Starting phenix.real_space_refine on Sat Feb 7 22:19:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o1d_70003/02_2026/9o1d_70003_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o1d_70003/02_2026/9o1d_70003.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9o1d_70003/02_2026/9o1d_70003_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o1d_70003/02_2026/9o1d_70003_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9o1d_70003/02_2026/9o1d_70003.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o1d_70003/02_2026/9o1d_70003.map" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.011 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 23553 2.51 5 N 6273 2.21 5 O 6993 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: 36997 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 3872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3872 Classifications: {'peptide': 512} Link IDs: {'PTRANS': 17, 'TRANS': 494} Chain: "B" Number of atoms: 3846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 3846 Classifications: {'peptide': 509} Link IDs: {'PTRANS': 17, 'TRANS': 491} Chain: "C" Number of atoms: 3817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3817 Classifications: {'peptide': 505} Link IDs: {'PTRANS': 16, 'TRANS': 488} Chain: "D" Number of atoms: 3464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3464 Classifications: {'peptide': 456} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 435} Chain: "E" Number of atoms: 3464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3464 Classifications: {'peptide': 456} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 435} Chain: "F" Number of atoms: 3464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3464 Classifications: {'peptide': 456} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 435} Chain: "G" Number of atoms: 2074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2074 Classifications: {'peptide': 269} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 261} Chain breaks: 2 Chain: "H" Number of atoms: 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: 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: 3 Unresolved non-hydrogen dihedrals: 3 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: 8.36, per 1000 atoms: 0.23 Number of scatterers: 36997 At special positions: 0 Unit cell: (131.14, 134.46, 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 6993 8.00 N 6273 7.00 C 23553 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.95 Conformation dependent library (CDL) restraints added in 1.4 seconds 9686 Ramachandran restraints generated. 4843 Oldfield, 0 Emsley, 4843 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8790 Finding SS restraints... Secondary structure from input PDB file: 213 helices and 29 sheets defined 62.4% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 9 through 19 removed outlier: 3.799A pdb=" N GLU A 18 " --> pdb=" O LYS A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 59 No H-bonds generated for 'chain 'A' and resid 57 through 59' Processing helix chain 'A' and resid 101 through 105 Processing helix chain 'A' and resid 136 through 140 Processing helix chain 'A' and resid 151 through 158 Processing helix chain 'A' and resid 175 through 186 removed outlier: 3.522A pdb=" N ALA A 180 " --> pdb=" O LYS A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 216 Processing helix chain 'A' and resid 218 through 220 No H-bonds generated for 'chain 'A' and resid 218 through 220' Processing helix chain 'A' and resid 232 through 253 Proline residue: A 240 - end of helix removed outlier: 4.466A pdb=" N PHE A 250 " --> pdb=" O MET A 246 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG A 251 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG A 253 " --> pdb=" O TYR A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 278 Processing helix chain 'A' and resid 283 through 287 Processing helix chain 'A' and resid 290 through 300 removed outlier: 3.600A pdb=" N HIS A 295 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU A 298 " --> pdb=" O LEU A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 314 Processing helix chain 'A' and resid 340 through 350 Processing helix chain 'A' and resid 357 through 363 Processing helix chain 'A' and resid 378 through 383 removed outlier: 3.560A pdb=" N ALA A 381 " --> pdb=" O VAL A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 405 removed outlier: 4.207A pdb=" N GLY A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N GLY A 393 " --> pdb=" O LYS A 389 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ILE A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 414 removed outlier: 4.290A pdb=" N GLN A 409 " --> pdb=" O ALA A 406 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA A 411 " --> pdb=" O ALA A 408 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N SER A 412 " --> pdb=" O GLN A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 432 removed outlier: 3.719A pdb=" N GLN A 421 " --> pdb=" O ALA A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 454 removed outlier: 3.567A pdb=" N SER A 448 " --> pdb=" O GLU A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 463 No H-bonds generated for 'chain 'A' and resid 461 through 463' Processing helix chain 'A' and resid 464 through 480 removed outlier: 3.524A pdb=" N ARG A 478 " --> pdb=" O SER A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 489 Processing helix chain 'A' and resid 494 through 510 Processing helix chain 'B' and resid 7 through 19 removed outlier: 3.721A pdb=" N ARG B 16 " --> pdb=" O ILE B 12 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS B 19 " --> pdb=" O GLY B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 59 No H-bonds generated for 'chain 'B' and resid 57 through 59' Processing helix chain 'B' and resid 101 through 105 Processing helix chain 'B' and resid 136 through 140 Processing helix chain 'B' and resid 151 through 158 Processing helix chain 'B' and resid 175 through 186 Processing helix chain 'B' and resid 202 through 216 Processing helix chain 'B' and resid 218 through 220 No H-bonds generated for 'chain 'B' and resid 218 through 220' Processing helix chain 'B' and resid 232 through 252 Proline residue: B 240 - end of helix removed outlier: 4.569A pdb=" N PHE B 250 " --> pdb=" O MET B 246 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG B 251 " --> pdb=" O GLY B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 278 Processing helix chain 'B' and resid 290 through 300 removed outlier: 3.780A pdb=" N HIS B 295 " --> pdb=" O VAL B 291 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU B 298 " --> pdb=" O LEU B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 314 Processing helix chain 'B' and resid 340 through 348 Processing helix chain 'B' and resid 357 through 363 Processing helix chain 'B' and resid 378 through 383 Processing helix chain 'B' and resid 384 through 392 Processing helix chain 'B' and resid 393 through 408 removed outlier: 3.592A pdb=" N GLU B 403 " --> pdb=" O ALA B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 432 removed outlier: 3.513A pdb=" N ARG B 427 " --> pdb=" O GLU B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 454 Processing helix chain 'B' and resid 455 through 460 removed outlier: 4.238A pdb=" N ASP B 459 " --> pdb=" O PHE B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 463 No H-bonds generated for 'chain 'B' and resid 461 through 463' Processing helix chain 'B' and resid 464 through 480 Processing helix chain 'B' and resid 480 through 488 Processing helix chain 'B' and resid 494 through 512 Processing helix chain 'C' and resid 10 through 19 Processing helix chain 'C' and resid 57 through 59 No H-bonds generated for 'chain 'C' and resid 57 through 59' Processing helix chain 'C' and resid 101 through 105 Processing helix chain 'C' and resid 136 through 140 removed outlier: 3.670A pdb=" N ARG C 140 " --> pdb=" O VAL C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 158 Processing helix chain 'C' and resid 175 through 186 Processing helix chain 'C' and resid 187 through 189 No H-bonds generated for 'chain 'C' and resid 187 through 189' Processing helix chain 'C' and resid 202 through 216 Processing helix chain 'C' and resid 218 through 220 No H-bonds generated for 'chain 'C' and resid 218 through 220' Processing helix chain 'C' and resid 232 through 253 Proline residue: C 240 - end of helix removed outlier: 4.346A pdb=" N PHE C 250 " --> pdb=" O MET C 246 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG C 251 " --> pdb=" O GLY C 247 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG C 253 " --> pdb=" O TYR C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 278 Processing helix chain 'C' and resid 283 through 287 Processing helix chain 'C' and resid 290 through 300 removed outlier: 3.697A pdb=" N HIS C 295 " --> pdb=" O VAL C 291 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU C 298 " --> pdb=" O LEU C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 314 Processing helix chain 'C' and resid 340 through 348 Processing helix chain 'C' and resid 357 through 363 Processing helix chain 'C' and resid 378 through 382 removed outlier: 3.599A pdb=" N ALA C 381 " --> pdb=" O VAL C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 403 removed outlier: 3.805A pdb=" N GLY C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N GLY C 393 " --> pdb=" O LYS C 389 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ILE C 394 " --> pdb=" O LEU C 390 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N THR C 396 " --> pdb=" O GLY C 392 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA C 397 " --> pdb=" O GLY C 393 " (cutoff:3.500A) removed outlier: 4.131A 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 432 Processing helix chain 'C' and resid 441 through 454 Processing helix chain 'C' and resid 461 through 463 No H-bonds generated for 'chain 'C' and resid 461 through 463' Processing helix chain 'C' and resid 464 through 480 Processing helix chain 'C' and resid 480 through 489 Processing helix chain 'C' and resid 494 through 512 Processing helix chain 'D' and resid 25 through 29 removed outlier: 4.064A pdb=" N VAL D 29 " --> pdb=" O ARG D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 89 Processing helix chain 'D' and resid 120 through 124 removed outlier: 3.694A pdb=" N GLN D 124 " --> pdb=" O TYR D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 142 Processing helix chain 'D' and resid 159 through 171 Processing helix chain 'D' and resid 187 through 201 Processing helix chain 'D' and resid 203 through 205 No H-bonds generated for 'chain 'D' and resid 203 through 205' Processing helix chain 'D' and resid 217 through 238 removed outlier: 5.228A pdb=" N ALA D 225 " --> pdb=" O ARG D 221 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N LEU D 226 " --> pdb=" O LEU D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 261 removed outlier: 3.924A pdb=" N THR D 253 " --> pdb=" O ILE D 249 " (cutoff:3.500A) removed outlier: 4.352A 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: 3.610A 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 Processing helix chain 'D' and resid 318 through 320 No H-bonds generated for 'chain 'D' and resid 318 through 320' Processing helix chain 'D' and resid 327 through 332 Processing helix chain 'D' and resid 355 through 383 removed outlier: 3.925A pdb=" N GLU D 374 " --> pdb=" O GLN D 370 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU D 375 " --> pdb=" O ARG D 371 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ASP D 377 " --> pdb=" O LYS D 373 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ILE D 378 " --> pdb=" O GLU D 374 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA D 380 " --> pdb=" O LYS D 376 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ILE D 381 " --> pdb=" O ASP D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 405 removed outlier: 3.572A pdb=" N LEU D 393 " --> pdb=" O GLU D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 411 No H-bonds generated for 'chain 'D' and resid 409 through 411' Processing helix chain 'D' and resid 412 through 417 Processing helix chain 'D' and resid 424 through 438 Processing helix chain 'D' and resid 444 through 449 removed outlier: 3.617A pdb=" N PHE D 448 " --> pdb=" O GLU D 445 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR D 449 " --> pdb=" O GLN D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 461 removed outlier: 3.942A pdb=" N ALA D 457 " --> pdb=" O GLY D 453 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 89 Processing helix chain 'E' and resid 120 through 124 removed outlier: 3.628A pdb=" N GLN E 124 " --> pdb=" O TYR E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 142 Processing helix chain 'E' and resid 159 through 172 removed outlier: 3.587A pdb=" N LEU E 167 " --> pdb=" O ASN E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 201 Processing helix chain 'E' and resid 203 through 205 No H-bonds generated for 'chain 'E' and resid 203 through 205' Processing helix chain 'E' and resid 217 through 238 removed outlier: 3.505A pdb=" N ARG E 221 " --> pdb=" O PRO E 217 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N ALA E 225 " --> pdb=" O ARG E 221 " (cutoff:3.500A) removed outlier: 5.449A 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: 3.593A pdb=" N VAL E 259 " --> pdb=" O ALA E 255 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ALA E 261 " --> pdb=" O THR E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 272 Processing helix chain 'E' and resid 275 through 285 removed outlier: 3.636A pdb=" N LEU E 283 " --> pdb=" O GLU E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 304 through 307 Processing helix chain 'E' and resid 310 through 317 Processing helix chain 'E' and resid 318 through 320 No H-bonds generated for 'chain 'E' and resid 318 through 320' Processing helix chain 'E' and resid 327 through 333 removed outlier: 3.584A pdb=" N LEU E 333 " --> pdb=" O ASP E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 355 Processing helix chain 'E' and resid 355 through 383 removed outlier: 3.533A pdb=" N LEU E 375 " --> pdb=" O ARG E 371 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS E 376 " --> pdb=" O TYR E 372 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ASP E 377 " --> pdb=" O LYS E 373 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ILE E 378 " --> pdb=" O GLU E 374 " (cutoff:3.500A) Processing helix chain 'E' and resid 384 through 387 Processing helix chain 'E' and resid 388 through 405 removed outlier: 3.513A pdb=" N LEU E 393 " --> pdb=" O GLU E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 412 through 417 removed outlier: 3.709A pdb=" N THR E 416 " --> pdb=" O ALA E 412 " (cutoff:3.500A) Processing helix chain 'E' and resid 424 through 438 Processing helix chain 'E' and resid 444 through 449 removed outlier: 3.616A pdb=" N PHE E 448 " --> pdb=" O GLU E 445 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR E 449 " --> pdb=" O GLN E 446 " (cutoff:3.500A) Processing helix chain 'E' and resid 453 through 461 removed outlier: 3.905A pdb=" N ALA E 457 " --> pdb=" O GLY E 453 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL E 458 " --> pdb=" O ILE E 454 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 89 Processing helix chain 'F' and resid 120 through 124 removed outlier: 3.770A pdb=" N GLN F 124 " --> pdb=" O TYR F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 142 Processing helix chain 'F' and resid 159 through 176 removed outlier: 3.644A pdb=" N ALA F 172 " --> pdb=" O ILE F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 201 Processing helix chain 'F' and resid 203 through 205 No H-bonds generated for 'chain 'F' and resid 203 through 205' Processing helix chain 'F' and resid 217 through 238 removed outlier: 3.588A pdb=" N ARG F 221 " --> pdb=" O PRO F 217 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N ALA F 225 " --> pdb=" O ARG F 221 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N LEU F 226 " --> pdb=" O LEU F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 263 removed outlier: 3.732A pdb=" N TYR F 252 " --> pdb=" O ASN F 248 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 272 Processing helix chain 'F' and resid 275 through 285 removed outlier: 3.596A pdb=" N LEU F 283 " --> pdb=" O GLU F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 307 Processing helix chain 'F' and resid 310 through 318 removed outlier: 3.860A pdb=" N ALA F 318 " --> pdb=" O ALA F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 333 Processing helix chain 'F' and resid 350 through 355 Processing helix chain 'F' and resid 355 through 380 removed outlier: 3.816A pdb=" N ASP F 377 " --> pdb=" O LYS F 373 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE F 378 " --> pdb=" O GLU F 374 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 387 Processing helix chain 'F' and resid 388 through 405 Processing helix chain 'F' and resid 412 through 417 Processing helix chain 'F' and resid 424 through 438 Processing helix chain 'F' and resid 444 through 448 Processing helix chain 'F' and resid 453 through 461 removed outlier: 3.760A pdb=" N ALA F 457 " --> pdb=" O GLY F 453 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 42 removed outlier: 3.863A pdb=" N ILE G 7 " --> pdb=" O GLY G 3 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE G 20 " --> pdb=" O SER G 16 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LYS G 26 " --> pdb=" O ASN G 22 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY G 42 " --> pdb=" O ARG G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 59 removed outlier: 3.899A pdb=" N ALA G 46 " --> pdb=" O GLY G 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 69 removed outlier: 3.584A pdb=" N VAL G 69 " --> pdb=" O PRO G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 110 removed outlier: 3.590A pdb=" N VAL G 100 " --> pdb=" O PHE G 96 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYS G 101 " --> pdb=" O LYS G 97 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP G 102 " --> pdb=" O SER G 98 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY G 105 " --> pdb=" O LYS G 101 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 130 Processing helix chain 'G' and resid 145 through 148 Processing helix chain 'G' and resid 149 through 162 removed outlier: 3.566A pdb=" N MET G 156 " --> pdb=" O SER G 152 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR G 160 " --> pdb=" O MET G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 210 through 286 removed outlier: 3.581A pdb=" N VAL G 220 " --> pdb=" O ASP G 216 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL G 286 " --> pdb=" O GLY G 282 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 102 removed outlier: 3.742A pdb=" N ALA H 95 " --> pdb=" O ASP H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 114 through 129 removed outlier: 3.706A pdb=" N ARG H 121 " --> pdb=" O ALA H 117 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 41 removed outlier: 3.533A pdb=" N ILE I 10 " --> pdb=" O GLY I 6 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLY I 19 " --> pdb=" O LEU I 15 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS I 33 " --> pdb=" O LEU I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 44 through 60 removed outlier: 3.554A pdb=" N GLY I 57 " --> pdb=" O PHE I 53 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU I 58 " --> pdb=" O ILE I 54 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP I 60 " --> pdb=" O ALA I 56 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 76 removed outlier: 3.579A pdb=" N ILE I 65 " --> pdb=" O ALA I 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 41 removed outlier: 3.586A pdb=" N ILE J 10 " --> pdb=" O GLY J 6 " (cutoff:3.500A) Processing helix chain 'J' and resid 44 through 60 removed outlier: 3.819A pdb=" N VAL J 50 " --> pdb=" O PRO J 46 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU J 58 " --> pdb=" O ILE J 54 " (cutoff:3.500A) Processing helix chain 'J' and resid 60 through 76 removed outlier: 3.533A pdb=" N ILE J 65 " --> pdb=" O ALA J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 83 removed outlier: 4.114A pdb=" N GLY J 81 " --> pdb=" O ASN J 77 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLN J 82 " --> pdb=" O PRO J 78 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 17 removed outlier: 3.572A pdb=" N ILE L 10 " --> pdb=" O GLY L 6 " (cutoff:3.500A) Processing helix chain 'L' and resid 18 through 41 removed outlier: 3.579A pdb=" N LYS L 33 " --> pdb=" O LEU L 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 44 through 76 removed outlier: 3.759A pdb=" N LEU L 58 " --> pdb=" O ILE L 54 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N VAL L 62 " --> pdb=" O LEU L 58 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N THR L 63 " --> pdb=" O LEU L 59 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'M' and resid 2 through 41 removed outlier: 3.721A pdb=" N GLY M 19 " --> pdb=" O LEU M 15 " (cutoff:3.500A) Processing helix chain 'M' and resid 44 through 76 removed outlier: 3.775A pdb=" N VAL M 50 " --> pdb=" O PRO M 46 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU M 58 " --> pdb=" O ILE M 54 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N VAL M 62 " --> pdb=" O LEU M 58 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N THR M 63 " --> pdb=" O LEU M 59 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE M 65 " --> pdb=" O ALA M 61 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 83 removed outlier: 3.857A pdb=" N ILE M 83 " --> pdb=" O VAL M 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 41 removed outlier: 3.667A pdb=" N ILE N 10 " --> pdb=" O GLY N 6 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLY N 19 " --> pdb=" O LEU N 15 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 60 removed outlier: 4.149A pdb=" N LEU N 58 " --> pdb=" O ILE N 54 " (cutoff:3.500A) Processing helix chain 'N' and resid 61 through 76 Processing helix chain 'N' and resid 79 through 83 Processing helix chain 'O' and resid 2 through 41 removed outlier: 3.514A pdb=" N ILE O 10 " --> pdb=" O GLY O 6 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY O 19 " --> pdb=" O LEU O 15 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS O 33 " --> pdb=" O LEU O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 44 through 76 removed outlier: 3.642A pdb=" N VAL O 55 " --> pdb=" O LYS O 51 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU O 58 " --> pdb=" O ILE O 54 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N VAL O 62 " --> pdb=" O LEU O 58 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N THR O 63 " --> pdb=" O LEU O 59 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE O 65 " --> pdb=" O ALA O 61 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 41 removed outlier: 4.068A pdb=" N GLY P 19 " --> pdb=" O LEU P 15 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS P 33 " --> pdb=" O LEU P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 44 through 76 removed outlier: 3.744A pdb=" N VAL P 50 " --> pdb=" O PRO P 46 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU P 58 " --> pdb=" O ILE P 54 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N VAL P 62 " --> pdb=" O LEU P 58 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N THR P 63 " --> pdb=" O LEU P 59 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE P 65 " --> pdb=" O ALA P 61 " (cutoff:3.500A) Processing helix chain 'P' and resid 78 through 82 Processing helix chain 'Q' and resid 2 through 41 removed outlier: 3.623A pdb=" N ILE Q 10 " --> pdb=" O GLY Q 6 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY Q 19 " --> pdb=" O LEU Q 15 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS Q 33 " --> pdb=" O LEU Q 29 " (cutoff:3.500A) Processing helix chain 'Q' and resid 44 through 60 removed outlier: 3.746A pdb=" N LEU Q 58 " --> pdb=" O ILE Q 54 " (cutoff:3.500A) Processing helix chain 'Q' and resid 60 through 76 Processing helix chain 'R' and resid 2 through 41 removed outlier: 3.622A pdb=" N ILE R 10 " --> pdb=" O GLY R 6 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY R 19 " --> pdb=" O LEU R 15 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS R 33 " --> pdb=" O LEU R 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 44 through 60 removed outlier: 3.732A pdb=" N VAL R 50 " --> pdb=" O PRO R 46 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU R 58 " --> pdb=" O ILE R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 75 removed outlier: 3.660A pdb=" N ILE R 65 " --> pdb=" O ALA R 61 " (cutoff:3.500A) Processing helix chain 'S' and resid 3 through 41 removed outlier: 4.012A pdb=" N LEU S 7 " --> pdb=" O THR S 3 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ALA S 9 " --> pdb=" O VAL S 5 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE S 10 " --> pdb=" O GLY S 6 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY S 19 " --> pdb=" O LEU S 15 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG S 40 " --> pdb=" O GLU S 36 " (cutoff:3.500A) Processing helix chain 'S' and resid 44 through 76 removed outlier: 3.847A pdb=" N VAL S 50 " --> pdb=" O PRO S 46 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU S 58 " --> pdb=" O ILE S 54 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N VAL S 62 " --> pdb=" O LEU S 58 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N THR S 63 " --> pdb=" O LEU S 59 " (cutoff:3.500A) Processing helix chain 'S' and resid 79 through 83 Processing helix chain 'W' and resid 3 through 22 Proline residue: W 10 - end of helix Processing helix chain 'W' and resid 24 through 40 Processing helix chain 'W' and resid 41 through 49 removed outlier: 3.674A pdb=" N GLN W 46 " --> pdb=" O ASP W 42 " (cutoff:3.500A) Processing helix chain 'W' and resid 54 through 67 Processing helix chain 'W' and resid 68 through 70 No H-bonds generated for 'chain 'W' and resid 68 through 70' Processing helix chain 'W' and resid 71 through 84 Processing helix chain 'W' and resid 86 through 88 No H-bonds generated for 'chain 'W' and resid 86 through 88' Processing helix chain 'W' and resid 89 through 105 removed outlier: 3.856A pdb=" N GLU W 95 " --> pdb=" O PRO W 91 " (cutoff:3.500A) Processing helix chain 'W' and resid 119 through 135 Processing helix chain 'W' and resid 164 through 178 removed outlier: 3.547A pdb=" N LYS W 168 " --> pdb=" O SER W 164 " (cutoff:3.500A) Processing helix chain 'X' and resid 3 through 7 removed outlier: 4.073A pdb=" N THR X 6 " --> pdb=" O ILE X 3 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU X 7 " --> pdb=" O ASN X 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 3 through 7' Processing helix chain 'X' and resid 8 through 25 removed outlier: 3.687A pdb=" N VAL X 12 " --> pdb=" O ILE X 8 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE X 15 " --> pdb=" O SER X 11 " (cutoff:3.500A) Processing helix chain 'X' and resid 26 through 137 removed outlier: 3.540A pdb=" N ALA X 31 " --> pdb=" O PRO X 27 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ALA X 32 " --> pdb=" O PRO X 28 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LEU X 33 " --> pdb=" O VAL X 29 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLN X 34 " --> pdb=" O ILE X 30 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE X 40 " --> pdb=" O ARG X 36 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLN X 85 " --> pdb=" O LYS X 81 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA X 90 " --> pdb=" O ILE X 86 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ASN X 114 " --> pdb=" O GLU X 110 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N SER X 115 " --> pdb=" O GLN X 111 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL X 116 " --> pdb=" O GLU X 112 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA X 119 " --> pdb=" O SER X 115 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N GLY X 125 " --> pdb=" O ARG X 121 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ALA X 126 " --> pdb=" O ALA X 122 " (cutoff:3.500A) Processing helix chain 'X' and resid 140 through 143 Processing helix chain 'X' and resid 144 through 152 removed outlier: 3.519A pdb=" N SER X 150 " --> pdb=" O GLU X 146 " (cutoff:3.500A) Processing helix chain 'X' and resid 153 through 155 No H-bonds generated for 'chain 'X' and resid 153 through 155' Processing helix chain 'Y' and resid 2 through 25 removed outlier: 4.177A pdb=" N LEU Y 7 " --> pdb=" O ILE Y 3 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE Y 8 " --> pdb=" O ASN Y 4 " (cutoff:3.500A) Processing helix chain 'Y' and resid 26 through 98 removed outlier: 3.554A pdb=" N GLN Y 37 " --> pdb=" O LEU Y 33 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU Y 55 " --> pdb=" O ALA Y 51 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY Y 98 " --> pdb=" O ALA Y 94 " (cutoff:3.500A) Processing helix chain 'Y' and resid 99 through 104 Processing helix chain 'Y' and resid 105 through 140 removed outlier: 3.570A pdb=" N GLN Y 123 " --> pdb=" O ALA Y 119 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA Y 138 " --> pdb=" O LYS Y 134 " (cutoff:3.500A) Processing helix chain 'Y' and resid 141 through 146 removed outlier: 3.610A pdb=" N GLU Y 146 " --> pdb=" O ALA Y 142 " (cutoff:3.500A) Processing helix chain 'Y' and resid 148 through 153 Processing helix chain 'a' and resid 5 through 14 removed outlier: 4.011A pdb=" N HIS a 12 " --> pdb=" O GLY a 8 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N HIS a 13 " --> pdb=" O TYR a 9 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU a 14 " --> pdb=" O ILE a 10 " (cutoff:3.500A) Processing helix chain 'a' and resid 33 through 38 removed outlier: 3.832A pdb=" N GLU a 38 " --> pdb=" O GLN a 35 " (cutoff:3.500A) Processing helix chain 'a' and resid 46 through 68 removed outlier: 3.604A pdb=" N GLY a 50 " --> pdb=" O VAL a 46 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU a 55 " --> pdb=" O TRP a 51 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY a 56 " --> pdb=" O SER a 52 " (cutoff:3.500A) Processing helix chain 'a' and resid 76 through 95 removed outlier: 4.016A pdb=" N PHE a 81 " --> pdb=" O GLY a 77 " (cutoff:3.500A) Processing helix chain 'a' and resid 103 through 121 removed outlier: 3.502A pdb=" N ILE a 121 " --> pdb=" O LEU a 117 " (cutoff:3.500A) Processing helix chain 'a' and resid 122 through 124 No H-bonds generated for 'chain 'a' and resid 122 through 124' Processing helix chain 'a' and resid 127 through 138 removed outlier: 4.133A pdb=" N MET a 131 " --> pdb=" O ASP a 127 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LEU a 132 " --> pdb=" O TYR a 128 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ALA a 133 " --> pdb=" O LEU a 129 " (cutoff:3.500A) Processing helix chain 'a' and resid 151 through 186 removed outlier: 4.062A pdb=" N THR a 155 " --> pdb=" O ASP a 151 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ILE a 176 " --> pdb=" O LYS a 172 " (cutoff:3.500A) removed outlier: 9.194A pdb=" N GLY a 177 " --> pdb=" O VAL a 173 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY a 178 " --> pdb=" O LYS a 174 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N HIS a 186 " --> pdb=" O GLU a 182 " (cutoff:3.500A) Processing helix chain 'a' and resid 192 through 242 removed outlier: 3.786A pdb=" N LEU a 198 " --> pdb=" O VAL a 194 " (cutoff:3.500A) Proline residue: a 201 - end of helix removed outlier: 3.683A pdb=" N VAL a 209 " --> pdb=" O LEU a 205 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS a 214 " --> pdb=" O THR a 210 " (cutoff:3.500A) Proline residue: a 215 - end of helix removed outlier: 3.952A pdb=" N MET a 239 " --> pdb=" O LEU a 235 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N PHE a 240 " --> pdb=" O ILE a 236 " (cutoff:3.500A) Processing helix chain 'a' and resid 244 through 259 removed outlier: 4.224A pdb=" N VAL a 252 " --> pdb=" O SER a 248 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N ALA a 253 " --> pdb=" O ALA a 249 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU a 254 " --> pdb=" O LEU a 250 " (cutoff:3.500A) Processing helix chain 'a' and resid 261 through 283 removed outlier: 4.554A pdb=" N ILE a 265 " --> pdb=" O PHE a 261 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA a 270 " --> pdb=" O ILE a 266 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE a 273 " --> pdb=" O GLN a 269 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET a 274 " --> pdb=" O ALA a 270 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL a 279 " --> pdb=" O MET a 275 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 36 removed outlier: 6.714A pdb=" N ARG A 41 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N VAL A 35 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE A 39 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL A 75 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ALA A 64 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N GLU A 52 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N MET A 53 " --> pdb=" O THR A 92 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 100 removed outlier: 4.118A pdb=" N ALA A 126 " --> pdb=" O VAL A 100 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 108 through 110 removed outlier: 6.501A pdb=" N VAL A 109 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR A 261 " --> pdb=" O LEU A 328 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY A 323 " --> pdb=" O VAL A 305 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 110 removed outlier: 6.501A pdb=" N VAL A 109 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR A 261 " --> pdb=" O LEU A 328 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU A 167 " --> pdb=" O ILE A 354 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'W' and resid 137 through 144 removed outlier: 7.041A pdb=" N VAL W 108 " --> pdb=" O ARG W 139 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N HIS W 141 " --> pdb=" O VAL W 108 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N VAL W 110 " --> pdb=" O HIS W 141 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N SER W 143 " --> pdb=" O VAL W 110 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N VAL W 112 " --> pdb=" O SER W 143 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU W 159 " --> pdb=" O ALA W 156 " (cutoff:3.500A) removed outlier: 12.773A pdb=" N ALA B 26 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N GLY B 93 " --> pdb=" O ALA B 26 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N ASN B 28 " --> pdb=" O CYS B 91 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N MET B 53 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLU B 52 " --> pdb=" O ALA B 64 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N ALA B 64 " --> pdb=" O VAL B 75 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL B 75 " --> pdb=" O ALA B 64 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ILE B 39 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N VAL B 35 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ARG B 41 " --> pdb=" O VAL B 33 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 97 through 99 Processing sheet with id=AA7, first strand: chain 'B' and resid 108 through 110 removed outlier: 6.473A pdb=" N VAL B 109 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ALA B 257 " --> pdb=" O THR B 326 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N LEU B 328 " --> pdb=" O ALA B 257 " (cutoff:3.500A) removed outlier: 6.911A 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=AA8, first strand: chain 'B' and resid 108 through 110 removed outlier: 6.473A pdb=" N VAL B 109 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ALA B 257 " --> pdb=" O THR B 326 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N LEU B 328 " --> pdb=" O ALA B 257 " (cutoff:3.500A) removed outlier: 6.911A 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: 6.564A pdb=" N LEU B 167 " --> pdb=" O ILE B 354 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 61 through 67 removed outlier: 4.428A pdb=" N GLU C 52 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N MET C 53 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ARG C 41 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N VAL C 35 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ILE C 39 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VAL C 75 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N ALA C 64 " --> pdb=" O VAL C 75 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ALA E 35 " --> pdb=" O THR E 76 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLU E 34 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ARG E 57 " --> pdb=" O GLN E 48 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N GLN E 50 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 7.321A 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: 6.691A pdb=" N ASP E 21 " --> pdb=" O VAL E 13 " (cutoff:3.500A) Processing sheet with id=AB1, 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=AB2, first strand: chain 'C' and resid 108 through 109 removed outlier: 6.536A pdb=" N VAL C 109 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N SER C 228 " --> pdb=" O VAL C 109 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 108 through 109 removed outlier: 6.536A pdb=" N VAL C 109 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N SER C 228 " --> pdb=" O VAL C 109 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LEU C 167 " --> pdb=" O ILE C 354 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N LEU C 356 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ILE C 169 " --> pdb=" O LEU C 356 " (cutoff:3.500A) Processing sheet with id=AB4, 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=AB5, first strand: chain 'D' and resid 9 through 16 removed outlier: 6.678A pdb=" N ASP D 21 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ILE D 15 " --> pdb=" O VAL D 19 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N VAL D 19 " --> pdb=" O ILE D 15 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N VAL D 55 " --> pdb=" O GLN D 50 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLN D 50 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ARG D 57 " --> pdb=" O GLN D 48 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLU D 34 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ALA D 35 " --> pdb=" O THR D 76 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 81 through 83 Processing sheet with id=AB7, first strand: chain 'D' and resid 92 through 93 removed outlier: 6.216A pdb=" N MET D 93 " --> pdb=" O TYR D 211 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N SER D 179 " --> pdb=" O ALA D 208 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N VAL D 210 " --> pdb=" O SER D 179 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N PHE D 181 " --> pdb=" O VAL D 210 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N GLY D 212 " --> pdb=" O PHE D 181 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N GLY D 183 " --> pdb=" O GLY D 212 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TYR D 178 " --> pdb=" O ASP D 241 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL D 242 " --> pdb=" O THR D 296 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ILE D 298 " --> pdb=" O VAL D 242 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU D 244 " --> pdb=" O ILE D 298 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N ALA D 300 " --> pdb=" O LEU D 244 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ILE D 246 " --> pdb=" O ALA D 300 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N TYR D 302 " --> pdb=" O ILE D 246 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LYS D 149 " --> pdb=" O ALA D 322 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N VAL D 324 " --> pdb=" O LYS D 149 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N GLY D 151 " --> pdb=" O VAL D 324 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 130 through 131 removed outlier: 4.170A pdb=" N PHE D 144 " --> pdb=" O LEU D 131 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 81 through 84 removed outlier: 4.915A pdb=" N GLU E 110 " --> pdb=" O VAL E 84 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 92 through 93 removed outlier: 6.625A pdb=" N MET E 93 " --> pdb=" O TYR E 211 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LYS E 149 " --> pdb=" O ALA E 322 " (cutoff:3.500A) removed outlier: 7.962A 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=AC2, first strand: chain 'E' and resid 130 through 131 removed outlier: 4.188A pdb=" N PHE E 144 " --> pdb=" O LEU E 131 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 9 through 16 removed outlier: 6.670A pdb=" N ASP F 21 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ILE F 15 " --> pdb=" O VAL F 19 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N VAL F 19 " --> pdb=" O ILE F 15 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N VAL F 55 " --> pdb=" O GLN F 50 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N GLN F 50 " --> pdb=" O VAL F 55 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ARG F 57 " --> pdb=" O GLN F 48 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N GLU F 34 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ALA F 35 " --> pdb=" O THR F 76 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 81 through 83 Processing sheet with id=AC5, first strand: chain 'F' and resid 92 through 93 removed outlier: 6.304A pdb=" N MET F 93 " --> pdb=" O TYR F 211 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N GLN F 213 " --> pdb=" O MET F 93 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N TYR F 178 " --> pdb=" O ASP F 241 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N VAL F 242 " --> pdb=" O THR F 296 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N ILE F 298 " --> pdb=" O VAL F 242 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LEU F 244 " --> pdb=" O ILE F 298 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N ALA F 300 " --> pdb=" O LEU F 244 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ILE F 246 " --> pdb=" O ALA F 300 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL F 150 " --> pdb=" O GLN F 299 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 130 through 131 removed outlier: 4.664A pdb=" N PHE F 144 " --> pdb=" O LEU F 131 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 133 through 137 removed outlier: 7.322A pdb=" N LEU G 115 " --> pdb=" O VAL G 134 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ALA G 136 " --> pdb=" O LEU G 115 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL G 117 " --> pdb=" O ALA G 136 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ILE G 79 " --> pdb=" O VAL G 171 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N ASN G 173 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 8.904A pdb=" N VAL G 81 " --> pdb=" O ASN G 173 " (cutoff:3.500A) removed outlier: 12.080A pdb=" N PHE G 175 " --> pdb=" O VAL G 81 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N THR G 180 " --> pdb=" O VAL G 176 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 15 through 21 removed outlier: 6.218A pdb=" N ILE H 9 " --> pdb=" O ILE H 16 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N SER H 18 " --> pdb=" O CYS H 7 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N CYS H 7 " --> pdb=" O SER H 18 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU H 20 " --> pdb=" O VAL H 5 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N VAL H 5 " --> pdb=" O LEU H 20 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 31 through 35 removed outlier: 3.639A pdb=" N MET H 23 " --> pdb=" O VAL H 54 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 49 through 50 removed outlier: 3.570A 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 20 2349 hydrogen bonds defined for protein. 6762 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: 7.97 Time building geometry restraints manager: 3.99 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: 6351 1.28 - 1.41: 8790 1.41 - 1.55: 22025 1.55 - 1.69: 96 1.69 - 1.83: 297 Bond restraints: 37559 Sorted by residual: bond pdb=" C GLY R 81 " pdb=" O GLY R 81 " ideal model delta sigma weight residual 1.239 1.141 0.097 7.10e-03 1.98e+04 1.88e+02 bond pdb=" C4 ADP F 501 " pdb=" C5 ADP F 501 " ideal model delta sigma weight residual 1.490 1.351 0.139 2.00e-02 2.50e+03 4.85e+01 bond pdb=" C4 ADP D 501 " pdb=" C5 ADP D 501 " ideal model delta sigma weight residual 1.490 1.352 0.138 2.00e-02 2.50e+03 4.74e+01 bond pdb=" C4 ADP E 501 " pdb=" C5 ADP E 501 " ideal model delta sigma weight residual 1.490 1.355 0.135 2.00e-02 2.50e+03 4.58e+01 bond pdb=" C GLU D 23 " pdb=" N PHE D 24 " ideal model delta sigma weight residual 1.325 1.245 0.080 1.25e-02 6.40e+03 4.09e+01 ... (remaining 37554 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.90: 50734 6.90 - 13.79: 89 13.79 - 20.69: 5 20.69 - 27.59: 2 27.59 - 34.48: 1 Bond angle restraints: 50831 Sorted by residual: angle pdb=" O GLY R 81 " pdb=" C GLY R 81 " pdb=" N GLN R 82 " ideal model delta sigma weight residual 121.97 95.08 26.89 9.50e-01 1.11e+00 8.01e+02 angle pdb=" O ALA a 284 " pdb=" C ALA a 284 " pdb=" N HIS a 285 " ideal model delta sigma weight residual 122.41 87.93 34.48 1.42e+00 4.96e-01 5.90e+02 angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 120.98 18.89 1.00e+00 1.00e+00 3.57e+02 angle pdb=" PB ATP C 600 " pdb=" O3B ATP C 600 " pdb=" PG ATP C 600 " ideal model delta sigma weight residual 139.87 122.87 17.00 1.00e+00 1.00e+00 2.89e+02 angle pdb=" PA ATP A 600 " pdb=" O3A ATP A 600 " pdb=" PB ATP A 600 " ideal model delta sigma weight residual 136.83 119.86 16.97 1.00e+00 1.00e+00 2.88e+02 ... (remaining 50826 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.49: 22195 35.49 - 70.98: 386 70.98 - 106.47: 28 106.47 - 141.96: 3 141.96 - 177.45: 2 Dihedral angle restraints: 22614 sinusoidal: 8833 harmonic: 13781 Sorted by residual: dihedral pdb=" C THR X 6 " pdb=" N THR X 6 " pdb=" CA THR X 6 " pdb=" CB THR X 6 " ideal model delta harmonic sigma weight residual -122.00 -144.04 22.04 0 2.50e+00 1.60e-01 7.77e+01 dihedral pdb=" N THR X 6 " pdb=" C THR X 6 " pdb=" CA THR X 6 " pdb=" CB THR X 6 " ideal model delta harmonic sigma weight residual 123.40 143.12 -19.72 0 2.50e+00 1.60e-01 6.22e+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 300.00 122.55 177.45 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 22611 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.178: 5587 0.178 - 0.357: 322 0.357 - 0.535: 19 0.535 - 0.714: 0 0.714 - 0.892: 1 Chirality restraints: 5929 Sorted by residual: chirality pdb=" CA THR X 6 " pdb=" N THR X 6 " pdb=" C THR X 6 " pdb=" CB THR X 6 " both_signs ideal model delta sigma weight residual False 2.53 1.63 0.89 2.00e-01 2.50e+01 1.99e+01 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 5.74e+00 chirality pdb=" CA ARG B 366 " pdb=" N ARG B 366 " pdb=" C ARG B 366 " pdb=" CB ARG B 366 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.50e+00 ... (remaining 5926 not shown) Planarity restraints: 6558 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA a 284 " -0.115 2.00e-02 2.50e+03 1.85e-01 3.41e+02 pdb=" C ALA a 284 " 0.320 2.00e-02 2.50e+03 pdb=" O ALA a 284 " -0.106 2.00e-02 2.50e+03 pdb=" N HIS a 285 " -0.099 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY R 81 " 0.104 2.00e-02 2.50e+03 1.81e-01 3.28e+02 pdb=" C GLY R 81 " -0.313 2.00e-02 2.50e+03 pdb=" O GLY R 81 " 0.117 2.00e-02 2.50e+03 pdb=" N GLN R 82 " 0.093 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ATP A 600 " -0.156 2.00e-02 2.50e+03 6.87e-02 1.30e+02 pdb=" C2 ATP A 600 " 0.022 2.00e-02 2.50e+03 pdb=" C4 ATP A 600 " 0.052 2.00e-02 2.50e+03 pdb=" C5 ATP A 600 " 0.046 2.00e-02 2.50e+03 pdb=" C6 ATP A 600 " -0.016 2.00e-02 2.50e+03 pdb=" C8 ATP A 600 " 0.025 2.00e-02 2.50e+03 pdb=" N1 ATP A 600 " -0.021 2.00e-02 2.50e+03 pdb=" N3 ATP A 600 " 0.054 2.00e-02 2.50e+03 pdb=" N6 ATP A 600 " -0.110 2.00e-02 2.50e+03 pdb=" N7 ATP A 600 " 0.067 2.00e-02 2.50e+03 pdb=" N9 ATP A 600 " 0.037 2.00e-02 2.50e+03 ... (remaining 6555 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 19 2.47 - 3.08: 22740 3.08 - 3.69: 54060 3.69 - 4.29: 82053 4.29 - 4.90: 136331 Nonbonded interactions: 295203 Sorted by model distance: nonbonded pdb=" O1G ATP A 600 " pdb="MG MG A 601 " model vdw 1.863 2.170 nonbonded pdb=" O2G ATP C 600 " pdb="MG MG C 601 " model vdw 1.869 2.170 nonbonded pdb=" O2G ATP B 600 " pdb="MG MG B 601 " model vdw 1.902 2.170 nonbonded pdb=" O1B ADP E 501 " pdb="MG MG E 502 " model vdw 1.905 2.170 nonbonded pdb=" OD2 ASP D 247 " pdb="MG MG D 502 " model vdw 1.916 2.170 ... (remaining 295198 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 8 through 601) selection = (chain 'B' and resid 8 through 601) selection = chain 'C' } ncs_group { reference = (chain 'D' and resid 8 through 501) selection = (chain 'E' and resid 8 through 501) selection = chain 'F' } ncs_group { reference = (chain 'I' and (resid 1 through 82 or (resid 83 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'J' and ((resid 1 and (name N or name CA or name C or name O or name CB ) \ ) or resid 2 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 and (name N or name CA or name C or name O or name CB ) \ ) or resid 2 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 and (name N or name CA or name C or name O or name CB ) \ ) or resid 2 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 and (name N or name CA or name C or name O or name CB ) \ ) or resid 2 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 and (name N or name CA or name C or name O or name CB ) \ ) or resid 2 through 82 or (resid 83 and (name N or name CA or name C or name O \ or name CB )))) selection = (chain 'P' and ((resid 1 and (name N or name CA or name C or name O or name CB ) \ ) or resid 2 through 83)) selection = (chain 'Q' and ((resid 1 and (name N or name CA or name C or name O or name CB ) \ ) or resid 2 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 and (name N or name CA or name C or name O or name CB ) \ ) or resid 2 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 and (name N or name CA or name C or name O or name CB ) \ ) or resid 2 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: 4.190 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: 0.640 Check model and map are aligned: 0.120 Set scattering table: 0.120 Process input model: 33.500 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.070 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:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.139 37559 Z= 0.780 Angle : 1.885 34.482 50831 Z= 1.282 Chirality : 0.099 0.892 5929 Planarity : 0.016 0.262 6558 Dihedral : 13.221 177.451 13824 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 0.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.46 % Favored : 97.50 % Rotamer: Outliers : 0.31 % Allowed : 3.38 % Favored : 96.31 % Cbeta Deviations : 0.66 % Peptide Plane: Cis-proline : 2.35 % 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: -0.59 (0.11), residues: 4843 helix: -0.29 (0.09), residues: 2632 sheet: 0.05 (0.21), residues: 503 loop : -0.40 (0.15), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.040 0.002 ARG C 251 TYR 0.129 0.018 TYR C 475 PHE 0.083 0.011 PHE a 63 TRP 0.125 0.023 TRP a 114 HIS 0.019 0.003 HIS a 13 Details of bonding type rmsd covalent geometry : bond 0.01267 (37559) covalent geometry : angle 1.88492 (50831) hydrogen bonds : bond 0.20866 ( 2307) hydrogen bonds : angle 7.29440 ( 6762) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9686 Ramachandran restraints generated. 4843 Oldfield, 0 Emsley, 4843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9686 Ramachandran restraints generated. 4843 Oldfield, 0 Emsley, 4843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 3818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 412 time to evaluate : 1.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 237 TYR cc_start: 0.8741 (OUTLIER) cc_final: 0.8338 (t80) REVERT: X 86 ILE cc_start: 0.7421 (mt) cc_final: 0.6624 (mt) outliers start: 12 outliers final: 0 residues processed: 423 average time/residue: 0.2552 time to fit residues: 168.5654 Evaluate side-chains 211 residues out of total 3818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 210 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 237 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 432 optimal weight: 6.9990 chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 9.9990 chunk 455 optimal weight: 7.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 4.9990 chunk 470 optimal weight: 6.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 GLN B 458 GLN C 400 GLN F 358 HIS G 248 ASN ** I 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 82 GLN M 49 GLN P 82 GLN ** R 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 141 HIS X 37 GLN Y 63 GLN Y 114 ASN ** Y 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 225 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.075651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.051035 restraints weight = 148186.620| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.51 r_work: 0.3039 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 37559 Z= 0.200 Angle : 0.679 14.238 50831 Z= 0.360 Chirality : 0.045 0.204 5929 Planarity : 0.004 0.050 6558 Dihedral : 7.845 172.201 5345 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.42 % Favored : 98.55 % Rotamer: Outliers : 1.28 % Allowed : 6.87 % Favored : 91.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: 1.07 (0.12), residues: 4843 helix: 1.33 (0.10), residues: 2673 sheet: 0.31 (0.20), residues: 549 loop : -0.05 (0.16), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 454 TYR 0.016 0.002 TYR D 252 PHE 0.025 0.002 PHE a 81 TRP 0.023 0.003 TRP a 114 HIS 0.008 0.001 HIS G 65 Details of bonding type rmsd covalent geometry : bond 0.00436 (37559) covalent geometry : angle 0.67908 (50831) hydrogen bonds : bond 0.06301 ( 2307) hydrogen bonds : angle 4.94163 ( 6762) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9686 Ramachandran restraints generated. 4843 Oldfield, 0 Emsley, 4843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9686 Ramachandran restraints generated. 4843 Oldfield, 0 Emsley, 4843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 3818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 229 time to evaluate : 1.483 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: C 237 TYR cc_start: 0.9346 (OUTLIER) cc_final: 0.9130 (t80) REVERT: D 280 MET cc_start: 0.8452 (tpp) cc_final: 0.8251 (tpp) REVERT: H 116 SER cc_start: 0.7314 (t) cc_final: 0.7055 (p) REVERT: I 44 MET cc_start: 0.8404 (mmp) cc_final: 0.7894 (mmt) REVERT: Q 1 MET cc_start: 0.7244 (OUTLIER) cc_final: 0.6084 (pmm) REVERT: W 5 THR cc_start: 0.9000 (OUTLIER) cc_final: 0.8523 (p) REVERT: X 84 ASN cc_start: 0.8873 (m-40) cc_final: 0.8580 (m-40) REVERT: X 88 ASP cc_start: 0.8039 (p0) cc_final: 0.7828 (p0) REVERT: a 85 MET cc_start: 0.7503 (OUTLIER) cc_final: 0.7191 (mpp) REVERT: a 244 MET cc_start: 0.2991 (tpt) cc_final: 0.2279 (mtt) REVERT: a 274 MET cc_start: 0.8022 (tmm) cc_final: 0.7379 (ppp) outliers start: 49 outliers final: 11 residues processed: 267 average time/residue: 0.2195 time to fit residues: 98.7366 Evaluate side-chains 214 residues out of total 3818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 199 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain C residue 91 CYS Chi-restraints excluded: chain C residue 237 TYR Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain G residue 65 HIS Chi-restraints excluded: chain G residue 106 TYR Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain H residue 128 GLN Chi-restraints excluded: chain L residue 65 ILE Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain W residue 5 THR Chi-restraints excluded: chain W residue 138 VAL Chi-restraints excluded: chain a residue 85 MET Chi-restraints excluded: chain a residue 200 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 356 optimal weight: 30.0000 chunk 258 optimal weight: 6.9990 chunk 39 optimal weight: 20.0000 chunk 316 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 237 optimal weight: 7.9990 chunk 239 optimal weight: 0.0570 chunk 279 optimal weight: 20.0000 chunk 37 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 overall best weight: 2.6104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 424 HIS P 49 GLN R 41 GLN Y 10 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.075233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.050675 restraints weight = 147371.355| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.52 r_work: 0.3027 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 37559 Z= 0.146 Angle : 0.568 9.595 50831 Z= 0.297 Chirality : 0.042 0.178 5929 Planarity : 0.004 0.044 6558 Dihedral : 7.503 170.513 5345 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.76 % Favored : 98.22 % Rotamer: Outliers : 1.31 % Allowed : 7.21 % Favored : 91.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: 1.47 (0.12), residues: 4843 helix: 1.71 (0.10), residues: 2692 sheet: 0.44 (0.20), residues: 552 loop : 0.03 (0.16), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG X 52 TYR 0.015 0.001 TYR D 252 PHE 0.024 0.001 PHE M 73 TRP 0.014 0.002 TRP Y 26 HIS 0.006 0.001 HIS G 55 Details of bonding type rmsd covalent geometry : bond 0.00319 (37559) covalent geometry : angle 0.56820 (50831) hydrogen bonds : bond 0.05170 ( 2307) hydrogen bonds : angle 4.51219 ( 6762) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9686 Ramachandran restraints generated. 4843 Oldfield, 0 Emsley, 4843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9686 Ramachandran restraints generated. 4843 Oldfield, 0 Emsley, 4843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 3818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 219 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 ILE cc_start: 0.9293 (OUTLIER) cc_final: 0.9014 (tp) REVERT: C 237 TYR cc_start: 0.9329 (OUTLIER) cc_final: 0.9119 (t80) REVERT: I 44 MET cc_start: 0.7931 (mmp) cc_final: 0.7461 (mmm) REVERT: O 48 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8537 (mt) REVERT: P 23 THR cc_start: 0.8095 (OUTLIER) cc_final: 0.7741 (p) REVERT: Q 1 MET cc_start: 0.6998 (OUTLIER) cc_final: 0.6218 (pmm) REVERT: R 44 MET cc_start: 0.6272 (mmm) cc_final: 0.5921 (mmm) REVERT: X 84 ASN cc_start: 0.8892 (m-40) cc_final: 0.8604 (m-40) REVERT: a 85 MET cc_start: 0.7354 (OUTLIER) cc_final: 0.7118 (mpp) outliers start: 50 outliers final: 17 residues processed: 260 average time/residue: 0.2242 time to fit residues: 96.1054 Evaluate side-chains 218 residues out of total 3818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 195 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain C residue 237 TYR Chi-restraints excluded: chain C residue 490 LYS Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain G residue 65 HIS Chi-restraints excluded: chain G residue 106 TYR Chi-restraints excluded: chain H residue 128 GLN Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain L residue 65 ILE Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain P residue 23 THR Chi-restraints excluded: chain P residue 52 MET Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain R residue 47 MET Chi-restraints excluded: chain W residue 5 THR Chi-restraints excluded: chain W residue 138 VAL Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain a residue 85 MET Chi-restraints excluded: chain a residue 200 ILE Chi-restraints excluded: chain a residue 281 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 398 optimal weight: 8.9990 chunk 132 optimal weight: 10.0000 chunk 102 optimal weight: 0.8980 chunk 372 optimal weight: 20.0000 chunk 154 optimal weight: 8.9990 chunk 73 optimal weight: 5.9990 chunk 278 optimal weight: 20.0000 chunk 53 optimal weight: 9.9990 chunk 134 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 126 optimal weight: 2.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 HIS B 424 HIS ** B 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 49 GLN W 141 HIS a 45 HIS ** a 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.075267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.050080 restraints weight = 147967.148| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.48 r_work: 0.3004 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 37559 Z= 0.165 Angle : 0.568 9.898 50831 Z= 0.294 Chirality : 0.042 0.176 5929 Planarity : 0.004 0.045 6558 Dihedral : 7.384 168.911 5345 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.76 % Favored : 98.22 % Rotamer: Outliers : 1.15 % Allowed : 7.99 % Favored : 90.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: 1.62 (0.12), residues: 4843 helix: 1.88 (0.10), residues: 2683 sheet: 0.47 (0.20), residues: 556 loop : 0.01 (0.16), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Y 52 TYR 0.016 0.001 TYR E 252 PHE 0.034 0.001 PHE a 271 TRP 0.011 0.001 TRP Y 26 HIS 0.008 0.001 HIS G 55 Details of bonding type rmsd covalent geometry : bond 0.00378 (37559) covalent geometry : angle 0.56841 (50831) hydrogen bonds : bond 0.04934 ( 2307) hydrogen bonds : angle 4.39112 ( 6762) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9686 Ramachandran restraints generated. 4843 Oldfield, 0 Emsley, 4843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9686 Ramachandran restraints generated. 4843 Oldfield, 0 Emsley, 4843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 3818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 204 time to evaluate : 1.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 ILE cc_start: 0.9339 (OUTLIER) cc_final: 0.9052 (tp) REVERT: F 450 MET cc_start: 0.8676 (mtp) cc_final: 0.8445 (mtp) REVERT: H 116 SER cc_start: 0.7282 (t) cc_final: 0.7046 (p) REVERT: I 44 MET cc_start: 0.7982 (mmp) cc_final: 0.7625 (mmt) REVERT: O 48 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8563 (mt) REVERT: P 43 GLU cc_start: 0.8091 (mp0) cc_final: 0.7844 (mp0) REVERT: Q 1 MET cc_start: 0.7091 (OUTLIER) cc_final: 0.6319 (pmm) REVERT: R 44 MET cc_start: 0.6230 (mmm) cc_final: 0.5911 (mmm) REVERT: R 64 MET cc_start: 0.7704 (mmp) cc_final: 0.7503 (mmp) REVERT: S 1 MET cc_start: 0.6005 (ppp) cc_final: 0.5664 (ppp) REVERT: X 84 ASN cc_start: 0.8950 (m-40) cc_final: 0.8502 (m-40) REVERT: a 39 MET cc_start: 0.4382 (ptp) cc_final: 0.4058 (mmp) REVERT: a 85 MET cc_start: 0.7476 (OUTLIER) cc_final: 0.7229 (mpp) outliers start: 44 outliers final: 25 residues processed: 237 average time/residue: 0.2008 time to fit residues: 81.3987 Evaluate side-chains 224 residues out of total 3818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 195 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain C residue 91 CYS Chi-restraints excluded: chain C residue 237 TYR Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain G residue 65 HIS Chi-restraints excluded: chain G residue 106 TYR Chi-restraints excluded: chain H residue 128 GLN Chi-restraints excluded: chain I residue 65 ILE Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain L residue 65 ILE Chi-restraints excluded: chain O residue 27 PHE Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain P residue 52 MET Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain W residue 138 VAL Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain Y residue 52 ARG Chi-restraints excluded: chain Y residue 145 HIS Chi-restraints excluded: chain a residue 85 MET Chi-restraints excluded: chain a residue 156 LEU Chi-restraints excluded: chain a residue 200 ILE Chi-restraints excluded: chain a residue 223 PHE Chi-restraints excluded: chain a residue 281 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 374 optimal weight: 8.9990 chunk 180 optimal weight: 9.9990 chunk 323 optimal weight: 10.0000 chunk 438 optimal weight: 7.9990 chunk 41 optimal weight: 20.0000 chunk 68 optimal weight: 0.9980 chunk 267 optimal weight: 0.9990 chunk 461 optimal weight: 9.9990 chunk 428 optimal weight: 9.9990 chunk 328 optimal weight: 7.9990 chunk 220 optimal weight: 5.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 458 GLN P 49 GLN ** a 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.073484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.048558 restraints weight = 146305.706| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.45 r_work: 0.2961 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 37559 Z= 0.203 Angle : 0.588 8.693 50831 Z= 0.305 Chirality : 0.043 0.201 5929 Planarity : 0.004 0.057 6558 Dihedral : 7.381 171.029 5345 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.19 % Favored : 97.79 % Rotamer: Outliers : 1.52 % Allowed : 8.75 % Favored : 89.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: 1.57 (0.12), residues: 4843 helix: 1.88 (0.10), residues: 2684 sheet: 0.40 (0.20), residues: 565 loop : -0.09 (0.16), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG X 52 TYR 0.017 0.001 TYR C 237 PHE 0.030 0.002 PHE a 271 TRP 0.010 0.001 TRP a 27 HIS 0.007 0.001 HIS G 55 Details of bonding type rmsd covalent geometry : bond 0.00476 (37559) covalent geometry : angle 0.58798 (50831) hydrogen bonds : bond 0.05011 ( 2307) hydrogen bonds : angle 4.39938 ( 6762) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9686 Ramachandran restraints generated. 4843 Oldfield, 0 Emsley, 4843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9686 Ramachandran restraints generated. 4843 Oldfield, 0 Emsley, 4843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 3818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 213 time to evaluate : 1.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 ILE cc_start: 0.9377 (OUTLIER) cc_final: 0.9112 (tp) REVERT: E 280 MET cc_start: 0.9207 (tpp) cc_final: 0.8996 (ttp) REVERT: F 450 MET cc_start: 0.8731 (mtp) cc_final: 0.8379 (mtp) REVERT: I 44 MET cc_start: 0.8024 (mmp) cc_final: 0.7698 (mmm) REVERT: L 44 MET cc_start: 0.8201 (mmt) cc_final: 0.7845 (mmt) REVERT: M 44 MET cc_start: 0.7946 (mmm) cc_final: 0.7650 (mmm) REVERT: O 48 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8576 (mt) REVERT: O 49 GLN cc_start: 0.8367 (tt0) cc_final: 0.8051 (tp40) REVERT: P 23 THR cc_start: 0.8224 (OUTLIER) cc_final: 0.7845 (p) REVERT: P 43 GLU cc_start: 0.8166 (mp0) cc_final: 0.7931 (mp0) REVERT: P 49 GLN cc_start: 0.7881 (OUTLIER) cc_final: 0.7675 (mm-40) REVERT: P 64 MET cc_start: 0.8582 (mmm) cc_final: 0.7202 (mtm) REVERT: Q 1 MET cc_start: 0.7185 (OUTLIER) cc_final: 0.6447 (pmm) REVERT: R 64 MET cc_start: 0.7935 (mmp) cc_final: 0.7669 (mmp) REVERT: S 1 MET cc_start: 0.6126 (ppp) cc_final: 0.5818 (ppp) REVERT: X 84 ASN cc_start: 0.8914 (m-40) cc_final: 0.8500 (m-40) REVERT: a 85 MET cc_start: 0.7505 (OUTLIER) cc_final: 0.7275 (mpp) outliers start: 58 outliers final: 28 residues processed: 257 average time/residue: 0.2210 time to fit residues: 96.7894 Evaluate side-chains 227 residues out of total 3818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 193 time to evaluate : 1.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASN Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain C residue 237 TYR Chi-restraints excluded: chain C residue 490 LYS Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain G residue 65 HIS Chi-restraints excluded: chain G residue 106 TYR Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain H residue 128 GLN Chi-restraints excluded: chain I residue 65 ILE Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain L residue 65 ILE Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain P residue 23 THR Chi-restraints excluded: chain P residue 49 GLN Chi-restraints excluded: chain P residue 52 MET Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain W residue 138 VAL Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain Y residue 52 ARG Chi-restraints excluded: chain Y residue 145 HIS Chi-restraints excluded: chain a residue 85 MET Chi-restraints excluded: chain a residue 156 LEU Chi-restraints excluded: chain a residue 200 ILE Chi-restraints excluded: chain a residue 223 PHE Chi-restraints excluded: chain a residue 281 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 284 optimal weight: 9.9990 chunk 107 optimal weight: 0.5980 chunk 242 optimal weight: 0.8980 chunk 103 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 chunk 408 optimal weight: 9.9990 chunk 340 optimal weight: 5.9990 chunk 415 optimal weight: 10.0000 chunk 24 optimal weight: 0.8980 chunk 394 optimal weight: 40.0000 chunk 19 optimal weight: 0.8980 overall best weight: 1.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 458 GLN Y 58 HIS ** a 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.074325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.049634 restraints weight = 147309.100| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.47 r_work: 0.2989 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 37559 Z= 0.124 Angle : 0.539 13.555 50831 Z= 0.275 Chirality : 0.041 0.167 5929 Planarity : 0.004 0.059 6558 Dihedral : 7.182 178.747 5345 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.73 % Favored : 98.24 % Rotamer: Outliers : 1.28 % Allowed : 9.22 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.12), residues: 4843 helix: 2.07 (0.10), residues: 2685 sheet: 0.47 (0.21), residues: 559 loop : -0.04 (0.16), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 169 TYR 0.013 0.001 TYR E 252 PHE 0.025 0.001 PHE a 271 TRP 0.008 0.001 TRP X 26 HIS 0.007 0.001 HIS G 55 Details of bonding type rmsd covalent geometry : bond 0.00260 (37559) covalent geometry : angle 0.53887 (50831) hydrogen bonds : bond 0.04483 ( 2307) hydrogen bonds : angle 4.22475 ( 6762) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9686 Ramachandran restraints generated. 4843 Oldfield, 0 Emsley, 4843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9686 Ramachandran restraints generated. 4843 Oldfield, 0 Emsley, 4843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 3818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 199 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 ILE cc_start: 0.9334 (OUTLIER) cc_final: 0.9087 (tp) REVERT: B 123 ASP cc_start: 0.8454 (m-30) cc_final: 0.7842 (p0) REVERT: F 450 MET cc_start: 0.8684 (mtp) cc_final: 0.8355 (mtp) REVERT: I 44 MET cc_start: 0.7969 (mmp) cc_final: 0.7454 (mtt) REVERT: M 44 MET cc_start: 0.8023 (mmm) cc_final: 0.7706 (mmm) REVERT: O 48 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8088 (mt) REVERT: O 49 GLN cc_start: 0.8307 (tt0) cc_final: 0.7691 (tp40) REVERT: O 52 MET cc_start: 0.8446 (mtp) cc_final: 0.8229 (mtm) REVERT: P 64 MET cc_start: 0.8634 (mmm) cc_final: 0.7283 (mtm) REVERT: Q 44 MET cc_start: 0.8446 (mmp) cc_final: 0.8203 (mmp) REVERT: Q 60 ASP cc_start: 0.7608 (p0) cc_final: 0.7373 (p0) REVERT: R 64 MET cc_start: 0.8007 (mmp) cc_final: 0.7693 (mmp) REVERT: S 1 MET cc_start: 0.6192 (ppp) cc_final: 0.5902 (ppp) REVERT: Y 1 MET cc_start: 0.3574 (mmm) cc_final: 0.3079 (mmm) REVERT: Y 58 HIS cc_start: 0.8317 (OUTLIER) cc_final: 0.8018 (m-70) REVERT: a 85 MET cc_start: 0.7464 (OUTLIER) cc_final: 0.7234 (mpp) REVERT: a 244 MET cc_start: 0.3046 (tpt) cc_final: 0.2289 (mtt) outliers start: 49 outliers final: 32 residues processed: 236 average time/residue: 0.2026 time to fit residues: 81.8407 Evaluate side-chains 226 residues out of total 3818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 190 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain C residue 237 TYR Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain G residue 24 MET Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 65 HIS Chi-restraints excluded: chain G residue 106 TYR Chi-restraints excluded: chain H residue 128 GLN Chi-restraints excluded: chain I residue 65 ILE Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain O residue 27 PHE Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain P residue 52 MET Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain W residue 44 VAL Chi-restraints excluded: chain W residue 138 VAL Chi-restraints excluded: chain Y residue 52 ARG Chi-restraints excluded: chain Y residue 58 HIS Chi-restraints excluded: chain Y residue 145 HIS Chi-restraints excluded: chain a residue 85 MET Chi-restraints excluded: chain a residue 156 LEU Chi-restraints excluded: chain a residue 200 ILE Chi-restraints excluded: chain a residue 223 PHE Chi-restraints excluded: chain a residue 260 VAL Chi-restraints excluded: chain a residue 281 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 365 optimal weight: 0.8980 chunk 254 optimal weight: 4.9990 chunk 387 optimal weight: 6.9990 chunk 20 optimal weight: 9.9990 chunk 59 optimal weight: 9.9990 chunk 332 optimal weight: 20.0000 chunk 46 optimal weight: 9.9990 chunk 345 optimal weight: 10.0000 chunk 267 optimal weight: 5.9990 chunk 455 optimal weight: 20.0000 chunk 78 optimal weight: 0.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.073586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.048701 restraints weight = 147070.710| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.47 r_work: 0.2968 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 37559 Z= 0.176 Angle : 0.571 14.910 50831 Z= 0.290 Chirality : 0.042 0.366 5929 Planarity : 0.004 0.064 6558 Dihedral : 7.161 173.724 5345 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.06 % Favored : 97.91 % Rotamer: Outliers : 1.15 % Allowed : 9.62 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.12), residues: 4843 helix: 2.05 (0.10), residues: 2687 sheet: 0.40 (0.21), residues: 565 loop : -0.08 (0.16), residues: 1591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Y 52 TYR 0.015 0.001 TYR E 252 PHE 0.024 0.001 PHE a 271 TRP 0.008 0.001 TRP X 26 HIS 0.030 0.001 HIS Y 58 Details of bonding type rmsd covalent geometry : bond 0.00410 (37559) covalent geometry : angle 0.57062 (50831) hydrogen bonds : bond 0.04641 ( 2307) hydrogen bonds : angle 4.27086 ( 6762) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9686 Ramachandran restraints generated. 4843 Oldfield, 0 Emsley, 4843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9686 Ramachandran restraints generated. 4843 Oldfield, 0 Emsley, 4843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 3818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 195 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 ILE cc_start: 0.9358 (OUTLIER) cc_final: 0.9097 (tp) REVERT: B 123 ASP cc_start: 0.8459 (m-30) cc_final: 0.7819 (p0) REVERT: F 450 MET cc_start: 0.8683 (mtp) cc_final: 0.8343 (mtp) REVERT: H 23 MET cc_start: 0.1236 (tpp) cc_final: 0.0520 (tpp) REVERT: I 44 MET cc_start: 0.7993 (mmp) cc_final: 0.7542 (mtt) REVERT: J 44 MET cc_start: 0.7735 (mpp) cc_final: 0.7515 (pmm) REVERT: O 48 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8550 (mt) REVERT: O 49 GLN cc_start: 0.8305 (tt0) cc_final: 0.8062 (tp40) REVERT: P 23 THR cc_start: 0.8232 (OUTLIER) cc_final: 0.7842 (p) REVERT: Q 47 MET cc_start: 0.7562 (ttp) cc_final: 0.7253 (tmm) REVERT: R 64 MET cc_start: 0.8064 (mmp) cc_final: 0.7699 (mmp) REVERT: S 1 MET cc_start: 0.6239 (ppp) cc_final: 0.5969 (ppp) REVERT: Y 1 MET cc_start: 0.3510 (mmm) cc_final: 0.3042 (mmm) REVERT: a 85 MET cc_start: 0.7485 (OUTLIER) cc_final: 0.7268 (mpp) REVERT: a 271 PHE cc_start: 0.9090 (OUTLIER) cc_final: 0.8728 (t80) outliers start: 44 outliers final: 33 residues processed: 229 average time/residue: 0.1964 time to fit residues: 77.5218 Evaluate side-chains 229 residues out of total 3818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 191 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain C residue 237 TYR Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain G residue 24 MET Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 65 HIS Chi-restraints excluded: chain G residue 106 TYR Chi-restraints excluded: chain H residue 128 GLN Chi-restraints excluded: chain I residue 65 ILE Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain O residue 27 PHE Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain P residue 23 THR Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain W residue 44 VAL Chi-restraints excluded: chain W residue 138 VAL Chi-restraints excluded: chain Y residue 52 ARG Chi-restraints excluded: chain Y residue 58 HIS Chi-restraints excluded: chain Y residue 145 HIS Chi-restraints excluded: chain a residue 85 MET Chi-restraints excluded: chain a residue 156 LEU Chi-restraints excluded: chain a residue 200 ILE Chi-restraints excluded: chain a residue 223 PHE Chi-restraints excluded: chain a residue 260 VAL Chi-restraints excluded: chain a residue 271 PHE Chi-restraints excluded: chain a residue 281 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 409 optimal weight: 1.9990 chunk 447 optimal weight: 6.9990 chunk 369 optimal weight: 9.9990 chunk 363 optimal weight: 0.7980 chunk 36 optimal weight: 9.9990 chunk 344 optimal weight: 6.9990 chunk 370 optimal weight: 7.9990 chunk 450 optimal weight: 7.9990 chunk 52 optimal weight: 9.9990 chunk 91 optimal weight: 30.0000 chunk 264 optimal weight: 0.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 41 GLN Y 58 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.073486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.048725 restraints weight = 145967.992| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 2.45 r_work: 0.2970 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.4075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 37559 Z= 0.162 Angle : 0.564 13.450 50831 Z= 0.286 Chirality : 0.042 0.174 5929 Planarity : 0.004 0.064 6558 Dihedral : 7.050 167.139 5345 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.96 % Favored : 98.02 % Rotamer: Outliers : 1.21 % Allowed : 9.83 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: 1.73 (0.12), residues: 4843 helix: 2.07 (0.10), residues: 2688 sheet: 0.41 (0.21), residues: 565 loop : -0.11 (0.16), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG X 52 TYR 0.015 0.001 TYR E 252 PHE 0.020 0.001 PHE a 271 TRP 0.008 0.001 TRP a 27 HIS 0.007 0.001 HIS G 55 Details of bonding type rmsd covalent geometry : bond 0.00375 (37559) covalent geometry : angle 0.56369 (50831) hydrogen bonds : bond 0.04530 ( 2307) hydrogen bonds : angle 4.23829 ( 6762) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9686 Ramachandran restraints generated. 4843 Oldfield, 0 Emsley, 4843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9686 Ramachandran restraints generated. 4843 Oldfield, 0 Emsley, 4843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 3818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 194 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 ILE cc_start: 0.9349 (OUTLIER) cc_final: 0.9089 (tp) REVERT: B 123 ASP cc_start: 0.8411 (m-30) cc_final: 0.7815 (p0) REVERT: F 450 MET cc_start: 0.8689 (mtp) cc_final: 0.8358 (mtp) REVERT: H 23 MET cc_start: 0.1299 (tpp) cc_final: 0.0644 (tpp) REVERT: I 44 MET cc_start: 0.7918 (mmp) cc_final: 0.7611 (mtt) REVERT: J 44 MET cc_start: 0.7725 (mpp) cc_final: 0.7521 (pmm) REVERT: O 48 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8087 (mt) REVERT: O 49 GLN cc_start: 0.8296 (tt0) cc_final: 0.7646 (tp40) REVERT: O 52 MET cc_start: 0.8302 (mtp) cc_final: 0.7810 (mtm) REVERT: P 23 THR cc_start: 0.8234 (OUTLIER) cc_final: 0.7858 (p) REVERT: P 64 MET cc_start: 0.8653 (mmp) cc_final: 0.7080 (mtm) REVERT: R 64 MET cc_start: 0.8151 (mmp) cc_final: 0.7780 (mmp) REVERT: S 1 MET cc_start: 0.6211 (ppp) cc_final: 0.5955 (ppp) REVERT: Y 58 HIS cc_start: 0.8335 (OUTLIER) cc_final: 0.8028 (m-70) REVERT: a 39 MET cc_start: 0.4538 (OUTLIER) cc_final: 0.2064 (ptp) REVERT: a 85 MET cc_start: 0.7494 (OUTLIER) cc_final: 0.7278 (mpp) REVERT: a 271 PHE cc_start: 0.9055 (OUTLIER) cc_final: 0.8569 (t80) REVERT: a 283 MET cc_start: 0.3643 (mmp) cc_final: 0.2049 (ppp) outliers start: 46 outliers final: 33 residues processed: 227 average time/residue: 0.2078 time to fit residues: 80.6541 Evaluate side-chains 229 residues out of total 3818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 189 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain C residue 237 TYR Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain G residue 24 MET Chi-restraints excluded: chain G residue 65 HIS Chi-restraints excluded: chain G residue 106 TYR Chi-restraints excluded: chain H residue 128 GLN Chi-restraints excluded: chain I residue 65 ILE Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain O residue 27 PHE Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain P residue 23 THR Chi-restraints excluded: chain P residue 52 MET Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain W residue 44 VAL Chi-restraints excluded: chain W residue 138 VAL Chi-restraints excluded: chain Y residue 52 ARG Chi-restraints excluded: chain Y residue 58 HIS Chi-restraints excluded: chain Y residue 145 HIS Chi-restraints excluded: chain a residue 39 MET Chi-restraints excluded: chain a residue 85 MET Chi-restraints excluded: chain a residue 156 LEU Chi-restraints excluded: chain a residue 200 ILE Chi-restraints excluded: chain a residue 223 PHE Chi-restraints excluded: chain a residue 260 VAL Chi-restraints excluded: chain a residue 271 PHE Chi-restraints excluded: chain a residue 281 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 306 optimal weight: 5.9990 chunk 142 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 130 optimal weight: 7.9990 chunk 135 optimal weight: 3.9990 chunk 367 optimal weight: 20.0000 chunk 311 optimal weight: 5.9990 chunk 458 optimal weight: 10.0000 chunk 139 optimal weight: 6.9990 chunk 188 optimal weight: 50.0000 chunk 275 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 58 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.072988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.048108 restraints weight = 146691.128| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 2.45 r_work: 0.2948 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 37559 Z= 0.215 Angle : 0.603 12.936 50831 Z= 0.307 Chirality : 0.043 0.427 5929 Planarity : 0.004 0.089 6558 Dihedral : 7.093 166.328 5345 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.29 % Favored : 97.69 % Rotamer: Outliers : 1.21 % Allowed : 9.96 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: 1.60 (0.12), residues: 4843 helix: 1.96 (0.10), residues: 2691 sheet: 0.36 (0.21), residues: 564 loop : -0.19 (0.16), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.035 0.001 ARG X 52 TYR 0.016 0.001 TYR C 237 PHE 0.022 0.001 PHE a 271 TRP 0.009 0.001 TRP a 27 HIS 0.032 0.001 HIS Y 58 Details of bonding type rmsd covalent geometry : bond 0.00509 (37559) covalent geometry : angle 0.60264 (50831) hydrogen bonds : bond 0.04800 ( 2307) hydrogen bonds : angle 4.32830 ( 6762) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9686 Ramachandran restraints generated. 4843 Oldfield, 0 Emsley, 4843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9686 Ramachandran restraints generated. 4843 Oldfield, 0 Emsley, 4843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 3818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 195 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 169 ILE cc_start: 0.9360 (OUTLIER) cc_final: 0.9095 (tp) REVERT: F 91 ARG cc_start: 0.9097 (OUTLIER) cc_final: 0.8496 (mmm160) REVERT: F 450 MET cc_start: 0.8733 (mtp) cc_final: 0.8519 (mtp) REVERT: I 34 PHE cc_start: 0.8618 (t80) cc_final: 0.8271 (t80) REVERT: O 48 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8055 (mt) REVERT: O 49 GLN cc_start: 0.8310 (tt0) cc_final: 0.7660 (tp40) REVERT: O 52 MET cc_start: 0.8292 (mtp) cc_final: 0.7793 (mtm) REVERT: P 23 THR cc_start: 0.8249 (OUTLIER) cc_final: 0.7861 (p) REVERT: P 64 MET cc_start: 0.8653 (mmp) cc_final: 0.7064 (mtm) REVERT: R 64 MET cc_start: 0.8202 (mmp) cc_final: 0.7816 (mmp) REVERT: S 1 MET cc_start: 0.6168 (ppp) cc_final: 0.5943 (ppp) REVERT: a 39 MET cc_start: 0.4653 (mpp) cc_final: 0.2059 (ptp) REVERT: a 85 MET cc_start: 0.7555 (OUTLIER) cc_final: 0.7335 (mpp) REVERT: a 271 PHE cc_start: 0.9084 (OUTLIER) cc_final: 0.8639 (t80) outliers start: 46 outliers final: 33 residues processed: 229 average time/residue: 0.2081 time to fit residues: 81.2384 Evaluate side-chains 227 residues out of total 3818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 188 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain C residue 237 TYR Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain F residue 91 ARG Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain G residue 24 MET Chi-restraints excluded: chain G residue 65 HIS Chi-restraints excluded: chain G residue 106 TYR Chi-restraints excluded: chain H residue 128 GLN Chi-restraints excluded: chain I residue 65 ILE Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain O residue 27 PHE Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain P residue 23 THR Chi-restraints excluded: chain P residue 52 MET Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain R residue 60 ASP Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain W residue 44 VAL Chi-restraints excluded: chain W residue 138 VAL Chi-restraints excluded: chain Y residue 145 HIS Chi-restraints excluded: chain a residue 85 MET Chi-restraints excluded: chain a residue 156 LEU Chi-restraints excluded: chain a residue 200 ILE Chi-restraints excluded: chain a residue 223 PHE Chi-restraints excluded: chain a residue 260 VAL Chi-restraints excluded: chain a residue 271 PHE Chi-restraints excluded: chain a residue 281 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 445 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 281 optimal weight: 3.9990 chunk 457 optimal weight: 0.0870 chunk 70 optimal weight: 1.9990 chunk 414 optimal weight: 9.9990 chunk 158 optimal weight: 0.0050 chunk 297 optimal weight: 7.9990 chunk 163 optimal weight: 9.9990 chunk 272 optimal weight: 5.9990 chunk 235 optimal weight: 0.9990 overall best weight: 1.0178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 175 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.074035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.049432 restraints weight = 146764.386| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.47 r_work: 0.2994 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.4288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 37559 Z= 0.111 Angle : 0.555 11.998 50831 Z= 0.280 Chirality : 0.041 0.165 5929 Planarity : 0.004 0.066 6558 Dihedral : 6.756 166.457 5345 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.71 % Favored : 98.27 % Rotamer: Outliers : 0.92 % Allowed : 10.17 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: 1.81 (0.12), residues: 4843 helix: 2.11 (0.10), residues: 2715 sheet: 0.44 (0.21), residues: 554 loop : -0.07 (0.16), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG Y 52 TYR 0.014 0.001 TYR H 115 PHE 0.020 0.001 PHE a 271 TRP 0.014 0.001 TRP a 114 HIS 0.006 0.001 HIS G 55 Details of bonding type rmsd covalent geometry : bond 0.00225 (37559) covalent geometry : angle 0.55466 (50831) hydrogen bonds : bond 0.04178 ( 2307) hydrogen bonds : angle 4.14695 ( 6762) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9686 Ramachandran restraints generated. 4843 Oldfield, 0 Emsley, 4843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9686 Ramachandran restraints generated. 4843 Oldfield, 0 Emsley, 4843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 3818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 196 time to evaluate : 1.454 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 169 ILE cc_start: 0.9334 (OUTLIER) cc_final: 0.9065 (tp) REVERT: B 123 ASP cc_start: 0.8394 (m-30) cc_final: 0.7857 (p0) REVERT: F 450 MET cc_start: 0.8697 (mtp) cc_final: 0.8385 (mtp) REVERT: H 23 MET cc_start: 0.1144 (tpp) cc_final: 0.0478 (tpp) REVERT: O 48 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.7996 (mt) REVERT: O 49 GLN cc_start: 0.8282 (tt0) cc_final: 0.7583 (mt0) REVERT: O 52 MET cc_start: 0.8247 (mtp) cc_final: 0.7797 (mtm) REVERT: P 64 MET cc_start: 0.8600 (mmp) cc_final: 0.7028 (mtm) REVERT: R 64 MET cc_start: 0.8270 (mmp) cc_final: 0.7879 (mmp) REVERT: S 1 MET cc_start: 0.6178 (ppp) cc_final: 0.5951 (ppp) REVERT: a 39 MET cc_start: 0.4346 (mpp) cc_final: 0.1766 (ptp) REVERT: a 85 MET cc_start: 0.7496 (OUTLIER) cc_final: 0.7272 (mpp) REVERT: a 271 PHE cc_start: 0.9027 (OUTLIER) cc_final: 0.8540 (t80) REVERT: a 283 MET cc_start: 0.3574 (mmp) cc_final: 0.1978 (ttt) outliers start: 35 outliers final: 26 residues processed: 223 average time/residue: 0.2032 time to fit residues: 77.3016 Evaluate side-chains 218 residues out of total 3818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 188 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain C residue 237 TYR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 142 CYS Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain G residue 24 MET Chi-restraints excluded: chain G residue 65 HIS Chi-restraints excluded: chain H residue 128 GLN Chi-restraints excluded: chain I residue 65 ILE Chi-restraints excluded: chain O residue 27 PHE Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain R residue 60 ASP Chi-restraints excluded: chain W residue 44 VAL Chi-restraints excluded: chain W residue 138 VAL Chi-restraints excluded: chain Y residue 145 HIS Chi-restraints excluded: chain a residue 85 MET Chi-restraints excluded: chain a residue 156 LEU Chi-restraints excluded: chain a residue 200 ILE Chi-restraints excluded: chain a residue 223 PHE Chi-restraints excluded: chain a residue 260 VAL Chi-restraints excluded: chain a residue 271 PHE Chi-restraints excluded: chain a residue 281 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 333 optimal weight: 20.0000 chunk 133 optimal weight: 3.9990 chunk 185 optimal weight: 4.9990 chunk 340 optimal weight: 5.9990 chunk 423 optimal weight: 0.4980 chunk 253 optimal weight: 9.9990 chunk 134 optimal weight: 4.9990 chunk 415 optimal weight: 6.9990 chunk 313 optimal weight: 20.0000 chunk 342 optimal weight: 30.0000 chunk 456 optimal weight: 20.0000 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 49 GLN R 41 GLN Y 58 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.073251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.048440 restraints weight = 146782.252| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.46 r_work: 0.2960 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.4369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 37559 Z= 0.181 Angle : 0.589 13.947 50831 Z= 0.297 Chirality : 0.042 0.178 5929 Planarity : 0.004 0.062 6558 Dihedral : 6.790 166.724 5345 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.21 % Favored : 97.77 % Rotamer: Outliers : 0.92 % Allowed : 10.32 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.12), residues: 4843 helix: 2.09 (0.10), residues: 2691 sheet: 0.38 (0.21), residues: 564 loop : -0.17 (0.16), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.000 ARG X 52 TYR 0.015 0.001 TYR E 252 PHE 0.025 0.001 PHE a 271 TRP 0.009 0.001 TRP Y 26 HIS 0.006 0.001 HIS G 55 Details of bonding type rmsd covalent geometry : bond 0.00426 (37559) covalent geometry : angle 0.58911 (50831) hydrogen bonds : bond 0.04491 ( 2307) hydrogen bonds : angle 4.22657 ( 6762) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11376.13 seconds wall clock time: 194 minutes 22.79 seconds (11662.79 seconds total)