) REVERT: X 81 LYS cc_start: 0.8087 (OUTLIER) cc_final: 0.7573 (mtpt) REVERT: X 100 ARG cc_start: 0.7782 (ttp-170) cc_final: 0.7524 (ttp-110) REVERT: X 151 LYS cc_start: 0.8182 (mmtp) cc_final: 0.7975 (mtmm) REVERT: Y 22 MET cc_start: 0.5385 (tpp) cc_final: 0.5098 (tpt) REVERT: a 206 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.7399 (mt) REVERT: a 239 MET cc_start: 0.6758 (ptp) cc_final: 0.6379 (ppp) outliers start: 77 outliers final: 33 residues processed: 364 average time/residue: 0.7826 time to fit residues: 338.9435 Evaluate side-chains 342 residues out of total 3818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 295 time to evaluate : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 GLN Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 489 GLU Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 237 TYR Chi-restraints excluded: chain C residue 407 PHE Chi-restraints excluded: chain C residue 469 GLU Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 297 SER Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain F residue 142 CYS Chi-restraints excluded: chain F residue 198 MET Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 106 TYR Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 186 GLU Chi-restraints excluded: chain H residue 60 GLN Chi-restraints excluded: chain H residue 91 ASP Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 115 TYR Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain I residue 36 GLU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain M residue 3 THR Chi-restraints excluded: chain N residue 23 THR Chi-restraints excluded: chain N residue 69 ILE Chi-restraints excluded: chain Q residue 10 ILE Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain R residue 47 MET Chi-restraints excluded: chain R residue 52 MET Chi-restraints excluded: chain R residue 83 ILE Chi-restraints excluded: chain S residue 23 THR Chi-restraints excluded: chain S residue 44 MET Chi-restraints excluded: chain W residue 114 SER Chi-restraints excluded: chain X residue 16 ILE Chi-restraints excluded: chain X residue 40 ILE Chi-restraints excluded: chain X residue 81 LYS Chi-restraints excluded: chain Y residue 116 VAL Chi-restraints excluded: chain Y residue 140 ILE Chi-restraints excluded: chain a residue 149 THR Chi-restraints excluded: chain a residue 206 LEU Chi-restraints excluded: chain a residue 231 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 427 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 357 optimal weight: 5.9990 chunk 152 optimal weight: 5.9990 chunk 146 optimal weight: 0.9980 chunk 291 optimal weight: 5.9990 chunk 428 optimal weight: 6.9990 chunk 33 optimal weight: 0.5980 chunk 445 optimal weight: 8.9990 chunk 451 optimal weight: 9.9990 chunk 363 optimal weight: 2.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 66 ASN E 437 ASN F 175 HIS O 49 GLN P 82 GLN X 145 HIS ** a 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.104022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.072568 restraints weight = 80984.976| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.11 r_work: 0.3108 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 37567 Z= 0.171 Angle : 0.575 10.136 50842 Z= 0.295 Chirality : 0.042 0.186 5929 Planarity : 0.004 0.050 6560 Dihedral : 6.772 160.481 5345 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.86 % Favored : 98.12 % Rotamer: Outliers : 1.99 % Allowed : 13.68 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 1.84 (0.12), residues: 4846 helix: 2.20 (0.10), residues: 2707 sheet: 0.26 (0.21), residues: 528 loop : -0.07 (0.16), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG X 82 TYR 0.023 0.001 TYR C 475 PHE 0.015 0.001 PHE N 72 TRP 0.007 0.001 TRP a 256 HIS 0.005 0.001 HIS a 141 Details of bonding type rmsd covalent geometry : bond 0.00404 (37567) covalent geometry : angle 0.57479 (50842) hydrogen bonds : bond 0.05227 ( 2232) hydrogen bonds : angle 4.18610 ( 6465) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9692 Ramachandran restraints generated. 4846 Oldfield, 0 Emsley, 4846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9692 Ramachandran restraints generated. 4846 Oldfield, 0 Emsley, 4846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 3818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 305 time to evaluate : 1.516 Fit side-chains revert: symmetry clash REVERT: B 426 GLN cc_start: 0.7702 (mt0) cc_final: 0.7489 (mt0) REVERT: B 489 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7253 (pm20) REVERT: B 502 LYS cc_start: 0.8839 (tttt) cc_final: 0.8547 (ttpp) REVERT: C 391 SER cc_start: 0.7738 (p) cc_final: 0.7519 (m) REVERT: C 407 PHE cc_start: 0.4970 (OUTLIER) cc_final: 0.4469 (t80) REVERT: D 128 ASN cc_start: 0.7779 (p0) cc_final: 0.7044 (m-40) REVERT: E 402 GLN cc_start: 0.8561 (tt0) cc_final: 0.8275 (mt0) REVERT: E 446 GLN cc_start: 0.8373 (tm-30) cc_final: 0.8039 (tm-30) REVERT: F 392 LYS cc_start: 0.7402 (mttt) cc_final: 0.7117 (mptt) REVERT: H 60 GLN cc_start: 0.6962 (OUTLIER) cc_final: 0.6368 (mp-120) REVERT: H 91 ASP cc_start: 0.8297 (OUTLIER) cc_final: 0.8034 (t70) REVERT: H 96 GLN cc_start: 0.8076 (mm-40) cc_final: 0.7736 (mm-40) REVERT: H 106 LEU cc_start: 0.6246 (OUTLIER) cc_final: 0.6032 (mm) REVERT: H 122 LEU cc_start: 0.6761 (OUTLIER) cc_final: 0.6537 (mm) REVERT: H 128 GLN cc_start: 0.6204 (mm-40) cc_final: 0.5896 (mm-40) REVERT: H 129 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7511 (tp) REVERT: J 41 GLN cc_start: 0.7233 (mp10) cc_final: 0.6706 (mt0) REVERT: J 43 GLU cc_start: 0.8257 (pm20) cc_final: 0.8032 (pm20) REVERT: J 44 MET cc_start: 0.7216 (mtt) cc_final: 0.6867 (mtp) REVERT: J 54 ILE cc_start: 0.7978 (mt) cc_final: 0.7733 (mt) REVERT: L 1 MET cc_start: 0.6897 (mmp) cc_final: 0.6609 (mmp) REVERT: N 1 MET cc_start: 0.6869 (ttp) cc_final: 0.6494 (tmt) REVERT: O 47 MET cc_start: 0.7842 (ptm) cc_final: 0.7617 (tmm) REVERT: P 82 GLN cc_start: 0.6791 (OUTLIER) cc_final: 0.5533 (mp-120) REVERT: Q 43 GLU cc_start: 0.8446 (pm20) cc_final: 0.8053 (pm20) REVERT: Q 82 GLN cc_start: 0.7128 (mm-40) cc_final: 0.6851 (tp-100) REVERT: R 83 ILE cc_start: 0.6520 (OUTLIER) cc_final: 0.6035 (mt) REVERT: S 44 MET cc_start: 0.7451 (OUTLIER) cc_final: 0.7250 (mtp) REVERT: X 16 ILE cc_start: 0.7364 (OUTLIER) cc_final: 0.7138 (mp) REVERT: X 20 PHE cc_start: 0.6128 (t80) cc_final: 0.5852 (t80) REVERT: X 81 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7707 (mtpt) REVERT: X 100 ARG cc_start: 0.7893 (ttp-170) cc_final: 0.7621 (ttp-110) REVERT: Y 22 MET cc_start: 0.5443 (tpp) cc_final: 0.5134 (tpt) REVERT: a 62 ILE cc_start: 0.6981 (OUTLIER) cc_final: 0.6629 (mt) REVERT: a 187 PRO cc_start: 0.8211 (Cg_endo) cc_final: 0.7989 (Cg_exo) REVERT: a 206 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7415 (mt) REVERT: a 239 MET cc_start: 0.6806 (ptp) cc_final: 0.6449 (ppp) outliers start: 76 outliers final: 39 residues processed: 358 average time/residue: 0.8181 time to fit residues: 348.1337 Evaluate side-chains 348 residues out of total 3818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 295 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain B residue 25 GLN Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 489 GLU Chi-restraints excluded: chain C residue 237 TYR Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 407 PHE Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 297 SER Chi-restraints excluded: chain D residue 426 LYS Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain F residue 142 CYS Chi-restraints excluded: chain F residue 198 MET Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 186 GLU Chi-restraints excluded: chain G residue 276 ILE Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain H residue 60 GLN Chi-restraints excluded: chain H residue 91 ASP Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 115 TYR Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain I residue 36 GLU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain M residue 3 THR Chi-restraints excluded: chain N residue 23 THR Chi-restraints excluded: chain N residue 69 ILE Chi-restraints excluded: chain P residue 82 GLN Chi-restraints excluded: chain Q residue 10 ILE Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain R residue 47 MET Chi-restraints excluded: chain R residue 52 MET Chi-restraints excluded: chain R residue 83 ILE Chi-restraints excluded: chain S residue 23 THR Chi-restraints excluded: chain S residue 44 MET Chi-restraints excluded: chain W residue 114 SER Chi-restraints excluded: chain X residue 16 ILE Chi-restraints excluded: chain X residue 40 ILE Chi-restraints excluded: chain X residue 81 LYS Chi-restraints excluded: chain Y residue 116 VAL Chi-restraints excluded: chain Y residue 140 ILE Chi-restraints excluded: chain a residue 62 ILE Chi-restraints excluded: chain a residue 149 THR Chi-restraints excluded: chain a residue 206 LEU Chi-restraints excluded: chain a residue 231 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 69 optimal weight: 4.9990 chunk 418 optimal weight: 0.0980 chunk 400 optimal weight: 7.9990 chunk 196 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 335 optimal weight: 0.9990 chunk 326 optimal weight: 8.9990 chunk 317 optimal weight: 5.9990 chunk 163 optimal weight: 10.0000 chunk 147 optimal weight: 7.9990 overall best weight: 2.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 437 ASN O 49 GLN a 11 GLN ** a 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.104396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.073017 restraints weight = 81554.570| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.11 r_work: 0.3119 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 37567 Z= 0.147 Angle : 0.563 10.964 50842 Z= 0.290 Chirality : 0.041 0.189 5929 Planarity : 0.004 0.050 6560 Dihedral : 6.597 143.208 5345 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.63 % Favored : 98.35 % Rotamer: Outliers : 1.70 % Allowed : 14.07 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 1.87 (0.12), residues: 4846 helix: 2.21 (0.10), residues: 2711 sheet: 0.27 (0.21), residues: 527 loop : -0.06 (0.16), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG X 82 TYR 0.028 0.001 TYR C 475 PHE 0.019 0.001 PHE C 456 TRP 0.006 0.001 TRP a 256 HIS 0.005 0.001 HIS a 141 Details of bonding type rmsd covalent geometry : bond 0.00338 (37567) covalent geometry : angle 0.56336 (50842) hydrogen bonds : bond 0.05002 ( 2232) hydrogen bonds : angle 4.15605 ( 6465) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9692 Ramachandran restraints generated. 4846 Oldfield, 0 Emsley, 4846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9692 Ramachandran restraints generated. 4846 Oldfield, 0 Emsley, 4846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 3818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 304 time to evaluate : 1.541 Fit side-chains revert: symmetry clash REVERT: B 426 GLN cc_start: 0.7687 (mt0) cc_final: 0.7477 (mt0) REVERT: B 489 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7268 (pm20) REVERT: B 502 LYS cc_start: 0.8830 (tttt) cc_final: 0.8551 (ttpp) REVERT: C 391 SER cc_start: 0.7714 (p) cc_final: 0.7488 (m) REVERT: C 407 PHE cc_start: 0.4992 (OUTLIER) cc_final: 0.4451 (t80) REVERT: D 128 ASN cc_start: 0.7797 (p0) cc_final: 0.7069 (m-40) REVERT: D 384 MET cc_start: 0.7053 (tmm) cc_final: 0.6544 (tpt) REVERT: E 402 GLN cc_start: 0.8534 (tt0) cc_final: 0.8251 (mt0) REVERT: E 446 GLN cc_start: 0.8394 (tm-30) cc_final: 0.8067 (tm-30) REVERT: F 392 LYS cc_start: 0.7402 (mttt) cc_final: 0.7182 (mptt) REVERT: H 60 GLN cc_start: 0.7006 (OUTLIER) cc_final: 0.6394 (mp-120) REVERT: H 91 ASP cc_start: 0.8282 (OUTLIER) cc_final: 0.7958 (t70) REVERT: H 96 GLN cc_start: 0.8084 (mm-40) cc_final: 0.7757 (mm-40) REVERT: H 106 LEU cc_start: 0.6258 (OUTLIER) cc_final: 0.5996 (mm) REVERT: H 122 LEU cc_start: 0.6720 (OUTLIER) cc_final: 0.6520 (mm) REVERT: H 128 GLN cc_start: 0.6295 (mm-40) cc_final: 0.6014 (mm-40) REVERT: H 129 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7499 (tp) REVERT: J 41 GLN cc_start: 0.7177 (mp10) cc_final: 0.6656 (mt0) REVERT: J 43 GLU cc_start: 0.8262 (pm20) cc_final: 0.8034 (pm20) REVERT: J 44 MET cc_start: 0.7166 (mtt) cc_final: 0.6848 (mtp) REVERT: J 54 ILE cc_start: 0.7985 (mt) cc_final: 0.7728 (mt) REVERT: L 1 MET cc_start: 0.6885 (mmp) cc_final: 0.6605 (mmp) REVERT: O 49 GLN cc_start: 0.7993 (OUTLIER) cc_final: 0.7751 (tp40) REVERT: Q 43 GLU cc_start: 0.8460 (pm20) cc_final: 0.8058 (pm20) REVERT: Q 82 GLN cc_start: 0.7146 (mm-40) cc_final: 0.6894 (tp-100) REVERT: R 52 MET cc_start: 0.8619 (OUTLIER) cc_final: 0.8417 (ttp) REVERT: R 83 ILE cc_start: 0.6619 (OUTLIER) cc_final: 0.6110 (mt) REVERT: S 43 GLU cc_start: 0.8080 (mp0) cc_final: 0.7797 (mp0) REVERT: S 44 MET cc_start: 0.7392 (OUTLIER) cc_final: 0.7187 (mtp) REVERT: X 16 ILE cc_start: 0.7384 (OUTLIER) cc_final: 0.7132 (mp) REVERT: X 20 PHE cc_start: 0.6133 (t80) cc_final: 0.5732 (t80) REVERT: X 81 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.7716 (mtpt) REVERT: X 100 ARG cc_start: 0.7907 (ttp-170) cc_final: 0.7629 (ttp-110) REVERT: Y 22 MET cc_start: 0.5346 (tpp) cc_final: 0.5086 (tpt) REVERT: a 62 ILE cc_start: 0.6997 (OUTLIER) cc_final: 0.6660 (mt) REVERT: a 187 PRO cc_start: 0.8201 (Cg_endo) cc_final: 0.7999 (Cg_exo) REVERT: a 206 LEU cc_start: 0.7801 (OUTLIER) cc_final: 0.7397 (mt) REVERT: a 239 MET cc_start: 0.6886 (ptp) cc_final: 0.6564 (ppp) outliers start: 65 outliers final: 37 residues processed: 349 average time/residue: 0.8064 time to fit residues: 334.2421 Evaluate side-chains 347 residues out of total 3818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 295 time to evaluate : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 432 MET Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain B residue 25 GLN Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 489 GLU Chi-restraints excluded: chain C residue 237 TYR Chi-restraints excluded: chain C residue 407 PHE Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 297 SER Chi-restraints excluded: chain D residue 426 LYS Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain F residue 142 CYS Chi-restraints excluded: chain F residue 198 MET Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 186 GLU Chi-restraints excluded: chain G residue 276 ILE Chi-restraints excluded: chain H residue 60 GLN Chi-restraints excluded: chain H residue 91 ASP Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 115 TYR Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain I residue 36 GLU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain M residue 3 THR Chi-restraints excluded: chain N residue 23 THR Chi-restraints excluded: chain N residue 64 MET Chi-restraints excluded: chain N residue 69 ILE Chi-restraints excluded: chain O residue 49 GLN Chi-restraints excluded: chain Q residue 10 ILE Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain R residue 52 MET Chi-restraints excluded: chain R residue 83 ILE Chi-restraints excluded: chain S residue 23 THR Chi-restraints excluded: chain S residue 44 MET Chi-restraints excluded: chain W residue 114 SER Chi-restraints excluded: chain X residue 16 ILE Chi-restraints excluded: chain X residue 40 ILE Chi-restraints excluded: chain X residue 81 LYS Chi-restraints excluded: chain Y residue 116 VAL Chi-restraints excluded: chain Y residue 140 ILE Chi-restraints excluded: chain a residue 62 ILE Chi-restraints excluded: chain a residue 149 THR Chi-restraints excluded: chain a residue 206 LEU Chi-restraints excluded: chain a residue 231 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 131 optimal weight: 7.9990 chunk 391 optimal weight: 3.9990 chunk 115 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 342 optimal weight: 5.9990 chunk 97 optimal weight: 0.3980 chunk 296 optimal weight: 7.9990 chunk 312 optimal weight: 10.0000 chunk 431 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 overall best weight: 4.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 421 GLN N 82 GLN O 49 GLN P 82 GLN Y 10 GLN ** a 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 285 HIS ** 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 = 0.3781 r_free = 0.3781 target = 0.102900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.071333 restraints weight = 81142.240| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.10 r_work: 0.3080 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 37567 Z= 0.221 Angle : 0.637 11.042 50842 Z= 0.326 Chirality : 0.044 0.224 5929 Planarity : 0.005 0.050 6560 Dihedral : 6.755 122.767 5345 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.19 % Favored : 97.79 % Rotamer: Outliers : 1.76 % Allowed : 14.30 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 1.60 (0.12), residues: 4846 helix: 2.00 (0.10), residues: 2706 sheet: 0.15 (0.21), residues: 539 loop : -0.17 (0.16), residues: 1601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 121 TYR 0.025 0.002 TYR C 475 PHE 0.019 0.002 PHE N 72 TRP 0.006 0.001 TRP a 256 HIS 0.007 0.001 HIS D 358 Details of bonding type rmsd covalent geometry : bond 0.00535 (37567) covalent geometry : angle 0.63701 (50842) hydrogen bonds : bond 0.05760 ( 2232) hydrogen bonds : angle 4.32395 ( 6465) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9692 Ramachandran restraints generated. 4846 Oldfield, 0 Emsley, 4846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9692 Ramachandran restraints generated. 4846 Oldfield, 0 Emsley, 4846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 3818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 289 time to evaluate : 1.443 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 426 GLN cc_start: 0.7858 (mt0) cc_final: 0.7635 (mt0) REVERT: B 489 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7324 (pm20) REVERT: B 502 LYS cc_start: 0.8845 (tttt) cc_final: 0.8573 (ttpp) REVERT: C 391 SER cc_start: 0.7801 (p) cc_final: 0.7592 (m) REVERT: C 407 PHE cc_start: 0.4987 (OUTLIER) cc_final: 0.4390 (t80) REVERT: C 470 GLN cc_start: 0.7517 (tp40) cc_final: 0.7282 (mm110) REVERT: E 280 MET cc_start: 0.8994 (ttm) cc_final: 0.8572 (mtt) REVERT: E 402 GLN cc_start: 0.8596 (tt0) cc_final: 0.8300 (mt0) REVERT: E 446 GLN cc_start: 0.8497 (tm-30) cc_final: 0.8159 (tm-30) REVERT: F 392 LYS cc_start: 0.7460 (mttt) cc_final: 0.7214 (mptt) REVERT: H 91 ASP cc_start: 0.8310 (OUTLIER) cc_final: 0.7996 (t70) REVERT: H 96 GLN cc_start: 0.8085 (mm-40) cc_final: 0.7762 (mm-40) REVERT: H 106 LEU cc_start: 0.6323 (OUTLIER) cc_final: 0.6025 (mm) REVERT: H 122 LEU cc_start: 0.6731 (OUTLIER) cc_final: 0.6388 (mm) REVERT: H 128 GLN cc_start: 0.6286 (mm-40) cc_final: 0.6031 (mm-40) REVERT: H 129 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7469 (tp) REVERT: J 41 GLN cc_start: 0.7374 (mp10) cc_final: 0.6831 (mt0) REVERT: J 44 MET cc_start: 0.7265 (mtt) cc_final: 0.6994 (mtp) REVERT: J 54 ILE cc_start: 0.8059 (mt) cc_final: 0.7829 (mt) REVERT: L 1 MET cc_start: 0.6806 (mmp) cc_final: 0.6512 (mmp) REVERT: O 49 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7619 (tp40) REVERT: Q 43 GLU cc_start: 0.8489 (pm20) cc_final: 0.8082 (pm20) REVERT: R 83 ILE cc_start: 0.6608 (OUTLIER) cc_final: 0.6035 (mt) REVERT: S 43 GLU cc_start: 0.8079 (mp0) cc_final: 0.7798 (mp0) REVERT: S 44 MET cc_start: 0.7481 (OUTLIER) cc_final: 0.7265 (mtp) REVERT: X 16 ILE cc_start: 0.7391 (OUTLIER) cc_final: 0.7158 (mp) REVERT: X 20 PHE cc_start: 0.6146 (t80) cc_final: 0.5853 (t80) REVERT: X 75 ILE cc_start: 0.7903 (OUTLIER) cc_final: 0.7647 (mp) REVERT: X 81 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7682 (mtpt) REVERT: X 100 ARG cc_start: 0.7863 (ttp-170) cc_final: 0.7596 (ttp-110) REVERT: Y 22 MET cc_start: 0.5407 (tpp) cc_final: 0.5152 (tpt) REVERT: a 62 ILE cc_start: 0.6924 (OUTLIER) cc_final: 0.6586 (mt) REVERT: a 68 LYS cc_start: 0.5552 (ttpp) cc_final: 0.4839 (tmtt) REVERT: a 206 LEU cc_start: 0.7750 (OUTLIER) cc_final: 0.7374 (mt) REVERT: a 239 MET cc_start: 0.6979 (ptp) cc_final: 0.6587 (ppp) outliers start: 67 outliers final: 36 residues processed: 339 average time/residue: 0.7732 time to fit residues: 311.3217 Evaluate side-chains 331 residues out of total 3818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 281 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 MET Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain B residue 25 GLN Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 489 GLU Chi-restraints excluded: chain C residue 237 TYR Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 407 PHE Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 426 LYS Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain F residue 142 CYS Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 186 GLU Chi-restraints excluded: chain G residue 276 ILE Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain H residue 91 ASP Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 115 TYR Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain I residue 36 GLU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain M residue 3 THR Chi-restraints excluded: chain N residue 23 THR Chi-restraints excluded: chain N residue 64 MET Chi-restraints excluded: chain N residue 69 ILE Chi-restraints excluded: chain O residue 49 GLN Chi-restraints excluded: chain Q residue 10 ILE Chi-restraints excluded: chain R residue 83 ILE Chi-restraints excluded: chain S residue 23 THR Chi-restraints excluded: chain S residue 44 MET Chi-restraints excluded: chain W residue 114 SER Chi-restraints excluded: chain X residue 16 ILE Chi-restraints excluded: chain X residue 40 ILE Chi-restraints excluded: chain X residue 75 ILE Chi-restraints excluded: chain X residue 81 LYS Chi-restraints excluded: chain Y residue 116 VAL Chi-restraints excluded: chain Y residue 140 ILE Chi-restraints excluded: chain a residue 62 ILE Chi-restraints excluded: chain a residue 149 THR Chi-restraints excluded: chain a residue 206 LEU Chi-restraints excluded: chain a residue 231 LEU Chi-restraints excluded: chain a residue 287 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 62 optimal weight: 0.0980 chunk 227 optimal weight: 1.9990 chunk 399 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 97 optimal weight: 0.4980 chunk 228 optimal weight: 4.9990 chunk 172 optimal weight: 1.9990 chunk 345 optimal weight: 2.9990 chunk 332 optimal weight: 9.9990 chunk 213 optimal weight: 0.9980 chunk 315 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 HIS B 424 HIS C 421 GLN N 41 GLN O 49 GLN ** Q 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 285 HIS ** 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 = 0.3811 r_free = 0.3811 target = 0.104716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.074144 restraints weight = 81192.492| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.22 r_work: 0.3126 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 37567 Z= 0.122 Angle : 0.557 11.111 50842 Z= 0.286 Chirality : 0.040 0.192 5929 Planarity : 0.004 0.050 6560 Dihedral : 6.391 107.156 5345 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.51 % Favored : 98.47 % Rotamer: Outliers : 1.62 % Allowed : 14.59 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 1.87 (0.12), residues: 4846 helix: 2.24 (0.10), residues: 2705 sheet: 0.23 (0.21), residues: 537 loop : -0.09 (0.16), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 121 TYR 0.032 0.001 TYR C 475 PHE 0.017 0.001 PHE C 468 TRP 0.006 0.001 TRP a 256 HIS 0.005 0.001 HIS a 141 Details of bonding type rmsd covalent geometry : bond 0.00257 (37567) covalent geometry : angle 0.55676 (50842) hydrogen bonds : bond 0.04820 ( 2232) hydrogen bonds : angle 4.15180 ( 6465) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16843.21 seconds wall clock time: 286 minutes 3.13 seconds (17163.13 seconds total)