Starting phenix.real_space_refine on Sat Feb 7 22:06:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o1j_70009/02_2026/9o1j_70009_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o1j_70009/02_2026/9o1j_70009.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9o1j_70009/02_2026/9o1j_70009.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o1j_70009/02_2026/9o1j_70009.map" model { file = "/net/cci-nas-00/data/ceres_data/9o1j_70009/02_2026/9o1j_70009_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o1j_70009/02_2026/9o1j_70009_neut.cif" } resolution = 3.02 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= 0.003 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: 6 Type Number sf(0) Gaussians P 15 5.49 5 Mg 5 5.21 5 S 158 5.16 5 C 23505 2.51 5 N 6259 2.21 5 O 6977 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 216 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: 36919 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 3823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3823 Classifications: {'peptide': 506} Link IDs: {'PTRANS': 16, 'TRANS': 489} Chain: "B" Number of atoms: 3808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3808 Classifications: {'peptide': 504} Link IDs: {'PTRANS': 16, 'TRANS': 487} Chain: "C" Number of atoms: 3823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3823 Classifications: {'peptide': 506} Link IDs: {'PTRANS': 16, 'TRANS': 489} 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: {'PTRANS': 20, '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: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 261} Chain breaks: 2 Chain: "H" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 929 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain breaks: 1 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} Time building chain proxies: 9.03, per 1000 atoms: 0.24 Number of scatterers: 36919 At special positions: 0 Unit cell: (127.82, 136.12, 240.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 158 16.00 P 15 15.00 Mg 5 11.99 O 6977 8.00 N 6259 7.00 C 23505 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: 3.36 Conformation dependent library (CDL) restraints added in 1.7 seconds 9666 Ramachandran restraints generated. 4833 Oldfield, 0 Emsley, 4833 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8770 Finding SS restraints... Secondary structure from input PDB file: 201 helices and 29 sheets defined 61.8% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.46 Creating SS restraints... Processing helix chain 'A' and resid 9 through 18 removed outlier: 3.809A pdb=" N ILE A 13 " --> pdb=" O ILE A 9 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS A 14 " --> pdb=" O SER A 10 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N GLY A 15 " --> pdb=" O GLU A 11 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ARG A 16 " --> pdb=" O ILE A 12 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE A 17 " --> pdb=" O ILE A 13 " (cutoff:3.500A) 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 187 through 189 No H-bonds generated for 'chain 'A' and resid 187 through 189' 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: 3.505A pdb=" N TYR A 249 " --> pdb=" O THR A 245 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N PHE A 250 " --> pdb=" O MET A 246 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG A 251 " --> pdb=" O GLY A 247 " (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: 3.601A 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: 3.562A pdb=" N ALA A 381 " --> pdb=" O VAL A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 404 removed outlier: 4.409A pdb=" N GLY A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N GLY A 393 " --> pdb=" O LYS A 389 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ILE A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 removed outlier: 3.598A pdb=" N ALA A 408 " --> pdb=" O ALA A 405 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN A 409 " --> pdb=" O ALA A 406 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA A 411 " --> pdb=" O ALA A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 432 removed outlier: 3.518A pdb=" N MET A 432 " --> pdb=" O VAL A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 454 removed outlier: 3.623A pdb=" N SER A 448 " --> pdb=" O GLU A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 480 removed outlier: 3.507A pdb=" N ARG A 478 " --> pdb=" O SER A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 488 Processing helix chain 'A' and resid 494 through 512 removed outlier: 3.527A pdb=" N THR A 511 " --> pdb=" O LYS A 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 16 through 20 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 232 through 252 Proline residue: B 240 - end of helix removed outlier: 4.568A pdb=" N PHE B 250 " --> pdb=" O MET B 246 " (cutoff:3.500A) removed outlier: 3.634A 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: 3.658A 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: 3.507A pdb=" N ALA B 381 " --> pdb=" O VAL B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 391 Processing helix chain 'B' and resid 393 through 408 removed outlier: 3.591A pdb=" N GLU B 403 " --> pdb=" O ALA B 399 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA B 406 " --> pdb=" O ARG B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 432 removed outlier: 3.807A pdb=" N ARG B 427 " --> pdb=" O GLU B 423 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL B 428 " --> pdb=" O HIS B 424 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU B 430 " --> pdb=" O GLN B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 455 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 489 Processing helix chain 'B' and resid 494 through 512 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: 3.608A pdb=" N ARG C 251 " --> pdb=" O GLY C 247 " (cutoff:3.500A) removed outlier: 3.859A 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: 3.701A pdb=" N HIS C 295 " --> pdb=" O VAL C 291 " (cutoff:3.500A) removed outlier: 3.872A 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 384 through 391 Processing helix chain 'C' and resid 391 through 403 removed outlier: 3.694A pdb=" N ARG C 395 " --> pdb=" O SER C 391 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N THR C 396 " --> pdb=" O GLY C 392 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA C 397 " --> pdb=" O GLY C 393 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU C 403 " --> pdb=" O ALA C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 411 Processing helix chain 'C' and resid 415 through 433 removed outlier: 3.577A pdb=" N LYS C 433 " --> pdb=" O THR C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 455 Processing helix chain 'C' and resid 461 through 480 removed outlier: 4.446A pdb=" N GLY C 466 " --> pdb=" O ILE C 462 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N SER C 467 " --> pdb=" O ALA C 463 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG C 478 " --> pdb=" O SER C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 489 Processing helix chain 'C' and resid 494 through 512 removed outlier: 3.612A pdb=" N ALA C 510 " --> pdb=" O GLU C 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 89 Processing helix chain 'D' and resid 120 through 124 removed outlier: 3.705A 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 172 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: 5.313A pdb=" N ALA D 225 " --> pdb=" O ARG D 221 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N LEU D 226 " --> pdb=" O LEU D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 261 removed outlier: 3.794A pdb=" N THR D 253 " --> pdb=" O ILE D 249 " (cutoff:3.500A) removed outlier: 4.355A 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: 3.662A 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 381 removed outlier: 3.929A pdb=" N GLU D 374 " --> pdb=" O GLN D 370 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N ASP D 377 " --> pdb=" O LYS D 373 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE D 378 " --> pdb=" O GLU D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 405 removed outlier: 3.501A pdb=" N ARG D 397 " --> pdb=" O LEU D 393 " (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: 3.604A pdb=" N PHE D 448 " --> pdb=" O GLU D 445 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TYR D 449 " --> pdb=" O GLN D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 461 removed outlier: 3.528A 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: 3.541A 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: 3.749A pdb=" N LEU E 167 " --> pdb=" O ASN E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 201 removed outlier: 3.561A pdb=" N GLY E 191 " --> pdb=" O ARG E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 205 No H-bonds generated for 'chain 'E' and resid 203 through 205' Processing helix chain 'E' and resid 217 through 238 removed outlier: 3.503A pdb=" N ARG E 221 " --> pdb=" O PRO E 217 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N ALA E 225 " --> pdb=" O ARG E 221 " (cutoff:3.500A) removed outlier: 5.485A 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 287 removed outlier: 4.208A pdb=" N ARG E 286 " --> pdb=" O VAL E 282 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE E 287 " --> pdb=" O LEU E 283 " (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 Processing helix chain 'E' and resid 350 through 355 Processing helix chain 'E' and resid 355 through 383 removed outlier: 5.041A pdb=" N ASP E 377 " --> pdb=" O LYS E 373 " (cutoff:3.500A) removed outlier: 5.420A 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 424 through 438 Processing helix chain 'E' and resid 444 through 448 Processing helix chain 'E' and resid 453 through 461 removed outlier: 3.696A pdb=" N ALA E 457 " --> pdb=" O GLY E 453 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 89 Processing helix chain 'F' and resid 120 through 124 removed outlier: 3.739A 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 175 removed outlier: 3.584A 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 239 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: 4.911A pdb=" N LEU F 226 " --> pdb=" O LEU F 222 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE F 235 " --> pdb=" O MET F 231 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 263 removed outlier: 3.738A 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 Processing helix chain 'F' and resid 310 through 318 removed outlier: 3.518A pdb=" N ALA F 318 " --> pdb=" O ALA F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 334 Processing helix chain 'F' and resid 350 through 382 removed outlier: 8.107A pdb=" N GLN F 356 " --> pdb=" O LEU F 352 " (cutoff:3.500A) removed outlier: 9.180A pdb=" N ASP F 357 " --> pdb=" O VAL F 353 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N HIS F 358 " --> pdb=" O ILE F 354 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASP F 377 " --> pdb=" O LYS F 373 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 387 removed outlier: 3.599A pdb=" N LEU F 387 " --> pdb=" O MET F 384 " (cutoff:3.500A) 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 removed outlier: 3.517A pdb=" N ILE F 435 " --> pdb=" O GLY F 431 " (cutoff:3.500A) Processing helix chain 'F' and resid 444 through 449 Processing helix chain 'F' and resid 453 through 463 removed outlier: 3.799A pdb=" N ALA F 457 " --> pdb=" O GLY F 453 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS F 463 " --> pdb=" O GLU F 459 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 41 removed outlier: 3.872A pdb=" N ILE G 7 " --> pdb=" O GLY G 3 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER G 9 " --> pdb=" O LYS G 5 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR G 17 " --> pdb=" O SER G 13 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE G 20 " --> pdb=" O SER G 16 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS G 26 " --> pdb=" O ASN G 22 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA G 40 " --> pdb=" O GLN G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 60 removed outlier: 3.610A pdb=" N ALA G 46 " --> pdb=" O GLY G 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 69 Processing helix chain 'G' and resid 90 through 110 Processing helix chain 'G' and resid 119 through 128 removed outlier: 3.698A pdb=" N ALA G 123 " --> pdb=" O GLY G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 162 removed outlier: 4.123A pdb=" N LEU G 149 " --> pdb=" O SER G 145 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLY G 151 " --> pdb=" O ASN G 147 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N SER G 152 " --> pdb=" O ASP G 148 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N MET G 156 " --> pdb=" O SER G 152 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA G 159 " --> pdb=" O VAL G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 210 through 284 removed outlier: 3.601A pdb=" N GLY G 217 " --> pdb=" O SER G 213 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL G 220 " --> pdb=" O ASP G 216 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 103 removed outlier: 3.590A pdb=" N ASP H 91 " --> pdb=" O ALA H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 130 removed outlier: 3.623A pdb=" N ARG H 130 " --> pdb=" O ALA H 126 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 41 removed outlier: 3.521A pdb=" N ALA I 9 " --> pdb=" O VAL I 5 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE I 10 " --> pdb=" O GLY I 6 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY I 19 " --> pdb=" O LEU I 15 " (cutoff:3.500A) Processing helix chain 'I' and resid 44 through 76 removed outlier: 3.507A pdb=" N VAL I 55 " --> pdb=" O LYS I 51 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY I 57 " --> pdb=" O PHE I 53 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU I 58 " --> pdb=" O ILE I 54 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N VAL I 62 " --> pdb=" O LEU I 58 " (cutoff:3.500A) removed outlier: 5.140A 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: 3.546A pdb=" N ALA J 9 " --> pdb=" O VAL J 5 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE J 10 " --> pdb=" O GLY J 6 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY J 19 " --> pdb=" O LEU J 15 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS J 33 " --> pdb=" O LEU J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 44 through 60 removed outlier: 3.686A pdb=" N LEU J 58 " --> pdb=" O ILE J 54 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 76 removed outlier: 3.568A pdb=" N ILE J 65 " --> pdb=" O ALA J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 79 through 83 Processing helix chain 'L' and resid 2 through 41 removed outlier: 3.703A pdb=" N ILE L 10 " --> pdb=" O GLY L 6 " (cutoff:3.500A) Processing helix chain 'L' and resid 44 through 76 removed outlier: 3.756A pdb=" N VAL L 50 " --> pdb=" O PRO L 46 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU L 58 " --> pdb=" O ILE L 54 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N VAL L 62 " --> pdb=" O LEU L 58 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N THR L 63 " --> pdb=" O LEU L 59 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE L 65 " --> pdb=" O ALA L 61 " (cutoff:3.500A) Processing helix chain 'L' and resid 77 through 83 removed outlier: 3.613A pdb=" N GLY L 81 " --> pdb=" O ASN L 77 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 41 removed outlier: 3.502A pdb=" N GLY M 19 " --> pdb=" O LEU M 15 " (cutoff:3.500A) Processing helix chain 'M' and resid 44 through 76 removed outlier: 4.139A pdb=" N VAL M 50 " --> pdb=" O PRO M 46 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL M 55 " --> pdb=" O LYS M 51 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU M 58 " --> pdb=" O ILE M 54 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N VAL M 62 " --> pdb=" O LEU M 58 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N THR M 63 " --> pdb=" O LEU M 59 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE M 65 " --> pdb=" O ALA M 61 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 83 removed outlier: 3.862A pdb=" N ILE M 83 " --> pdb=" O VAL M 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 41 removed outlier: 3.883A pdb=" N GLY N 19 " --> pdb=" O LEU N 15 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN N 41 " --> pdb=" O GLY N 37 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 60 removed outlier: 3.615A pdb=" N GLY N 57 " --> pdb=" O PHE N 53 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU N 58 " --> pdb=" O ILE N 54 " (cutoff:3.500A) Processing helix chain 'N' and resid 60 through 74 removed outlier: 3.692A pdb=" N MET N 64 " --> pdb=" O ASP N 60 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 83 Processing helix chain 'O' and resid 2 through 41 removed outlier: 3.584A pdb=" N ALA O 9 " --> pdb=" O VAL O 5 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE O 10 " --> pdb=" O GLY O 6 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY O 19 " --> pdb=" O LEU O 15 " (cutoff:3.500A) Processing helix chain 'O' and resid 44 through 75 removed outlier: 3.591A pdb=" N VAL O 50 " --> pdb=" O PRO O 46 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU O 58 " --> pdb=" O ILE O 54 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N VAL O 62 " --> pdb=" O LEU O 58 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N THR O 63 " --> pdb=" O LEU O 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 41 removed outlier: 3.867A pdb=" N THR P 8 " --> pdb=" O VAL P 4 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE P 10 " --> pdb=" O GLY P 6 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLY P 19 " --> pdb=" O LEU P 15 " (cutoff:3.500A) Processing helix chain 'P' and resid 44 through 60 removed outlier: 3.769A pdb=" N VAL P 50 " --> pdb=" O PRO P 46 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU P 58 " --> pdb=" O ILE P 54 " (cutoff:3.500A) Processing helix chain 'P' and resid 60 through 76 removed outlier: 3.528A pdb=" N ILE P 65 " --> pdb=" O ALA P 61 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 41 removed outlier: 3.662A pdb=" N LYS Q 33 " --> pdb=" O LEU Q 29 " (cutoff:3.500A) Processing helix chain 'Q' and resid 44 through 60 removed outlier: 3.783A pdb=" N ILE Q 54 " --> pdb=" O VAL Q 50 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL Q 55 " --> pdb=" O LYS Q 51 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU Q 58 " --> pdb=" O ILE Q 54 " (cutoff:3.500A) Processing helix chain 'Q' and resid 60 through 76 removed outlier: 3.634A pdb=" N ILE Q 65 " --> pdb=" O ALA Q 61 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 83 removed outlier: 3.981A pdb=" N ILE Q 83 " --> pdb=" O VAL Q 80 " (cutoff:3.500A) Processing helix chain 'R' and resid 2 through 41 removed outlier: 3.587A pdb=" N ILE R 10 " --> pdb=" O GLY R 6 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY R 19 " --> pdb=" O LEU R 15 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS R 33 " --> pdb=" O LEU R 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 44 through 60 removed outlier: 3.841A pdb=" N VAL R 50 " --> pdb=" O PRO R 46 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU R 58 " --> pdb=" O ILE R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 76 removed outlier: 3.716A pdb=" N ILE R 65 " --> pdb=" O ALA R 61 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 41 removed outlier: 3.735A pdb=" N ILE S 10 " --> pdb=" O GLY S 6 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS S 33 " --> pdb=" O LEU S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 44 through 76 removed outlier: 3.650A pdb=" N VAL S 50 " --> pdb=" O PRO S 46 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU S 58 " --> pdb=" O ILE S 54 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N VAL S 62 " --> pdb=" O LEU S 58 " (cutoff:3.500A) removed outlier: 4.833A 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 26 through 41 removed outlier: 3.525A pdb=" N ALA W 30 " --> pdb=" O ALA W 26 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASP W 41 " --> pdb=" O ALA W 37 " (cutoff:3.500A) Processing helix chain 'W' and resid 41 through 49 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 106 removed outlier: 3.537A pdb=" N TYR W 97 " --> pdb=" O ILE W 93 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU W 98 " --> pdb=" O ALA W 94 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN W 99 " --> pdb=" O GLU W 95 " (cutoff:3.500A) Processing helix chain 'W' and resid 119 through 135 removed outlier: 3.710A pdb=" N ASP W 124 " --> pdb=" O LYS W 120 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU W 126 " --> pdb=" O GLN W 122 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ALA W 129 " --> pdb=" O LYS W 125 " (cutoff:3.500A) Processing helix chain 'W' and resid 164 through 178 Processing helix chain 'X' and resid 5 through 25 removed outlier: 3.904A pdb=" N GLY X 9 " --> pdb=" O ALA X 5 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N MET X 22 " --> pdb=" O VAL X 18 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS X 23 " --> pdb=" O LEU X 19 " (cutoff:3.500A) Processing helix chain 'X' and resid 25 through 120 removed outlier: 3.970A pdb=" N VAL X 29 " --> pdb=" O VAL X 25 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG X 36 " --> pdb=" O ALA X 32 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA X 47 " --> pdb=" O GLY X 43 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU X 54 " --> pdb=" O ALA X 50 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLU X 55 " --> pdb=" O ALA X 51 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU X 56 " --> pdb=" O ARG X 52 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N HIS X 58 " --> pdb=" O LEU X 54 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ALA X 61 " --> pdb=" O ALA X 57 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N GLN X 64 " --> pdb=" O LYS X 60 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN X 85 " --> pdb=" O LYS X 81 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA X 90 " --> pdb=" O ILE X 86 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU X 110 " --> pdb=" O GLN X 106 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN X 111 " --> pdb=" O ALA X 107 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N SER X 115 " --> pdb=" O GLN X 111 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ASP X 118 " --> pdb=" O ASN X 114 " (cutoff:3.500A) Processing helix chain 'X' and resid 123 through 137 removed outlier: 3.587A pdb=" N LEU X 127 " --> pdb=" O GLN X 123 " (cutoff:3.500A) Processing helix chain 'X' and resid 140 through 143 Processing helix chain 'X' and resid 144 through 149 removed outlier: 3.658A pdb=" N VAL X 149 " --> pdb=" O HIS X 145 " (cutoff:3.500A) Processing helix chain 'X' and resid 150 through 155 removed outlier: 3.701A pdb=" N GLU X 155 " --> pdb=" O LEU X 152 " (cutoff:3.500A) Processing helix chain 'Y' and resid 2 through 24 Processing helix chain 'Y' and resid 25 through 137 removed outlier: 4.259A pdb=" N VAL Y 29 " --> pdb=" O VAL Y 25 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU Y 33 " --> pdb=" O VAL Y 29 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLU Y 55 " --> pdb=" O ALA Y 51 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS Y 69 " --> pdb=" O LEU Y 65 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE Y 75 " --> pdb=" O GLN Y 71 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL Y 76 " --> pdb=" O ALA Y 72 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA Y 103 " --> pdb=" O GLU Y 99 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN Y 104 " --> pdb=" O ARG Y 100 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA Y 105 " --> pdb=" O LEU Y 101 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE Y 109 " --> pdb=" O ALA Y 105 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLU Y 110 " --> pdb=" O GLN Y 106 " (cutoff:3.500A) Processing helix chain 'Y' and resid 141 through 153 removed outlier: 3.898A pdb=" N GLN Y 147 " --> pdb=" O ASN Y 143 " (cutoff:3.500A) Processing helix chain 'a' and resid 5 through 14 Processing helix chain 'a' and resid 32 through 39 Processing helix chain 'a' and resid 46 through 69 removed outlier: 3.800A pdb=" N ALA a 66 " --> pdb=" O ILE a 62 " (cutoff:3.500A) Processing helix chain 'a' and resid 76 through 97 removed outlier: 4.024A pdb=" N PHE a 81 " --> pdb=" O GLY a 77 " (cutoff:3.500A) Processing helix chain 'a' and resid 103 through 121 removed outlier: 3.623A pdb=" N ILE a 121 " --> pdb=" O LEU a 117 " (cutoff:3.500A) Processing helix chain 'a' and resid 127 through 138 Processing helix chain 'a' and resid 147 through 150 removed outlier: 3.805A pdb=" N THR a 150 " --> pdb=" O VAL a 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 147 through 150' Processing helix chain 'a' and resid 151 through 175 removed outlier: 3.588A pdb=" N THR a 155 " --> pdb=" O ASP a 151 " (cutoff:3.500A) Processing helix chain 'a' and resid 175 through 186 removed outlier: 3.905A pdb=" N HIS a 186 " --> pdb=" O GLU a 182 " (cutoff:3.500A) Processing helix chain 'a' and resid 192 through 241 removed outlier: 4.046A pdb=" N LEU a 198 " --> pdb=" O VAL a 194 " (cutoff:3.500A) Proline residue: a 201 - end of helix removed outlier: 4.073A pdb=" N VAL a 209 " --> pdb=" O LEU a 205 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N LYS a 214 " --> pdb=" O THR a 210 " (cutoff:3.500A) Proline residue: a 215 - end of helix removed outlier: 4.261A pdb=" N ASN a 225 " --> pdb=" O ARG a 221 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N MET a 226 " --> pdb=" O LEU a 222 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N MET a 239 " --> pdb=" O LEU a 235 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N PHE a 240 " --> pdb=" O ILE a 236 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLY a 241 " --> pdb=" O ALA a 237 " (cutoff:3.500A) Processing helix chain 'a' and resid 244 through 283 removed outlier: 4.231A pdb=" N LEU a 264 " --> pdb=" O VAL a 260 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE a 265 " --> pdb=" O PHE a 261 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR a 267 " --> pdb=" O ILE a 263 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA a 270 " --> pdb=" O ILE a 266 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'W' and resid 137 through 140 removed outlier: 6.654A pdb=" N VAL W 108 " --> pdb=" O ARG W 139 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG W 155 " --> pdb=" O GLU W 111 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG A 27 " --> pdb=" O VAL W 160 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'W' and resid 137 through 140 removed outlier: 6.654A pdb=" N VAL W 108 " --> pdb=" O ARG W 139 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 107 through 114 current: chain 'A' and resid 53 through 56 removed outlier: 3.686A pdb=" N VAL A 60 " --> pdb=" O PHE A 56 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N ALA A 64 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL A 75 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE A 39 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N VAL A 35 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ARG A 41 " --> pdb=" O VAL A 33 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 97 through 100 removed outlier: 4.117A pdb=" N ALA A 126 " --> pdb=" O VAL A 100 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 110 removed outlier: 6.502A pdb=" N VAL A 109 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR A 261 " --> pdb=" O LEU A 328 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU A 167 " --> pdb=" O ILE A 354 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 146 through 147 removed outlier: 4.593A pdb=" N VAL A 160 " --> pdb=" O VAL A 147 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 29 through 35 removed outlier: 6.714A pdb=" N ARG B 41 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N VAL B 35 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ILE B 39 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL B 75 " --> pdb=" O ALA B 64 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ALA B 64 " --> pdb=" O VAL B 75 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLU B 52 " --> pdb=" O ALA B 64 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N MET B 53 " --> pdb=" O THR B 92 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 97 through 99 Processing sheet with id=AA8, first strand: chain 'B' and resid 108 through 110 removed outlier: 6.876A pdb=" N CYS B 194 " --> pdb=" O ILE B 223 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N VAL B 225 " --> pdb=" O CYS B 194 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N TYR B 196 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ALA B 227 " --> pdb=" O TYR B 196 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ALA B 198 " --> pdb=" O ALA B 227 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ALA B 257 " --> pdb=" O THR B 326 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N LEU B 328 " --> pdb=" O ALA B 257 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ILE B 259 " --> pdb=" O LEU B 328 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N ILE B 330 " --> pdb=" O ILE B 259 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N TYR B 261 " --> pdb=" O ILE B 330 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N GLU B 332 " --> pdb=" O TYR B 261 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 108 through 110 removed outlier: 6.876A pdb=" N CYS B 194 " --> pdb=" O ILE B 223 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N VAL B 225 " --> pdb=" O CYS B 194 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N TYR B 196 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ALA B 227 " --> pdb=" O TYR B 196 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ALA B 198 " --> pdb=" O ALA B 227 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ALA B 257 " --> pdb=" O THR B 326 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N LEU B 328 " --> pdb=" O ALA B 257 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ILE B 259 " --> pdb=" O LEU B 328 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N ILE B 330 " --> pdb=" O ILE B 259 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N TYR B 261 " --> pdb=" O ILE B 330 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N GLU B 332 " --> pdb=" O TYR B 261 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU B 167 " --> pdb=" O ILE B 354 " (cutoff:3.500A) Processing sheet with id=AB1, 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: 7.177A pdb=" N MET C 53 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ARG C 41 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N VAL C 35 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE C 39 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 6.818A 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: 7.345A pdb=" N THR E 76 " --> pdb=" O LYS E 37 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N LYS E 37 " --> pdb=" O THR E 76 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N ALA E 78 " --> pdb=" O ALA E 35 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLU E 34 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ARG E 57 " --> pdb=" O GLN E 48 " (cutoff:3.500A) removed outlier: 5.105A 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: 4.683A pdb=" N ILE E 15 " --> pdb=" O VAL E 19 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ASP E 21 " --> pdb=" O VAL E 13 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 97 through 100 removed outlier: 3.984A pdb=" N ALA C 126 " --> pdb=" O VAL C 100 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 108 through 109 removed outlier: 6.537A pdb=" N VAL C 109 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N SER C 228 " --> pdb=" O VAL C 109 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 108 through 109 removed outlier: 6.537A pdb=" N VAL C 109 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N SER C 228 " --> pdb=" O VAL C 109 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU C 167 " --> pdb=" O ILE C 354 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 146 through 147 removed outlier: 4.429A pdb=" N VAL C 160 " --> pdb=" O VAL C 147 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 9 through 16 removed outlier: 5.928A pdb=" N ILE D 12 " --> pdb=" O GLU D 23 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N GLU D 23 " --> pdb=" O ILE D 12 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN D 14 " --> pdb=" O ASP D 21 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N VAL D 55 " --> pdb=" O GLN D 50 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N GLN D 50 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ARG D 57 " --> pdb=" O GLN D 48 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 81 through 83 Processing sheet with id=AB8, first strand: chain 'D' and resid 92 through 93 removed outlier: 6.204A pdb=" N MET D 93 " --> pdb=" O TYR D 211 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N SER D 179 " --> pdb=" O ALA D 208 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N VAL D 210 " --> pdb=" O SER D 179 " (cutoff:3.500A) removed outlier: 6.365A 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: 6.306A pdb=" N GLY D 183 " --> pdb=" O GLY D 212 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TYR D 178 " --> pdb=" O ASP D 241 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL D 242 " --> pdb=" O THR D 296 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N ILE D 298 " --> pdb=" O VAL D 242 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LEU D 244 " --> pdb=" O ILE D 298 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N ALA D 300 " --> pdb=" O LEU D 244 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N ILE D 246 " --> pdb=" O ALA D 300 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N TYR D 302 " --> pdb=" O ILE D 246 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LYS D 149 " --> pdb=" O ALA D 322 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N VAL D 324 " --> pdb=" O LYS D 149 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N GLY D 151 " --> pdb=" O VAL D 324 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 130 through 131 removed outlier: 4.111A pdb=" N PHE D 144 " --> pdb=" O LEU D 131 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 81 through 83 Processing sheet with id=AC2, first strand: chain 'E' and resid 92 through 93 removed outlier: 6.624A pdb=" N MET E 93 " --> pdb=" O TYR E 211 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N TYR E 178 " --> pdb=" O ASP E 241 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LYS E 149 " --> pdb=" O ALA E 322 " (cutoff:3.500A) removed outlier: 7.962A 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=AC3, first strand: chain 'E' and resid 130 through 131 removed outlier: 4.481A pdb=" N PHE E 144 " --> pdb=" O LEU E 131 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 9 through 16 removed outlier: 6.669A pdb=" N ASP F 21 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ILE F 15 " --> pdb=" O VAL F 19 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N VAL F 19 " --> pdb=" O ILE F 15 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL F 55 " --> pdb=" O LEU F 51 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE F 59 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N VAL F 47 " --> pdb=" O ILE F 59 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N GLU F 34 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N ALA F 35 " --> pdb=" O THR F 76 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 81 through 83 Processing sheet with id=AC6, 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: 7.675A pdb=" N GLN F 213 " --> pdb=" O MET F 93 " (cutoff:3.500A) removed outlier: 3.876A 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: 7.614A pdb=" N ILE F 298 " --> pdb=" O VAL F 242 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU F 244 " --> pdb=" O ILE F 298 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N ALA F 300 " --> pdb=" O LEU F 244 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ILE F 246 " --> pdb=" O ALA F 300 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LYS F 149 " --> pdb=" O ALA F 322 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N VAL F 324 " --> pdb=" O LYS F 149 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N GLY F 151 " --> pdb=" O VAL F 324 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 135 through 137 removed outlier: 6.226A pdb=" N ILE G 79 " --> pdb=" O VAL G 171 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N ASN G 173 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 8.550A pdb=" N VAL G 81 " --> pdb=" O ASN G 173 " (cutoff:3.500A) removed outlier: 11.560A pdb=" N PHE G 175 " --> pdb=" O VAL G 81 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N VAL G 170 " --> pdb=" O GLN G 187 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N GLN G 187 " --> pdb=" O VAL G 170 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N SER G 172 " --> pdb=" O VAL G 185 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N VAL G 185 " --> pdb=" O SER G 172 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N LYS G 174 " --> pdb=" O PRO G 183 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL G 176 " --> pdb=" O GLN G 181 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N GLN G 181 " --> pdb=" O VAL G 176 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 206 through 208 removed outlier: 5.384A pdb=" N LEU G 206 " --> pdb=" O ILE H 43 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N ASP H 45 " --> pdb=" O LEU G 206 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N GLU G 208 " --> pdb=" O ASP H 45 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ILE H 9 " --> pdb=" O ILE H 16 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 206 through 208 removed outlier: 5.384A pdb=" N LEU G 206 " --> pdb=" O ILE H 43 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N ASP H 45 " --> pdb=" O LEU G 206 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N GLU G 208 " --> pdb=" O ASP H 45 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 31 through 35 removed outlier: 3.689A pdb=" N GLY H 31 " --> pdb=" O GLY H 28 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N HIS H 27 " --> pdb=" O PRO H 50 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE H 65 " --> pdb=" O GLY H 49 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'a' and resid 18 through 19 2321 hydrogen bonds defined for protein. 6690 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: 8.93 Time building geometry restraints manager: 4.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 6334 1.28 - 1.41: 8674 1.41 - 1.55: 21992 1.55 - 1.68: 182 1.68 - 1.82: 297 Bond restraints: 37479 Sorted by residual: bond pdb=" C4 ADP F 501 " pdb=" C5 ADP F 501 " ideal model delta sigma weight residual 1.490 1.350 0.140 2.00e-02 2.50e+03 4.88e+01 bond pdb=" C4 ADP E 501 " pdb=" C5 ADP E 501 " ideal model delta sigma weight residual 1.490 1.351 0.139 2.00e-02 2.50e+03 4.82e+01 bond pdb=" C GLN P 82 " pdb=" O GLN P 82 " ideal model delta sigma weight residual 1.234 1.140 0.093 1.44e-02 4.82e+03 4.18e+01 bond pdb=" C4 ADP D 501 " pdb=" C5 ADP D 501 " ideal model delta sigma weight residual 1.490 1.377 0.113 2.00e-02 2.50e+03 3.18e+01 bond pdb=" CZ ARG B 284 " pdb=" NH1 ARG B 284 " ideal model delta sigma weight residual 1.323 1.248 0.075 1.40e-02 5.10e+03 2.84e+01 ... (remaining 37474 not shown) Histogram of bond angle deviations from ideal: 0.00 - 12.24: 50706 12.24 - 24.48: 11 24.48 - 36.72: 2 36.72 - 48.96: 0 48.96 - 61.20: 1 Bond angle restraints: 50720 Sorted by residual: angle pdb=" O LYS X 60 " pdb=" C LYS X 60 " pdb=" N ALA X 61 " ideal model delta sigma weight residual 122.43 61.23 61.20 1.46e+00 4.69e-01 1.76e+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 90.67 31.67 1.25e+00 6.40e-01 6.42e+02 angle pdb=" O GLY R 81 " pdb=" C GLY R 81 " pdb=" N GLN R 82 " ideal model delta sigma weight residual 122.29 90.56 31.73 1.26e+00 6.30e-01 6.34e+02 angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 120.78 19.09 1.00e+00 1.00e+00 3.64e+02 angle pdb=" PB ATP B 600 " pdb=" O3B ATP B 600 " pdb=" PG ATP B 600 " ideal model delta sigma weight residual 139.87 121.92 17.95 1.00e+00 1.00e+00 3.22e+02 ... (remaining 50715 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.32: 22137 32.32 - 64.63: 385 64.63 - 96.95: 32 96.95 - 129.26: 4 129.26 - 161.58: 3 Dihedral angle restraints: 22561 sinusoidal: 8810 harmonic: 13751 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 -60.00 101.58 -161.58 1 2.00e+01 2.50e-03 4.68e+01 dihedral pdb=" C2' ADP E 501 " pdb=" C1' ADP E 501 " pdb=" N9 ADP E 501 " pdb=" C4 ADP E 501 " ideal model delta sinusoidal sigma weight residual 91.55 -109.66 -158.79 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 93.98 -153.98 1 2.00e+01 2.50e-03 4.56e+01 ... (remaining 22558 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 4072 0.101 - 0.202: 1647 0.202 - 0.303: 161 0.303 - 0.403: 28 0.403 - 0.504: 9 Chirality restraints: 5917 Sorted by residual: chirality pdb=" CA LYS G 121 " pdb=" N LYS G 121 " pdb=" C LYS G 121 " pdb=" CB LYS G 121 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.35e+00 chirality pdb=" CA GLU B 453 " pdb=" N GLU B 453 " pdb=" C GLU B 453 " pdb=" CB GLU B 453 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.92e+00 chirality pdb=" CA VAL E 270 " pdb=" N VAL E 270 " pdb=" C VAL E 270 " pdb=" CB VAL E 270 " both_signs ideal model delta sigma weight residual False 2.44 1.96 0.48 2.00e-01 2.50e+01 5.84e+00 ... (remaining 5914 not shown) Planarity restraints: 6541 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS X 60 " -0.199 2.00e-02 2.50e+03 2.82e-01 7.96e+02 pdb=" C LYS X 60 " 0.485 2.00e-02 2.50e+03 pdb=" O LYS X 60 " -0.103 2.00e-02 2.50e+03 pdb=" N ALA X 61 " -0.183 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY R 81 " 0.118 2.00e-02 2.50e+03 1.93e-01 3.74e+02 pdb=" C GLY R 81 " -0.335 2.00e-02 2.50e+03 pdb=" O GLY R 81 " 0.114 2.00e-02 2.50e+03 pdb=" N GLN R 82 " 0.103 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA a 284 " -0.109 2.00e-02 2.50e+03 1.78e-01 3.18e+02 pdb=" C ALA a 284 " 0.309 2.00e-02 2.50e+03 pdb=" O ALA a 284 " -0.108 2.00e-02 2.50e+03 pdb=" N HIS a 285 " -0.092 2.00e-02 2.50e+03 ... (remaining 6538 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.39: 12 2.39 - 3.02: 19040 3.02 - 3.64: 54052 3.64 - 4.27: 83946 4.27 - 4.90: 141787 Nonbonded interactions: 298837 Sorted by model distance: nonbonded pdb=" OG1 THR C 177 " pdb="MG MG C 601 " model vdw 1.759 2.170 nonbonded pdb=" O2G ATP B 600 " pdb="MG MG B 601 " model vdw 1.844 2.170 nonbonded pdb=" OE1 GLU E 186 " pdb="MG MG E 502 " model vdw 1.876 2.170 nonbonded pdb=" O2B ADP E 501 " pdb="MG MG E 502 " model vdw 1.878 2.170 nonbonded pdb=" O1G ATP A 600 " pdb="MG MG A 601 " model vdw 1.884 2.170 ... (remaining 298832 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 9 through 601) selection = chain 'B' selection = (chain 'C' and resid 9 through 601) } 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: 5.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.800 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 37.060 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.100 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 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 : 0.012 0.140 37479 Z= 0.792 Angle : 1.866 61.200 50720 Z= 1.291 Chirality : 0.099 0.504 5917 Planarity : 0.015 0.357 6541 Dihedral : 12.370 161.576 13791 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.75 % Favored : 97.21 % Rotamer: Outliers : 0.34 % Allowed : 3.68 % Favored : 95.98 % Cbeta Deviations : 0.46 % Peptide Plane: Cis-proline : 2.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.11), residues: 4833 helix: -0.79 (0.09), residues: 2673 sheet: -0.07 (0.21), residues: 486 loop : -0.93 (0.14), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.040 0.002 ARG C 251 TYR 0.184 0.016 TYR C 475 PHE 0.190 0.011 PHE N 75 TRP 0.157 0.021 TRP G 203 HIS 0.019 0.004 HIS a 45 Details of bonding type rmsd covalent geometry : bond 0.01247 (37479) covalent geometry : angle 1.86583 (50720) hydrogen bonds : bond 0.21049 ( 2284) hydrogen bonds : angle 7.43721 ( 6690) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9666 Ramachandran restraints generated. 4833 Oldfield, 0 Emsley, 4833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9666 Ramachandran restraints generated. 4833 Oldfield, 0 Emsley, 4833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 531 time to evaluate : 1.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 501 ILE cc_start: 0.8133 (mt) cc_final: 0.7928 (mt) REVERT: J 47 MET cc_start: 0.6342 (tmm) cc_final: 0.5831 (tmm) REVERT: Y 1 MET cc_start: 0.2639 (ttt) cc_final: 0.2219 (mmm) outliers start: 13 outliers final: 2 residues processed: 543 average time/residue: 0.2752 time to fit residues: 233.5372 Evaluate side-chains 267 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 265 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain P residue 4 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 432 optimal weight: 10.0000 chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 8.9990 chunk 455 optimal weight: 8.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 2.9990 chunk 470 optimal weight: 9.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 512 GLN B 470 GLN C 421 GLN C 470 GLN C 480 HIS D 437 ASN H 56 GLN H 60 GLN H 107 GLN ** M 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 82 GLN O 41 GLN O 49 GLN Q 77 ASN R 82 GLN S 82 GLN Y 48 ASN a 35 GLN a 269 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.093227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.063028 restraints weight = 105958.304| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.10 r_work: 0.3158 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 37479 Z= 0.154 Angle : 0.635 13.100 50720 Z= 0.335 Chirality : 0.044 0.197 5917 Planarity : 0.004 0.072 6541 Dihedral : 7.579 168.807 5335 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.14 % Favored : 98.84 % Rotamer: Outliers : 1.10 % Allowed : 7.49 % Favored : 91.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.12), residues: 4833 helix: 1.22 (0.09), residues: 2700 sheet: 0.24 (0.21), residues: 509 loop : -0.43 (0.15), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 26 TYR 0.026 0.002 TYR a 128 PHE 0.024 0.002 PHE I 34 TRP 0.012 0.002 TRP a 114 HIS 0.005 0.001 HIS a 12 Details of bonding type rmsd covalent geometry : bond 0.00305 (37479) covalent geometry : angle 0.63528 (50720) hydrogen bonds : bond 0.05671 ( 2284) hydrogen bonds : angle 4.79470 ( 6690) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9666 Ramachandran restraints generated. 4833 Oldfield, 0 Emsley, 4833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9666 Ramachandran restraints generated. 4833 Oldfield, 0 Emsley, 4833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 306 time to evaluate : 1.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 246 MET cc_start: 0.7890 (mmm) cc_final: 0.7651 (mmp) REVERT: H 6 HIS cc_start: 0.7609 (t70) cc_final: 0.7290 (t70) REVERT: I 47 MET cc_start: 0.7082 (mpp) cc_final: 0.6840 (mpp) REVERT: J 23 THR cc_start: 0.8442 (OUTLIER) cc_final: 0.8182 (p) REVERT: P 43 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7419 (pm20) REVERT: P 47 MET cc_start: 0.7614 (tmm) cc_final: 0.7313 (tmm) REVERT: R 36 GLU cc_start: 0.8309 (tt0) cc_final: 0.8024 (tm-30) REVERT: R 44 MET cc_start: 0.6148 (mtp) cc_final: 0.5603 (mtm) REVERT: X 91 ARG cc_start: 0.7673 (tpp80) cc_final: 0.7373 (mmm-85) REVERT: Y 1 MET cc_start: 0.3547 (ttt) cc_final: 0.2058 (mmm) REVERT: a 98 HIS cc_start: 0.6070 (m-70) cc_final: 0.5328 (p-80) REVERT: a 274 MET cc_start: 0.8138 (ttp) cc_final: 0.7721 (ttp) outliers start: 42 outliers final: 13 residues processed: 331 average time/residue: 0.2463 time to fit residues: 133.2103 Evaluate side-chains 267 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 252 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain C residue 237 TYR Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain E residue 174 GLU Chi-restraints excluded: chain I residue 25 ILE Chi-restraints excluded: chain I residue 36 GLU Chi-restraints excluded: chain I residue 65 ILE Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain P residue 43 GLU Chi-restraints excluded: chain Y residue 129 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 116 optimal weight: 9.9990 chunk 460 optimal weight: 10.0000 chunk 239 optimal weight: 8.9990 chunk 475 optimal weight: 50.0000 chunk 187 optimal weight: 0.9990 chunk 366 optimal weight: 20.0000 chunk 196 optimal weight: 2.9990 chunk 433 optimal weight: 8.9990 chunk 442 optimal weight: 9.9990 chunk 202 optimal weight: 5.9990 chunk 437 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN A 88 ASN B 25 GLN ** B 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 480 HIS C 315 ASN D 319 HIS G 226 GLN H 6 HIS M 49 GLN N 49 GLN P 82 GLN ** a 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.085632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.053448 restraints weight = 104869.660| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.27 r_work: 0.2890 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 37479 Z= 0.246 Angle : 0.672 10.298 50720 Z= 0.352 Chirality : 0.047 0.218 5917 Planarity : 0.005 0.075 6541 Dihedral : 7.595 173.656 5333 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.90 % Favored : 98.08 % Rotamer: Outliers : 1.71 % Allowed : 8.01 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.12), residues: 4833 helix: 1.49 (0.10), residues: 2689 sheet: 0.08 (0.20), residues: 543 loop : -0.45 (0.15), residues: 1601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 366 TYR 0.040 0.002 TYR C 475 PHE 0.023 0.002 PHE F 235 TRP 0.016 0.002 TRP A 139 HIS 0.006 0.001 HIS H 39 Details of bonding type rmsd covalent geometry : bond 0.00593 (37479) covalent geometry : angle 0.67184 (50720) hydrogen bonds : bond 0.05989 ( 2284) hydrogen bonds : angle 4.61942 ( 6690) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9666 Ramachandran restraints generated. 4833 Oldfield, 0 Emsley, 4833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9666 Ramachandran restraints generated. 4833 Oldfield, 0 Emsley, 4833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 278 time to evaluate : 1.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 ILE cc_start: 0.9361 (OUTLIER) cc_final: 0.9144 (tp) REVERT: I 44 MET cc_start: 0.7592 (mmm) cc_final: 0.7384 (mmt) REVERT: I 47 MET cc_start: 0.7324 (mpp) cc_final: 0.7096 (mpp) REVERT: J 23 THR cc_start: 0.8540 (OUTLIER) cc_final: 0.8178 (p) REVERT: J 52 MET cc_start: 0.8722 (ttp) cc_final: 0.8488 (ttp) REVERT: M 36 GLU cc_start: 0.7843 (tp30) cc_final: 0.7564 (tp30) REVERT: Y 1 MET cc_start: 0.3780 (ttt) cc_final: 0.2080 (mmm) REVERT: a 98 HIS cc_start: 0.5983 (m-70) cc_final: 0.5168 (p-80) REVERT: a 281 LEU cc_start: 0.8001 (tp) cc_final: 0.7757 (pp) outliers start: 65 outliers final: 32 residues processed: 323 average time/residue: 0.2400 time to fit residues: 128.9066 Evaluate side-chains 279 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 245 time to evaluate : 1.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain B residue 263 ASP Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 495 ASP Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 237 TYR Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 442 ILE Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain E residue 174 GLU Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain F residue 462 LYS Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 64 MET Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 63 THR Chi-restraints excluded: chain P residue 23 THR Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain X residue 87 VAL Chi-restraints excluded: chain X residue 116 VAL Chi-restraints excluded: chain Y residue 12 VAL Chi-restraints excluded: chain Y residue 17 PHE Chi-restraints excluded: chain Y residue 109 ILE Chi-restraints excluded: chain Y residue 129 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 255 optimal weight: 3.9990 chunk 167 optimal weight: 8.9990 chunk 371 optimal weight: 6.9990 chunk 352 optimal weight: 6.9990 chunk 110 optimal weight: 3.9990 chunk 120 optimal weight: 0.9990 chunk 199 optimal weight: 2.9990 chunk 253 optimal weight: 8.9990 chunk 180 optimal weight: 0.9990 chunk 317 optimal weight: 8.9990 chunk 37 optimal weight: 9.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN ** B 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 470 GLN C 424 HIS O 49 GLN P 49 GLN X 114 ASN a 269 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.087113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.055544 restraints weight = 104651.421| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.06 r_work: 0.2970 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 37479 Z= 0.150 Angle : 0.552 10.113 50720 Z= 0.286 Chirality : 0.042 0.157 5917 Planarity : 0.004 0.049 6541 Dihedral : 7.125 170.435 5333 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.45 % Favored : 98.53 % Rotamer: Outliers : 0.97 % Allowed : 9.56 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.12), residues: 4833 helix: 1.81 (0.10), residues: 2689 sheet: 0.24 (0.20), residues: 553 loop : -0.40 (0.15), residues: 1591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 27 TYR 0.037 0.001 TYR C 475 PHE 0.017 0.001 PHE H 113 TRP 0.007 0.001 TRP G 203 HIS 0.003 0.001 HIS D 358 Details of bonding type rmsd covalent geometry : bond 0.00341 (37479) covalent geometry : angle 0.55194 (50720) hydrogen bonds : bond 0.04837 ( 2284) hydrogen bonds : angle 4.32992 ( 6690) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9666 Ramachandran restraints generated. 4833 Oldfield, 0 Emsley, 4833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9666 Ramachandran restraints generated. 4833 Oldfield, 0 Emsley, 4833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 268 time to evaluate : 1.520 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 169 ILE cc_start: 0.9321 (OUTLIER) cc_final: 0.9101 (tp) REVERT: E 91 ARG cc_start: 0.9219 (OUTLIER) cc_final: 0.7841 (mmt180) REVERT: I 44 MET cc_start: 0.7674 (mmm) cc_final: 0.7466 (mmt) REVERT: J 23 THR cc_start: 0.8425 (OUTLIER) cc_final: 0.8077 (p) REVERT: M 36 GLU cc_start: 0.7713 (tp30) cc_final: 0.7451 (tp30) REVERT: M 51 LYS cc_start: 0.7815 (mmmm) cc_final: 0.7443 (mmtt) REVERT: O 73 PHE cc_start: 0.7454 (m-10) cc_final: 0.7156 (m-80) REVERT: R 36 GLU cc_start: 0.8364 (tt0) cc_final: 0.7977 (tm-30) REVERT: X 91 ARG cc_start: 0.7308 (mmm160) cc_final: 0.7077 (mmm160) REVERT: Y 1 MET cc_start: 0.3720 (ttt) cc_final: 0.2128 (mmm) REVERT: a 98 HIS cc_start: 0.5975 (m-70) cc_final: 0.5161 (p-80) REVERT: a 274 MET cc_start: 0.8299 (ttp) cc_final: 0.8008 (ptm) outliers start: 37 outliers final: 19 residues processed: 293 average time/residue: 0.2387 time to fit residues: 115.8767 Evaluate side-chains 266 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 244 time to evaluate : 1.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain B residue 366 ARG Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 495 ASP Chi-restraints excluded: chain C residue 237 TYR Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain E residue 91 ARG Chi-restraints excluded: chain E residue 174 GLU Chi-restraints excluded: chain F residue 462 LYS Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain J residue 10 ILE Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain O residue 44 MET Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain P residue 23 THR Chi-restraints excluded: chain R residue 45 VAL Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain X residue 87 VAL Chi-restraints excluded: chain Y residue 129 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 89 optimal weight: 7.9990 chunk 298 optimal weight: 0.6980 chunk 374 optimal weight: 10.0000 chunk 106 optimal weight: 7.9990 chunk 223 optimal weight: 0.0570 chunk 282 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 139 optimal weight: 6.9990 chunk 177 optimal weight: 3.9990 chunk 404 optimal weight: 7.9990 chunk 44 optimal weight: 0.9990 overall best weight: 2.3504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 HIS ** B 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 470 GLN G 202 HIS P 49 GLN Y 143 ASN a 269 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.087148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.055758 restraints weight = 103840.638| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.03 r_work: 0.2973 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.4296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 37479 Z= 0.141 Angle : 0.535 9.572 50720 Z= 0.276 Chirality : 0.042 0.151 5917 Planarity : 0.004 0.049 6541 Dihedral : 6.766 150.204 5333 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.86 % Favored : 98.12 % Rotamer: Outliers : 1.18 % Allowed : 9.72 % Favored : 89.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.12), residues: 4833 helix: 1.94 (0.10), residues: 2693 sheet: 0.32 (0.21), residues: 552 loop : -0.34 (0.15), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG X 121 TYR 0.025 0.001 TYR C 475 PHE 0.022 0.001 PHE H 113 TRP 0.007 0.001 TRP a 114 HIS 0.003 0.001 HIS D 358 Details of bonding type rmsd covalent geometry : bond 0.00321 (37479) covalent geometry : angle 0.53540 (50720) hydrogen bonds : bond 0.04615 ( 2284) hydrogen bonds : angle 4.19749 ( 6690) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9666 Ramachandran restraints generated. 4833 Oldfield, 0 Emsley, 4833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9666 Ramachandran restraints generated. 4833 Oldfield, 0 Emsley, 4833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 262 time to evaluate : 1.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 ILE cc_start: 0.9346 (OUTLIER) cc_final: 0.9130 (tp) REVERT: E 91 ARG cc_start: 0.9231 (OUTLIER) cc_final: 0.7910 (mmt180) REVERT: I 44 MET cc_start: 0.7736 (mmm) cc_final: 0.7516 (mmt) REVERT: J 23 THR cc_start: 0.8524 (OUTLIER) cc_final: 0.8166 (p) REVERT: L 52 MET cc_start: 0.8893 (ttm) cc_final: 0.8437 (ttt) REVERT: L 64 MET cc_start: 0.7838 (mmm) cc_final: 0.7580 (mmm) REVERT: M 36 GLU cc_start: 0.7742 (tp30) cc_final: 0.7486 (tp30) REVERT: M 51 LYS cc_start: 0.7775 (mmmm) cc_final: 0.7453 (mmtt) REVERT: O 73 PHE cc_start: 0.7508 (m-10) cc_final: 0.7176 (m-80) REVERT: R 36 GLU cc_start: 0.8358 (tt0) cc_final: 0.7965 (tm-30) REVERT: R 83 ILE cc_start: 0.3625 (OUTLIER) cc_final: 0.3382 (pt) REVERT: W 68 ASP cc_start: 0.8642 (p0) cc_final: 0.8336 (t0) REVERT: X 91 ARG cc_start: 0.7378 (mmm160) cc_final: 0.7154 (mmm160) REVERT: Y 1 MET cc_start: 0.3740 (ttt) cc_final: 0.2118 (mmm) REVERT: Y 22 MET cc_start: 0.5865 (mpp) cc_final: 0.5081 (mpp) REVERT: a 98 HIS cc_start: 0.5912 (m-70) cc_final: 0.5093 (p-80) outliers start: 45 outliers final: 25 residues processed: 295 average time/residue: 0.2384 time to fit residues: 116.2501 Evaluate side-chains 275 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 246 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain B residue 366 ARG Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 495 ASP Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 237 TYR Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain C residue 442 ILE Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 91 ARG Chi-restraints excluded: chain F residue 142 CYS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain J residue 10 ILE Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain O residue 44 MET Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain P residue 23 THR Chi-restraints excluded: chain R residue 45 VAL Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain R residue 83 ILE Chi-restraints excluded: chain X residue 22 MET Chi-restraints excluded: chain X residue 87 VAL Chi-restraints excluded: chain X residue 116 VAL Chi-restraints excluded: chain Y residue 129 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 158 optimal weight: 3.9990 chunk 101 optimal weight: 0.6980 chunk 407 optimal weight: 6.9990 chunk 349 optimal weight: 20.0000 chunk 464 optimal weight: 30.0000 chunk 30 optimal weight: 6.9990 chunk 320 optimal weight: 20.0000 chunk 288 optimal weight: 6.9990 chunk 45 optimal weight: 0.8980 chunk 459 optimal weight: 9.9990 chunk 97 optimal weight: 2.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.086508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.054953 restraints weight = 104208.572| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.06 r_work: 0.2950 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.4470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 37479 Z= 0.164 Angle : 0.544 12.572 50720 Z= 0.280 Chirality : 0.042 0.160 5917 Planarity : 0.004 0.049 6541 Dihedral : 6.653 154.006 5333 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.70 % Favored : 98.28 % Rotamer: Outliers : 1.29 % Allowed : 10.14 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.12), residues: 4833 helix: 1.98 (0.10), residues: 2695 sheet: 0.29 (0.21), residues: 559 loop : -0.32 (0.16), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 16 TYR 0.022 0.001 TYR C 475 PHE 0.019 0.001 PHE H 113 TRP 0.005 0.001 TRP G 203 HIS 0.004 0.001 HIS D 358 Details of bonding type rmsd covalent geometry : bond 0.00385 (37479) covalent geometry : angle 0.54428 (50720) hydrogen bonds : bond 0.04657 ( 2284) hydrogen bonds : angle 4.17638 ( 6690) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9666 Ramachandran restraints generated. 4833 Oldfield, 0 Emsley, 4833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9666 Ramachandran restraints generated. 4833 Oldfield, 0 Emsley, 4833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 259 time to evaluate : 1.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 ILE cc_start: 0.9358 (OUTLIER) cc_final: 0.9138 (tp) REVERT: A 490 LYS cc_start: 0.9275 (mtmt) cc_final: 0.9073 (ptmt) REVERT: E 91 ARG cc_start: 0.9239 (OUTLIER) cc_final: 0.7975 (mmt180) REVERT: H 52 ARG cc_start: 0.8121 (ttp-110) cc_final: 0.7726 (mtp180) REVERT: L 64 MET cc_start: 0.8000 (mmm) cc_final: 0.7788 (mmm) REVERT: M 36 GLU cc_start: 0.7792 (tp30) cc_final: 0.7509 (tp30) REVERT: M 51 LYS cc_start: 0.7786 (mmmm) cc_final: 0.7501 (mmtt) REVERT: O 73 PHE cc_start: 0.7490 (m-10) cc_final: 0.7193 (m-80) REVERT: R 36 GLU cc_start: 0.8356 (tt0) cc_final: 0.7947 (tm-30) REVERT: S 55 VAL cc_start: 0.7702 (t) cc_final: 0.7442 (p) REVERT: W 68 ASP cc_start: 0.8724 (p0) cc_final: 0.8439 (t0) REVERT: X 1 MET cc_start: 0.5334 (tmm) cc_final: 0.4843 (tmm) REVERT: X 91 ARG cc_start: 0.7514 (mmm160) cc_final: 0.7269 (mmm160) REVERT: Y 1 MET cc_start: 0.3867 (ttt) cc_final: 0.2188 (mmm) REVERT: a 98 HIS cc_start: 0.6052 (m-70) cc_final: 0.4663 (p-80) outliers start: 49 outliers final: 26 residues processed: 295 average time/residue: 0.2527 time to fit residues: 122.2207 Evaluate side-chains 276 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 248 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain B residue 366 ARG Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 495 ASP Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 237 TYR Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain C residue 442 ILE Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain E residue 91 ARG Chi-restraints excluded: chain F residue 142 CYS Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain J residue 10 ILE Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain P residue 23 THR Chi-restraints excluded: chain Q residue 82 GLN Chi-restraints excluded: chain R residue 45 VAL Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain X residue 87 VAL Chi-restraints excluded: chain X residue 116 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 73 optimal weight: 2.9990 chunk 363 optimal weight: 20.0000 chunk 137 optimal weight: 9.9990 chunk 184 optimal weight: 0.1980 chunk 149 optimal weight: 10.0000 chunk 192 optimal weight: 10.0000 chunk 204 optimal weight: 0.5980 chunk 351 optimal weight: 8.9990 chunk 112 optimal weight: 2.9990 chunk 224 optimal weight: 5.9990 chunk 325 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 216 ASN G 60 ASN H 6 HIS M 41 GLN a 269 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.087250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.056135 restraints weight = 104282.499| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.31 r_work: 0.2959 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.4609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 37479 Z= 0.121 Angle : 0.514 10.633 50720 Z= 0.264 Chirality : 0.041 0.155 5917 Planarity : 0.004 0.048 6541 Dihedral : 6.365 154.316 5333 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.55 % Favored : 98.43 % Rotamer: Outliers : 1.13 % Allowed : 10.45 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.12), residues: 4833 helix: 2.14 (0.10), residues: 2685 sheet: 0.34 (0.21), residues: 544 loop : -0.26 (0.15), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Y 49 TYR 0.017 0.001 TYR C 475 PHE 0.025 0.001 PHE H 113 TRP 0.005 0.001 TRP G 203 HIS 0.003 0.000 HIS D 358 Details of bonding type rmsd covalent geometry : bond 0.00264 (37479) covalent geometry : angle 0.51440 (50720) hydrogen bonds : bond 0.04248 ( 2284) hydrogen bonds : angle 4.05582 ( 6690) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9666 Ramachandran restraints generated. 4833 Oldfield, 0 Emsley, 4833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9666 Ramachandran restraints generated. 4833 Oldfield, 0 Emsley, 4833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 258 time to evaluate : 1.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 ILE cc_start: 0.9347 (OUTLIER) cc_final: 0.9131 (tp) REVERT: H 52 ARG cc_start: 0.8100 (ttp-110) cc_final: 0.7753 (mtm-85) REVERT: J 44 MET cc_start: 0.8799 (mmm) cc_final: 0.8344 (mmm) REVERT: M 36 GLU cc_start: 0.7765 (tp30) cc_final: 0.7466 (tp30) REVERT: M 51 LYS cc_start: 0.7803 (mmmm) cc_final: 0.7465 (mmtt) REVERT: O 44 MET cc_start: 0.7335 (OUTLIER) cc_final: 0.6933 (ptp) REVERT: O 73 PHE cc_start: 0.7535 (m-10) cc_final: 0.7225 (m-80) REVERT: P 52 MET cc_start: 0.7975 (tmm) cc_final: 0.7763 (tmm) REVERT: Q 1 MET cc_start: 0.5172 (tpp) cc_final: 0.4958 (tpp) REVERT: Q 52 MET cc_start: 0.9188 (tmm) cc_final: 0.8814 (tmm) REVERT: Q 64 MET cc_start: 0.6934 (ppp) cc_final: 0.6706 (ppp) REVERT: R 36 GLU cc_start: 0.8354 (tt0) cc_final: 0.7920 (tm-30) REVERT: W 68 ASP cc_start: 0.8754 (p0) cc_final: 0.8489 (t0) REVERT: X 91 ARG cc_start: 0.7478 (mmm160) cc_final: 0.7218 (mmm160) REVERT: Y 1 MET cc_start: 0.3923 (ttt) cc_final: 0.2320 (mmm) REVERT: Y 22 MET cc_start: 0.5809 (mpp) cc_final: 0.5004 (mpp) REVERT: a 98 HIS cc_start: 0.6050 (m-70) cc_final: 0.4630 (p-80) outliers start: 43 outliers final: 26 residues processed: 291 average time/residue: 0.2454 time to fit residues: 119.1307 Evaluate side-chains 277 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 249 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain B residue 366 ARG Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 495 ASP Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 237 TYR Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain C residue 442 ILE Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain F residue 142 CYS Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain J residue 10 ILE Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain O residue 44 MET Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain P residue 23 THR Chi-restraints excluded: chain Q residue 82 GLN Chi-restraints excluded: chain R residue 45 VAL Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain X residue 87 VAL Chi-restraints excluded: chain X residue 116 VAL Chi-restraints excluded: chain Y residue 129 VAL Chi-restraints excluded: chain a residue 147 VAL Chi-restraints excluded: chain a residue 268 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 109 optimal weight: 0.0770 chunk 441 optimal weight: 7.9990 chunk 260 optimal weight: 0.9990 chunk 136 optimal weight: 9.9990 chunk 451 optimal weight: 20.0000 chunk 105 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 chunk 52 optimal weight: 6.9990 chunk 323 optimal weight: 20.0000 chunk 173 optimal weight: 10.0000 chunk 137 optimal weight: 4.9990 overall best weight: 3.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.085764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.053766 restraints weight = 104047.335| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 2.29 r_work: 0.2897 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.4719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 37479 Z= 0.190 Angle : 0.572 10.215 50720 Z= 0.294 Chirality : 0.043 0.166 5917 Planarity : 0.004 0.051 6541 Dihedral : 6.512 159.765 5333 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.82 % Favored : 98.16 % Rotamer: Outliers : 1.13 % Allowed : 10.61 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.12), residues: 4833 helix: 2.03 (0.10), residues: 2690 sheet: 0.24 (0.21), residues: 561 loop : -0.28 (0.16), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Y 49 TYR 0.019 0.001 TYR D 252 PHE 0.021 0.001 PHE H 113 TRP 0.007 0.001 TRP a 114 HIS 0.005 0.001 HIS D 358 Details of bonding type rmsd covalent geometry : bond 0.00455 (37479) covalent geometry : angle 0.57174 (50720) hydrogen bonds : bond 0.04746 ( 2284) hydrogen bonds : angle 4.18481 ( 6690) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9666 Ramachandran restraints generated. 4833 Oldfield, 0 Emsley, 4833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9666 Ramachandran restraints generated. 4833 Oldfield, 0 Emsley, 4833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 251 time to evaluate : 1.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 ILE cc_start: 0.9394 (OUTLIER) cc_final: 0.9193 (tp) REVERT: H 52 ARG cc_start: 0.8210 (ttp-110) cc_final: 0.7788 (mtm-85) REVERT: I 34 PHE cc_start: 0.8687 (t80) cc_final: 0.8442 (t80) REVERT: M 36 GLU cc_start: 0.7831 (tp30) cc_final: 0.7557 (tp30) REVERT: M 51 LYS cc_start: 0.7835 (mmmm) cc_final: 0.7609 (mmmt) REVERT: O 73 PHE cc_start: 0.7431 (m-10) cc_final: 0.7117 (m-80) REVERT: Q 64 MET cc_start: 0.6951 (ppp) cc_final: 0.6724 (ppp) REVERT: Q 82 GLN cc_start: 0.6538 (OUTLIER) cc_final: 0.6329 (mp10) REVERT: R 36 GLU cc_start: 0.8389 (tt0) cc_final: 0.7956 (tm-30) REVERT: S 55 VAL cc_start: 0.7763 (t) cc_final: 0.7499 (p) REVERT: W 68 ASP cc_start: 0.8802 (p0) cc_final: 0.8582 (t0) REVERT: X 91 ARG cc_start: 0.7638 (mmm160) cc_final: 0.7400 (mmm160) REVERT: Y 1 MET cc_start: 0.4052 (ttt) cc_final: 0.2397 (mmm) REVERT: a 98 HIS cc_start: 0.5998 (m-70) cc_final: 0.4644 (p-80) REVERT: a 283 MET cc_start: 0.8058 (pmm) cc_final: 0.7167 (tpp) outliers start: 43 outliers final: 32 residues processed: 285 average time/residue: 0.2441 time to fit residues: 115.0798 Evaluate side-chains 280 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 246 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain B residue 366 ARG Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 495 ASP Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 237 TYR Chi-restraints excluded: chain C residue 442 ILE Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain F residue 142 CYS Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain J residue 10 ILE Chi-restraints excluded: chain N residue 23 THR Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain O residue 44 MET Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain P residue 10 ILE Chi-restraints excluded: chain P residue 23 THR Chi-restraints excluded: chain Q residue 82 GLN Chi-restraints excluded: chain R residue 45 VAL Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain X residue 87 VAL Chi-restraints excluded: chain X residue 116 VAL Chi-restraints excluded: chain Y residue 129 VAL Chi-restraints excluded: chain a residue 147 VAL Chi-restraints excluded: chain a residue 268 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 360 optimal weight: 1.9990 chunk 339 optimal weight: 20.0000 chunk 127 optimal weight: 7.9990 chunk 169 optimal weight: 9.9990 chunk 229 optimal weight: 6.9990 chunk 371 optimal weight: 6.9990 chunk 341 optimal weight: 9.9990 chunk 97 optimal weight: 0.9980 chunk 31 optimal weight: 10.0000 chunk 125 optimal weight: 5.9990 chunk 162 optimal weight: 10.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 145 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.085321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.053597 restraints weight = 105001.751| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 2.53 r_work: 0.2869 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.4850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 37479 Z= 0.218 Angle : 0.596 12.709 50720 Z= 0.305 Chirality : 0.044 0.176 5917 Planarity : 0.004 0.051 6541 Dihedral : 6.648 164.083 5333 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.92 % Favored : 98.06 % Rotamer: Outliers : 1.05 % Allowed : 10.82 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.12), residues: 4833 helix: 1.93 (0.10), residues: 2691 sheet: 0.14 (0.21), residues: 551 loop : -0.35 (0.15), residues: 1591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG X 121 TYR 0.019 0.002 TYR D 252 PHE 0.025 0.001 PHE H 113 TRP 0.008 0.001 TRP Y 26 HIS 0.006 0.001 HIS D 358 Details of bonding type rmsd covalent geometry : bond 0.00527 (37479) covalent geometry : angle 0.59575 (50720) hydrogen bonds : bond 0.04949 ( 2284) hydrogen bonds : angle 4.25724 ( 6690) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9666 Ramachandran restraints generated. 4833 Oldfield, 0 Emsley, 4833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9666 Ramachandran restraints generated. 4833 Oldfield, 0 Emsley, 4833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 251 time to evaluate : 1.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 ILE cc_start: 0.9403 (OUTLIER) cc_final: 0.9200 (tp) REVERT: G 139 HIS cc_start: 0.8469 (t70) cc_final: 0.8262 (t-90) REVERT: H 52 ARG cc_start: 0.8181 (ttp-110) cc_final: 0.7661 (mtm-85) REVERT: H 60 GLN cc_start: 0.7456 (tt0) cc_final: 0.7037 (tm-30) REVERT: M 36 GLU cc_start: 0.7802 (tp30) cc_final: 0.7529 (tp30) REVERT: M 51 LYS cc_start: 0.7864 (mmmm) cc_final: 0.7657 (mmmt) REVERT: O 73 PHE cc_start: 0.7513 (m-10) cc_final: 0.7280 (m-80) REVERT: Q 64 MET cc_start: 0.6938 (ppp) cc_final: 0.6716 (ppp) REVERT: Q 82 GLN cc_start: 0.6537 (OUTLIER) cc_final: 0.6265 (mp10) REVERT: R 36 GLU cc_start: 0.8343 (tt0) cc_final: 0.7909 (tm-30) REVERT: S 55 VAL cc_start: 0.7610 (t) cc_final: 0.7377 (p) REVERT: X 91 ARG cc_start: 0.7528 (mmm160) cc_final: 0.7295 (mmm160) REVERT: Y 1 MET cc_start: 0.4224 (ttt) cc_final: 0.2598 (mmm) REVERT: a 98 HIS cc_start: 0.6073 (m-70) cc_final: 0.4711 (p-80) REVERT: a 283 MET cc_start: 0.8124 (pmm) cc_final: 0.6906 (tpp) REVERT: a 289 HIS cc_start: 0.5003 (m90) cc_final: 0.4431 (t70) outliers start: 40 outliers final: 36 residues processed: 280 average time/residue: 0.2329 time to fit residues: 108.1365 Evaluate side-chains 286 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 248 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain B residue 366 ARG Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 495 ASP Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 237 TYR Chi-restraints excluded: chain C residue 442 ILE Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain F residue 142 CYS Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain J residue 10 ILE Chi-restraints excluded: chain N residue 23 THR Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain O residue 44 MET Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain P residue 10 ILE Chi-restraints excluded: chain P residue 23 THR Chi-restraints excluded: chain Q residue 82 GLN Chi-restraints excluded: chain R residue 45 VAL Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain X residue 87 VAL Chi-restraints excluded: chain X residue 116 VAL Chi-restraints excluded: chain Y residue 129 VAL Chi-restraints excluded: chain Y residue 143 ASN Chi-restraints excluded: chain a residue 85 MET Chi-restraints excluded: chain a residue 147 VAL Chi-restraints excluded: chain a residue 268 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 411 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 145 optimal weight: 6.9990 chunk 143 optimal weight: 7.9990 chunk 390 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 323 optimal weight: 20.0000 chunk 429 optimal weight: 6.9990 chunk 256 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 183 optimal weight: 5.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 348 GLN ** D 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.085443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.053965 restraints weight = 104650.348| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.08 r_work: 0.2919 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.4931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 37479 Z= 0.188 Angle : 0.578 11.158 50720 Z= 0.296 Chirality : 0.043 0.165 5917 Planarity : 0.004 0.050 6541 Dihedral : 6.550 165.735 5333 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.92 % Favored : 98.06 % Rotamer: Outliers : 1.00 % Allowed : 11.08 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.12), residues: 4833 helix: 1.98 (0.10), residues: 2684 sheet: 0.21 (0.21), residues: 547 loop : -0.31 (0.16), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Y 49 TYR 0.027 0.001 TYR G 222 PHE 0.031 0.001 PHE I 34 TRP 0.008 0.001 TRP a 114 HIS 0.005 0.001 HIS D 358 Details of bonding type rmsd covalent geometry : bond 0.00450 (37479) covalent geometry : angle 0.57769 (50720) hydrogen bonds : bond 0.04744 ( 2284) hydrogen bonds : angle 4.20813 ( 6690) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9666 Ramachandran restraints generated. 4833 Oldfield, 0 Emsley, 4833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9666 Ramachandran restraints generated. 4833 Oldfield, 0 Emsley, 4833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 251 time to evaluate : 1.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 ILE cc_start: 0.9376 (OUTLIER) cc_final: 0.9172 (tp) REVERT: B 462 ILE cc_start: 0.7852 (pt) cc_final: 0.7487 (mt) REVERT: C 464 LYS cc_start: 0.9044 (mttt) cc_final: 0.8393 (tptt) REVERT: H 52 ARG cc_start: 0.8005 (ttp-110) cc_final: 0.7554 (mtm-85) REVERT: H 60 GLN cc_start: 0.7529 (OUTLIER) cc_final: 0.7110 (tm-30) REVERT: M 36 GLU cc_start: 0.7732 (tp30) cc_final: 0.7451 (tp30) REVERT: M 51 LYS cc_start: 0.7870 (mmmm) cc_final: 0.7657 (mmmt) REVERT: O 44 MET cc_start: 0.7220 (OUTLIER) cc_final: 0.6677 (ptp) REVERT: O 73 PHE cc_start: 0.7479 (m-10) cc_final: 0.7201 (m-80) REVERT: P 64 MET cc_start: 0.8020 (ptp) cc_final: 0.7702 (mpp) REVERT: Q 43 GLU cc_start: 0.8416 (pp20) cc_final: 0.8081 (pp20) REVERT: Q 82 GLN cc_start: 0.6509 (OUTLIER) cc_final: 0.6249 (mp10) REVERT: R 36 GLU cc_start: 0.8309 (tt0) cc_final: 0.7863 (tm-30) REVERT: S 55 VAL cc_start: 0.7694 (t) cc_final: 0.7452 (p) REVERT: X 1 MET cc_start: 0.4765 (tmm) cc_final: 0.4018 (pmm) REVERT: X 91 ARG cc_start: 0.7623 (mmm160) cc_final: 0.7392 (mmm160) REVERT: Y 1 MET cc_start: 0.4115 (ttt) cc_final: 0.2626 (mmt) REVERT: a 98 HIS cc_start: 0.6066 (m-70) cc_final: 0.4587 (p-80) REVERT: a 283 MET cc_start: 0.8120 (pmm) cc_final: 0.6863 (tpp) REVERT: a 289 HIS cc_start: 0.5061 (m90) cc_final: 0.4455 (t70) outliers start: 38 outliers final: 31 residues processed: 280 average time/residue: 0.2272 time to fit residues: 105.4625 Evaluate side-chains 281 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 246 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain B residue 366 ARG Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 495 ASP Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 237 TYR Chi-restraints excluded: chain C residue 442 ILE Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain F residue 142 CYS Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 60 GLN Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain J residue 10 ILE Chi-restraints excluded: chain N residue 23 THR Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain O residue 44 MET Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain P residue 23 THR Chi-restraints excluded: chain Q residue 82 GLN Chi-restraints excluded: chain R residue 45 VAL Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain X residue 87 VAL Chi-restraints excluded: chain X residue 116 VAL Chi-restraints excluded: chain Y residue 129 VAL Chi-restraints excluded: chain a residue 147 VAL Chi-restraints excluded: chain a residue 268 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 260 optimal weight: 2.9990 chunk 247 optimal weight: 0.5980 chunk 385 optimal weight: 6.9990 chunk 299 optimal weight: 10.0000 chunk 196 optimal weight: 0.8980 chunk 313 optimal weight: 3.9990 chunk 322 optimal weight: 20.0000 chunk 216 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 314 optimal weight: 5.9990 chunk 40 optimal weight: 8.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 437 ASN ** H 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 12 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.086268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.054830 restraints weight = 104056.924| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.07 r_work: 0.2933 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.4992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 37479 Z= 0.145 Angle : 0.557 11.837 50720 Z= 0.284 Chirality : 0.041 0.165 5917 Planarity : 0.004 0.050 6541 Dihedral : 6.367 166.092 5333 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.70 % Favored : 98.28 % Rotamer: Outliers : 0.89 % Allowed : 11.16 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.12), residues: 4833 helix: 2.09 (0.10), residues: 2684 sheet: 0.29 (0.21), residues: 551 loop : -0.27 (0.16), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG Y 49 TYR 0.017 0.001 TYR D 252 PHE 0.026 0.001 PHE H 113 TRP 0.008 0.001 TRP a 114 HIS 0.004 0.001 HIS D 358 Details of bonding type rmsd covalent geometry : bond 0.00336 (37479) covalent geometry : angle 0.55665 (50720) hydrogen bonds : bond 0.04438 ( 2284) hydrogen bonds : angle 4.11859 ( 6690) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13887.65 seconds wall clock time: 237 minutes 1.35 seconds (14221.35 seconds total)