Starting phenix.real_space_refine on Sat Feb 7 22:23:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o1a_70000/02_2026/9o1a_70000_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o1a_70000/02_2026/9o1a_70000.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9o1a_70000/02_2026/9o1a_70000.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o1a_70000/02_2026/9o1a_70000.map" model { file = "/net/cci-nas-00/data/ceres_data/9o1a_70000/02_2026/9o1a_70000_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o1a_70000/02_2026/9o1a_70000_neut.cif" } resolution = 2.77 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 15 5.49 5 Mg 5 5.21 5 S 159 5.16 5 C 23585 2.51 5 N 6287 2.21 5 O 6999 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 220 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 37051 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 3823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3823 Classifications: {'peptide': 506} Link IDs: {'PTRANS': 16, 'TRANS': 489} Chain: "B" Number of atoms: 3872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3872 Classifications: {'peptide': 512} Link IDs: {'PTRANS': 17, 'TRANS': 494} Chain: "C" 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: "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: 2132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2132 Classifications: {'peptide': 276} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 268} Chain breaks: 1 Chain: "H" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 933 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "I" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 594 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain: "J" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 594 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain: "L" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 594 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain: "M" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 594 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain: "N" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 594 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain: "O" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 594 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain: "P" Number of atoms: 591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 591 Classifications: {'peptide': 83} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "Q" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 594 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain: "R" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 594 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain: "S" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 594 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain: "W" Number of atoms: 1345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1345 Classifications: {'peptide': 177} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 172} Chain: "X" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1174 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 2, 'TRANS': 151} Chain: "Y" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1174 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 2, 'TRANS': 151} Chain: "a" Number of atoms: 2243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2243 Classifications: {'peptide': 286} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 275} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.71, per 1000 atoms: 0.24 Number of scatterers: 37051 At special positions: 0 Unit cell: (123.67, 136.95, 241.53, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 159 16.00 P 15 15.00 Mg 5 11.99 O 6999 8.00 N 6287 7.00 C 23585 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.20 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN a 301 " pdb="ZN ZN a 301 " - pdb=" ND1 HIS a 186 " 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8800 Finding SS restraints... Secondary structure from input PDB file: 216 helices and 27 sheets defined 63.0% alpha, 13.4% 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 10 through 18 Processing helix chain 'A' and resid 57 through 59 No H-bonds generated for 'chain 'A' and resid 57 through 59' Processing helix chain 'A' and resid 101 through 105 Processing helix chain 'A' and resid 136 through 140 Processing helix chain 'A' and resid 151 through 158 Processing helix chain 'A' and resid 175 through 186 Processing helix chain 'A' and resid 202 through 216 Processing helix chain 'A' and resid 218 through 220 No H-bonds generated for 'chain 'A' and resid 218 through 220' Processing helix chain 'A' and resid 232 through 253 Proline residue: A 240 - end of helix removed outlier: 3.513A pdb=" N TYR A 249 " --> pdb=" O THR A 245 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N PHE A 250 " --> pdb=" O MET A 246 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG A 251 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 3.658A 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: 3.702A pdb=" N HIS A 295 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 3.614A 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 Processing helix chain 'A' and resid 384 through 405 removed outlier: 4.067A pdb=" N GLY A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N GLY A 393 " --> pdb=" O LYS A 389 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ILE A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 414 removed outlier: 4.326A pdb=" N GLN A 409 " --> pdb=" O ALA A 406 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA A 411 " --> pdb=" O ALA A 408 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N SER A 412 " --> pdb=" O GLN A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 432 Processing helix chain 'A' and resid 441 through 454 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: 3.679A pdb=" N ARG A 478 " --> pdb=" O SER A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 488 Processing helix chain 'A' and resid 494 through 512 removed outlier: 3.515A pdb=" N THR A 511 " --> pdb=" O LYS A 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 19 Processing helix chain 'B' and resid 21 through 25 removed outlier: 3.680A pdb=" N SER B 24 " --> pdb=" O ASP B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 105 Processing helix chain 'B' and resid 136 through 140 removed outlier: 3.547A pdb=" N ARG B 140 " --> pdb=" O VAL B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 158 Processing helix chain 'B' and resid 175 through 186 Processing helix chain 'B' and resid 202 through 216 Processing helix chain 'B' and resid 218 through 220 No H-bonds generated for 'chain 'B' and resid 218 through 220' Processing helix chain 'B' and resid 232 through 253 Proline residue: B 240 - end of helix removed outlier: 3.609A pdb=" N TYR B 249 " --> pdb=" O THR B 245 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N PHE B 250 " --> pdb=" O MET B 246 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG B 251 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG B 253 " --> pdb=" O TYR B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 278 Processing helix chain 'B' and resid 283 through 287 Processing helix chain 'B' and resid 288 through 289 No H-bonds generated for 'chain 'B' and resid 288 through 289' Processing helix chain 'B' and resid 290 through 300 removed outlier: 3.700A pdb=" N HIS B 295 " --> pdb=" O VAL B 291 " (cutoff:3.500A) removed outlier: 3.569A 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 350 Processing helix chain 'B' and resid 357 through 363 Processing helix chain 'B' and resid 378 through 383 removed outlier: 3.558A pdb=" N ALA B 381 " --> pdb=" O VAL B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 392 Processing helix chain 'B' and resid 393 through 408 Processing helix chain 'B' and resid 415 through 432 Processing helix chain 'B' and resid 441 through 454 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 490 removed outlier: 4.218A pdb=" N LYS B 490 " --> pdb=" O LYS B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 512 Processing helix chain 'C' and resid 6 through 11 removed outlier: 3.707A pdb=" N SER C 10 " --> pdb=" O PRO C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 20 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: 3.593A 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 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: 4.534A pdb=" N PHE C 250 " --> pdb=" O MET C 246 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG C 251 " --> pdb=" O GLY C 247 " (cutoff:3.500A) removed outlier: 3.651A 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: 3.729A pdb=" N HIS C 295 " --> pdb=" O VAL C 291 " (cutoff:3.500A) removed outlier: 3.626A 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 334 through 337 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: 3.802A pdb=" N ALA C 381 " --> pdb=" O VAL C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 391 Processing helix chain 'C' and resid 391 through 405 removed outlier: 3.833A pdb=" N ARG C 395 " --> pdb=" O SER C 391 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N THR C 396 " --> pdb=" O GLY C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 414 removed outlier: 4.090A pdb=" N GLN C 409 " --> pdb=" O ALA C 406 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALA C 411 " --> pdb=" O ALA C 408 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N SER C 412 " --> pdb=" O GLN C 409 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU C 414 " --> pdb=" O ALA C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 432 Processing helix chain 'C' and resid 441 through 454 Processing helix chain 'C' and resid 461 through 463 No H-bonds generated for 'chain 'C' and resid 461 through 463' Processing helix chain 'C' and resid 464 through 480 removed outlier: 3.587A pdb=" N ARG C 478 " --> pdb=" O SER C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 491 removed outlier: 4.478A pdb=" N LYS C 490 " --> pdb=" O LYS C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 512 Processing helix chain 'D' and resid 85 through 89 Processing helix chain 'D' and resid 120 through 124 removed outlier: 3.603A pdb=" N GLN D 124 " --> pdb=" O TYR D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 142 Processing helix chain 'D' and resid 159 through 172 Processing helix chain 'D' and resid 187 through 201 Processing helix chain 'D' and resid 203 through 205 No H-bonds generated for 'chain 'D' and resid 203 through 205' Processing helix chain 'D' and resid 217 through 238 removed outlier: 3.560A pdb=" N ARG D 221 " --> pdb=" O PRO D 217 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N ALA D 225 " --> pdb=" O ARG D 221 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N LEU D 226 " --> pdb=" O LEU D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 261 removed outlier: 3.866A pdb=" N THR D 253 " --> pdb=" O ILE D 249 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY D 256 " --> pdb=" O TYR D 252 " (cutoff:3.500A) removed outlier: 4.547A 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: 3.655A 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 350 through 355 Processing helix chain 'D' and resid 355 through 383 removed outlier: 3.772A pdb=" N GLU D 374 " --> pdb=" O GLN D 370 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU D 375 " --> pdb=" O ARG D 371 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASP D 377 " --> pdb=" O LYS D 373 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N ILE D 378 " --> pdb=" O GLU D 374 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE D 381 " --> pdb=" O ASP D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 387 Processing helix chain 'D' and resid 388 through 405 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: 3.670A pdb=" N PHE D 448 " --> pdb=" O GLU D 445 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR D 449 " --> pdb=" O GLN D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 462 removed outlier: 3.810A pdb=" N ALA D 457 " --> pdb=" O GLY D 453 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS D 462 " --> pdb=" O VAL D 458 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 89 Processing helix chain 'E' and resid 120 through 124 Processing helix chain 'E' and resid 135 through 142 Processing helix chain 'E' and resid 159 through 172 Processing helix chain 'E' and resid 187 through 201 removed outlier: 3.604A pdb=" N GLY E 191 " --> pdb=" O ARG E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 205 No H-bonds generated for 'chain 'E' and resid 203 through 205' Processing helix chain 'E' and resid 217 through 238 removed outlier: 5.182A pdb=" N ALA E 225 " --> pdb=" O ARG E 221 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N LEU E 226 " --> pdb=" O LEU E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 261 removed outlier: 3.869A pdb=" N THR E 253 " --> pdb=" O ILE E 249 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY E 256 " --> pdb=" O TYR E 252 " (cutoff:3.500A) removed outlier: 4.494A 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: 3.651A 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 Processing helix chain 'E' and resid 350 through 355 Processing helix chain 'E' and resid 355 through 375 removed outlier: 3.682A pdb=" N LEU E 375 " --> pdb=" O ARG E 371 " (cutoff:3.500A) Processing helix chain 'E' and resid 375 through 383 Processing helix chain 'E' and resid 384 through 387 Processing helix chain 'E' and resid 388 through 405 Processing helix chain 'E' and resid 412 through 417 removed outlier: 3.741A 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: 3.545A pdb=" N TYR E 449 " --> pdb=" O GLN E 446 " (cutoff:3.500A) Processing helix chain 'E' and resid 453 through 461 Processing helix chain 'F' and resid 85 through 89 Processing helix chain 'F' and resid 120 through 124 removed outlier: 3.532A pdb=" N GLN F 124 " --> pdb=" O TYR F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 142 Processing helix chain 'F' and resid 159 through 175 removed outlier: 3.533A 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: 3.528A pdb=" N ARG F 221 " --> pdb=" O PRO F 217 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ALA F 225 " --> pdb=" O ARG F 221 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N LEU F 226 " --> pdb=" O LEU F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 263 removed outlier: 3.775A pdb=" N TYR F 252 " --> pdb=" O ASN F 248 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 272 removed outlier: 3.527A pdb=" N TYR F 272 " --> pdb=" O ALA F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 275 through 285 removed outlier: 3.533A 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: 3.833A 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 383 removed outlier: 3.659A pdb=" N ASP F 377 " --> pdb=" O LYS F 373 " (cutoff:3.500A) Processing helix chain 'F' and resid 384 through 387 Processing helix chain 'F' and resid 388 through 405 Processing helix chain 'F' and resid 409 through 411 No H-bonds generated for 'chain 'F' and resid 409 through 411' Processing helix chain 'F' and resid 412 through 417 Processing helix chain 'F' and resid 424 through 438 Processing helix chain 'F' and resid 444 through 449 removed outlier: 3.563A pdb=" N TYR F 449 " --> pdb=" O GLN F 446 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 461 Processing helix chain 'G' and resid 3 through 60 removed outlier: 3.523A pdb=" N ARG G 8 " --> pdb=" O ALA G 4 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE G 20 " --> pdb=" O SER G 16 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYS G 26 " --> pdb=" O ASN G 22 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY G 42 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG G 43 " --> pdb=" O MET G 39 " (cutoff:3.500A) Proline residue: G 44 - end of helix removed outlier: 3.742A pdb=" N ARG G 48 " --> pdb=" O PRO G 44 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 69 removed outlier: 3.580A pdb=" N VAL G 69 " --> pdb=" O PRO G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 109 removed outlier: 3.519A pdb=" N LEU G 95 " --> pdb=" O LEU G 91 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLY G 105 " --> pdb=" O LYS G 101 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N TYR G 106 " --> pdb=" O ASP G 102 " (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: 3.559A pdb=" N MET G 156 " --> pdb=" O SER G 152 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR G 160 " --> pdb=" O MET G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 210 through 286 removed outlier: 4.438A pdb=" N VAL G 220 " --> pdb=" O ASP G 216 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA G 285 " --> pdb=" O GLY G 281 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 101 removed outlier: 4.181A pdb=" N ALA H 93 " --> pdb=" O ASP H 89 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA H 94 " --> pdb=" O LEU H 90 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA H 95 " --> pdb=" O ASP H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 129 removed outlier: 3.798A pdb=" N ALA H 117 " --> pdb=" O PHE H 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 41 removed outlier: 3.536A pdb=" N THR I 8 " --> pdb=" O VAL I 4 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE I 10 " --> pdb=" O GLY I 6 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY I 19 " --> pdb=" O LEU I 15 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS I 33 " --> pdb=" O LEU I 29 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU I 36 " --> pdb=" O GLY I 32 " (cutoff:3.500A) Processing helix chain 'I' and resid 44 through 76 removed outlier: 3.660A pdb=" N GLY I 57 " --> pdb=" O PHE I 53 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU I 58 " --> pdb=" O ILE I 54 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA I 61 " --> pdb=" O GLY I 57 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N VAL I 62 " --> pdb=" O LEU I 58 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N THR I 63 " --> pdb=" O LEU I 59 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 83 Processing helix chain 'J' and resid 2 through 41 removed outlier: 3.676A pdb=" N ALA J 11 " --> pdb=" O LEU J 7 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLY J 19 " --> pdb=" O LEU J 15 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS J 33 " --> pdb=" O LEU J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 44 through 60 removed outlier: 3.580A pdb=" N VAL J 50 " --> pdb=" O PRO J 46 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU J 58 " --> pdb=" O ILE J 54 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 76 removed outlier: 3.574A pdb=" N ILE J 65 " --> pdb=" O ALA J 61 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU J 71 " --> pdb=" O VAL J 67 " (cutoff:3.500A) Processing helix chain 'J' and resid 79 through 83 Processing helix chain 'L' and resid 2 through 41 removed outlier: 3.622A pdb=" N ILE L 10 " --> pdb=" O GLY L 6 " (cutoff:3.500A) Processing helix chain 'L' and resid 44 through 76 removed outlier: 3.599A pdb=" N VAL L 50 " --> pdb=" O PRO L 46 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU L 58 " --> pdb=" O ILE L 54 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N VAL L 62 " --> pdb=" O LEU L 58 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N THR L 63 " --> pdb=" O LEU L 59 " (cutoff:3.500A) Processing helix chain 'L' and resid 77 through 82 removed outlier: 4.043A pdb=" N GLY L 81 " --> pdb=" O ASN L 77 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 41 Processing helix chain 'M' and resid 44 through 76 removed outlier: 3.544A pdb=" N VAL M 50 " --> pdb=" O PRO M 46 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU M 58 " --> pdb=" O ILE M 54 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N VAL M 62 " --> pdb=" O LEU M 58 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N THR M 63 " --> pdb=" O LEU M 59 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 83 removed outlier: 3.752A pdb=" N ILE M 83 " --> pdb=" O VAL M 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 41 removed outlier: 3.979A pdb=" N GLY N 19 " --> pdb=" O LEU N 15 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA N 24 " --> pdb=" O ALA N 20 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 60 removed outlier: 4.042A pdb=" N LEU N 58 " --> pdb=" O ILE N 54 " (cutoff:3.500A) Processing helix chain 'N' and resid 60 through 75 removed outlier: 3.700A pdb=" N MET N 64 " --> pdb=" O ASP N 60 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE N 65 " --> pdb=" O ALA N 61 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE N 75 " --> pdb=" O LEU N 71 " (cutoff:3.500A) Processing helix chain 'N' and resid 77 through 82 removed outlier: 4.158A pdb=" N GLY N 81 " --> pdb=" O ASN N 77 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLN N 82 " --> pdb=" O PRO N 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 77 through 82' Processing helix chain 'O' and resid 2 through 41 removed outlier: 3.601A pdb=" N ILE O 10 " --> pdb=" O GLY O 6 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY O 19 " --> pdb=" O LEU O 15 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS O 33 " --> pdb=" O LEU O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 44 through 75 removed outlier: 3.866A pdb=" N VAL O 50 " --> pdb=" O PRO O 46 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU O 58 " --> pdb=" O ILE O 54 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N VAL O 62 " --> pdb=" O LEU O 58 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N THR O 63 " --> pdb=" O LEU O 59 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU O 71 " --> pdb=" O VAL O 67 " (cutoff:3.500A) Processing helix chain 'O' and resid 77 through 83 removed outlier: 4.472A pdb=" N GLY O 81 " --> pdb=" O ASN O 77 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLN O 82 " --> pdb=" O PRO O 78 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE O 83 " --> pdb=" O PHE O 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 77 through 83' Processing helix chain 'P' and resid 2 through 41 removed outlier: 3.511A pdb=" N ILE P 10 " --> pdb=" O GLY P 6 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLY P 19 " --> pdb=" O LEU P 15 " (cutoff:3.500A) Processing helix chain 'P' and resid 44 through 60 removed outlier: 3.586A pdb=" N VAL P 50 " --> pdb=" O PRO P 46 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU P 58 " --> pdb=" O ILE P 54 " (cutoff:3.500A) Processing helix chain 'P' and resid 60 through 76 Processing helix chain 'Q' and resid 2 through 41 removed outlier: 3.532A pdb=" N ILE Q 10 " --> pdb=" O GLY Q 6 " (cutoff:3.500A) Processing helix chain 'Q' and resid 44 through 60 removed outlier: 3.602A pdb=" N VAL Q 50 " --> pdb=" O PRO Q 46 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU Q 58 " --> pdb=" O ILE Q 54 " (cutoff:3.500A) Processing helix chain 'Q' and resid 60 through 76 Processing helix chain 'Q' and resid 79 through 83 removed outlier: 3.793A pdb=" N ILE Q 83 " --> pdb=" O VAL Q 80 " (cutoff:3.500A) Processing helix chain 'R' and resid 2 through 41 removed outlier: 3.638A pdb=" N ILE R 10 " --> pdb=" O GLY R 6 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY R 19 " --> pdb=" O LEU R 15 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS R 33 " --> pdb=" O LEU R 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 44 through 60 removed outlier: 3.831A pdb=" N VAL R 50 " --> pdb=" O PRO R 46 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU R 58 " --> pdb=" O ILE R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 76 removed outlier: 3.669A pdb=" N ILE R 65 " --> pdb=" O ALA R 61 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 41 removed outlier: 3.711A pdb=" N ILE S 10 " --> pdb=" O GLY S 6 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS S 33 " --> pdb=" O LEU S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 44 through 76 removed outlier: 3.726A pdb=" N LEU S 58 " --> pdb=" O ILE S 54 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N VAL S 62 " --> pdb=" O LEU S 58 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N THR S 63 " --> pdb=" O LEU S 59 " (cutoff:3.500A) Processing helix chain 'S' and resid 79 through 83 Processing helix chain 'W' and resid 3 through 22 Proline residue: W 10 - end of helix Processing helix chain 'W' and resid 24 through 40 Processing helix chain 'W' and resid 43 through 48 Processing helix chain 'W' and resid 54 through 67 Processing helix chain 'W' and resid 68 through 70 No H-bonds generated for 'chain 'W' and resid 68 through 70' Processing helix chain 'W' and resid 71 through 84 Processing helix chain 'W' and resid 86 through 88 No H-bonds generated for 'chain 'W' and resid 86 through 88' Processing helix chain 'W' and resid 89 through 106 Processing helix chain 'W' and resid 119 through 135 Processing helix chain 'W' and resid 164 through 178 removed outlier: 3.744A pdb=" N SER W 178 " --> pdb=" O GLU W 174 " (cutoff:3.500A) Processing helix chain 'X' and resid 6 through 24 removed outlier: 3.579A pdb=" N PHE X 15 " --> pdb=" O SER X 11 " (cutoff:3.500A) Processing helix chain 'X' and resid 25 through 120 removed outlier: 3.828A pdb=" N VAL X 29 " --> pdb=" O VAL X 25 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG X 36 " --> pdb=" O ALA X 32 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN X 37 " --> pdb=" O LEU X 33 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN X 114 " --> pdb=" O GLU X 110 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER X 115 " --> pdb=" O GLN X 111 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP X 118 " --> pdb=" O ASN X 114 " (cutoff:3.500A) Processing helix chain 'X' and resid 123 through 136 removed outlier: 3.634A pdb=" N LEU X 136 " --> pdb=" O ALA X 132 " (cutoff:3.500A) Processing helix chain 'X' and resid 139 through 154 removed outlier: 3.943A pdb=" N ALA X 144 " --> pdb=" O ILE X 140 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N HIS X 145 " --> pdb=" O ASP X 141 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU X 146 " --> pdb=" O ALA X 142 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N LEU X 148 " --> pdb=" O ALA X 144 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N VAL X 149 " --> pdb=" O HIS X 145 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N LEU X 152 " --> pdb=" O LEU X 148 " (cutoff:3.500A) Processing helix chain 'Y' and resid 2 through 25 removed outlier: 3.503A pdb=" N PHE Y 20 " --> pdb=" O ILE Y 16 " (cutoff:3.500A) Processing helix chain 'Y' and resid 25 through 124 removed outlier: 3.844A pdb=" N VAL Y 29 " --> pdb=" O VAL Y 25 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA Y 41 " --> pdb=" O GLN Y 37 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA Y 46 " --> pdb=" O ASP Y 42 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA Y 47 " --> pdb=" O GLY Y 43 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ALA Y 51 " --> pdb=" O ALA Y 47 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ARG Y 52 " --> pdb=" O ASN Y 48 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLU Y 55 " --> pdb=" O ALA Y 51 " (cutoff:3.500A) Processing helix chain 'Y' and resid 125 through 129 Processing helix chain 'Y' and resid 130 through 137 removed outlier: 4.144A pdb=" N LYS Y 134 " --> pdb=" O THR Y 130 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY Y 137 " --> pdb=" O GLU Y 133 " (cutoff:3.500A) Processing helix chain 'Y' and resid 139 through 153 Processing helix chain 'a' and resid 5 through 14 removed outlier: 3.539A pdb=" N LEU a 14 " --> pdb=" O ILE a 10 " (cutoff:3.500A) Processing helix chain 'a' and resid 32 through 39 removed outlier: 3.747A pdb=" N MET a 39 " --> pdb=" O GLN a 35 " (cutoff:3.500A) Processing helix chain 'a' and resid 46 through 66 removed outlier: 3.515A pdb=" N VAL a 53 " --> pdb=" O LEU a 49 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU a 54 " --> pdb=" O GLY a 50 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA a 66 " --> pdb=" O ILE a 62 " (cutoff:3.500A) Processing helix chain 'a' and resid 76 through 95 removed outlier: 3.691A pdb=" N PHE a 81 " --> pdb=" O GLY a 77 " (cutoff:3.500A) Processing helix chain 'a' and resid 103 through 121 removed outlier: 3.791A pdb=" N ILE a 121 " --> pdb=" O LEU a 117 " (cutoff:3.500A) Processing helix chain 'a' and resid 122 through 124 No H-bonds generated for 'chain 'a' and resid 122 through 124' Processing helix chain 'a' and resid 127 through 138 Processing helix chain 'a' and resid 147 through 150 Processing helix chain 'a' and resid 151 through 185 removed outlier: 3.567A pdb=" N VAL a 162 " --> pdb=" O LEU a 158 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ILE a 176 " --> pdb=" O LYS a 172 " (cutoff:3.500A) removed outlier: 8.871A pdb=" N GLY a 177 " --> pdb=" O VAL a 173 " (cutoff:3.500A) Processing helix chain 'a' and resid 192 through 242 Proline residue: a 201 - end of helix removed outlier: 3.557A pdb=" N THR a 210 " --> pdb=" O LEU a 206 " (cutoff:3.500A) Proline residue: a 215 - end of helix removed outlier: 3.619A pdb=" N LEU a 222 " --> pdb=" O LEU a 218 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE a 233 " --> pdb=" O GLY a 229 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N MET a 239 " --> pdb=" O LEU a 235 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N PHE a 240 " --> pdb=" O ILE a 236 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER a 242 " --> pdb=" O VAL a 238 " (cutoff:3.500A) Processing helix chain 'a' and resid 249 through 283 removed outlier: 3.617A pdb=" N ALA a 253 " --> pdb=" O ALA a 249 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU a 264 " --> pdb=" O VAL a 260 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA a 270 " --> pdb=" O ILE a 266 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 67 removed outlier: 4.383A pdb=" N GLU A 52 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N MET A 53 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ARG A 41 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N VAL A 35 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE A 39 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL A 75 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N ALA A 64 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ALA F 35 " --> pdb=" O THR F 76 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLU F 34 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ARG F 57 " --> pdb=" O GLN F 48 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N GLN F 50 " --> pdb=" O VAL F 55 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N VAL F 55 " --> pdb=" O GLN F 50 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N VAL F 19 " --> pdb=" O ILE F 15 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ILE F 15 " --> pdb=" O VAL F 19 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASP F 21 " --> pdb=" O VAL F 13 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 99 Processing sheet with id=AA3, first strand: chain 'A' and resid 108 through 110 removed outlier: 6.518A pdb=" N VAL A 109 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR A 261 " --> pdb=" O LEU A 328 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 110 removed outlier: 6.518A pdb=" N VAL A 109 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR A 261 " --> pdb=" O LEU A 328 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LEU A 167 " --> pdb=" O ILE A 354 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 29 through 35 removed outlier: 6.625A pdb=" N ARG B 41 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N VAL B 35 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ILE B 39 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL B 75 " --> pdb=" O ALA B 64 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N ALA B 64 " --> pdb=" O VAL B 75 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N GLU B 52 " --> pdb=" O ALA B 64 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N MET B 53 " --> pdb=" O THR B 92 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 97 through 100 removed outlier: 4.058A pdb=" N ALA B 126 " --> pdb=" O VAL B 100 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 108 through 110 removed outlier: 6.574A pdb=" N VAL B 109 " --> pdb=" O ALA B 226 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 108 through 110 removed outlier: 6.574A pdb=" N VAL B 109 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU B 167 " --> pdb=" O ILE B 354 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'W' and resid 137 through 144 removed outlier: 13.588A pdb=" N ALA C 26 " --> pdb=" O GLY C 93 " (cutoff:3.500A) removed outlier: 8.857A pdb=" N GLY C 93 " --> pdb=" O ALA C 26 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N ASN C 28 " --> pdb=" O CYS C 91 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N THR C 92 " --> pdb=" O GLU C 55 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N GLU C 55 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ARG C 94 " --> pdb=" O MET C 53 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N GLU C 52 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N GLY C 73 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE C 39 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL C 35 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ARG C 41 " --> pdb=" O VAL C 33 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 97 through 100 removed outlier: 4.162A 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 110 removed outlier: 6.691A pdb=" N ALA C 257 " --> pdb=" O THR C 326 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N LEU C 328 " --> pdb=" O ALA C 257 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ILE C 259 " --> pdb=" O LEU C 328 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ILE C 330 " --> pdb=" O ILE C 259 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N TYR C 261 " --> pdb=" O ILE C 330 " (cutoff:3.500A) removed outlier: 8.584A pdb=" N GLU C 332 " --> pdb=" O TYR C 261 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 108 through 110 removed outlier: 6.691A pdb=" N ALA C 257 " --> pdb=" O THR C 326 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N LEU C 328 " --> pdb=" O ALA C 257 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ILE C 259 " --> pdb=" O LEU C 328 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ILE C 330 " --> pdb=" O ILE C 259 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N TYR C 261 " --> pdb=" O ILE C 330 " (cutoff:3.500A) removed outlier: 8.584A pdb=" N GLU C 332 " --> pdb=" O TYR C 261 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU C 167 " --> pdb=" O ILE C 354 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 10 through 16 removed outlier: 6.716A pdb=" N ASP D 21 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ILE D 15 " --> pdb=" O VAL D 19 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N VAL D 19 " --> pdb=" O ILE D 15 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N VAL D 55 " --> pdb=" O GLN D 50 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N GLN D 50 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ARG D 57 " --> pdb=" O GLN D 48 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLU D 34 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA D 35 " --> pdb=" O THR D 76 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 81 through 83 Processing sheet with id=AB6, first strand: chain 'D' and resid 92 through 93 removed outlier: 6.413A pdb=" N MET D 93 " --> pdb=" O TYR D 211 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N TYR D 178 " --> pdb=" O ASP D 241 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL D 242 " --> pdb=" O THR D 296 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N ILE D 298 " --> pdb=" O VAL D 242 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU D 244 " --> pdb=" O ILE D 298 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N ALA D 300 " --> pdb=" O LEU D 244 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ILE D 246 " --> pdb=" O ALA D 300 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N TYR D 302 " --> pdb=" O ILE D 246 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LYS D 149 " --> pdb=" O ALA D 322 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N VAL D 324 " --> pdb=" O LYS D 149 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N GLY D 151 " --> pdb=" O VAL D 324 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 130 through 131 removed outlier: 4.189A pdb=" N PHE D 144 " --> pdb=" O LEU D 131 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 10 through 16 removed outlier: 6.682A pdb=" N ASP E 21 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ILE E 15 " --> pdb=" O VAL E 19 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N VAL E 19 " --> pdb=" O ILE E 15 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N VAL E 55 " --> pdb=" O GLN E 50 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N GLN E 50 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ARG E 57 " --> pdb=" O GLN E 48 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLU E 34 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ALA E 35 " --> pdb=" O THR E 76 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 81 through 83 Processing sheet with id=AC1, first strand: chain 'E' and resid 92 through 93 removed outlier: 6.751A pdb=" N LYS E 149 " --> pdb=" O ALA E 322 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N VAL E 324 " --> pdb=" O LYS E 149 " (cutoff:3.500A) removed outlier: 6.231A 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: 4.298A pdb=" N PHE E 144 " --> pdb=" O LEU E 131 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 81 through 83 Processing sheet with id=AC4, first strand: chain 'F' and resid 92 through 93 removed outlier: 6.267A pdb=" N MET F 93 " --> pdb=" O TYR F 211 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N GLN F 213 " --> pdb=" O MET F 93 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR F 178 " --> pdb=" O ASP F 241 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N VAL F 242 " --> pdb=" O THR F 296 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ILE F 298 " --> pdb=" O VAL F 242 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LEU F 244 " --> pdb=" O ILE F 298 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N ALA F 300 " --> pdb=" O LEU F 244 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ILE F 246 " --> pdb=" O ALA F 300 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 130 through 131 removed outlier: 4.611A pdb=" N PHE F 144 " --> pdb=" O LEU F 131 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 133 through 137 removed outlier: 7.674A pdb=" N VAL G 134 " --> pdb=" O ILE G 113 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N LEU G 115 " --> pdb=" O VAL G 134 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ALA G 136 " --> pdb=" O LEU G 115 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL G 117 " --> pdb=" O ALA G 136 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL G 76 " --> pdb=" O ASP G 114 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N CYS G 116 " --> pdb=" O VAL G 76 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N TYR G 78 " --> pdb=" O CYS G 116 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ILE G 118 " --> pdb=" O TYR G 78 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL G 80 " --> pdb=" O ILE G 118 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ARG G 75 " --> pdb=" O ARG G 167 " (cutoff:3.500A) removed outlier: 9.043A pdb=" N PHE G 169 " --> pdb=" O ARG G 75 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N GLY G 77 " --> pdb=" O PHE G 169 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N VAL G 171 " --> pdb=" O GLY G 77 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE G 79 " --> pdb=" O VAL G 171 " (cutoff:3.500A) removed outlier: 8.821A pdb=" N ASN G 173 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 9.242A pdb=" N VAL G 81 " --> pdb=" O ASN G 173 " (cutoff:3.500A) removed outlier: 12.116A pdb=" N PHE G 175 " --> pdb=" O VAL G 81 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR G 180 " --> pdb=" O VAL G 176 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 15 through 21 Processing sheet with id=AC8, first strand: chain 'H' and resid 32 through 35 removed outlier: 3.548A pdb=" N MET H 23 " --> pdb=" O VAL H 54 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N HIS H 27 " --> pdb=" O PRO H 50 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'a' and resid 18 through 20 2408 hydrogen bonds defined for protein. 6930 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.73 Time building geometry restraints manager: 4.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 6353 1.27 - 1.41: 8218 1.41 - 1.54: 22278 1.54 - 1.68: 466 1.68 - 1.82: 299 Bond restraints: 37614 Sorted by residual: bond pdb=" C GLY R 81 " pdb=" O GLY R 81 " ideal model delta sigma weight residual 1.235 1.130 0.105 1.15e-02 7.56e+03 8.31e+01 bond pdb=" C4 ADP F 501 " pdb=" C5 ADP F 501 " ideal model delta sigma weight residual 1.490 1.348 0.142 2.00e-02 2.50e+03 5.07e+01 bond pdb=" C4 ADP D 501 " pdb=" C5 ADP D 501 " ideal model delta sigma weight residual 1.490 1.350 0.140 2.00e-02 2.50e+03 4.91e+01 bond pdb=" C4 ADP E 501 " pdb=" C5 ADP E 501 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.04e+01 bond pdb=" C GLN P 82 " pdb=" O GLN P 82 " ideal model delta sigma weight residual 1.238 1.141 0.097 1.83e-02 2.99e+03 2.81e+01 ... (remaining 37609 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.54: 50815 6.54 - 13.08: 80 13.08 - 19.63: 9 19.63 - 26.17: 0 26.17 - 32.71: 1 Bond angle restraints: 50905 Sorted by residual: angle pdb=" O ALA a 284 " pdb=" C ALA a 284 " pdb=" N HIS a 285 " ideal model delta sigma weight residual 122.34 89.63 32.71 1.25e+00 6.40e-01 6.85e+02 angle pdb=" PB ATP B 600 " pdb=" O3B ATP B 600 " pdb=" PG ATP B 600 " ideal model delta sigma weight residual 139.87 121.68 18.19 1.00e+00 1.00e+00 3.31e+02 angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 121.89 17.98 1.00e+00 1.00e+00 3.23e+02 angle pdb=" PB ATP C 600 " pdb=" O3B ATP C 600 " pdb=" PG ATP C 600 " ideal model delta sigma weight residual 139.87 122.83 17.04 1.00e+00 1.00e+00 2.90e+02 angle pdb=" PA ATP A 600 " pdb=" O3A ATP A 600 " pdb=" PB ATP A 600 " ideal model delta sigma weight residual 136.83 120.47 16.36 1.00e+00 1.00e+00 2.68e+02 ... (remaining 50900 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.93: 22111 31.93 - 63.86: 473 63.86 - 95.79: 62 95.79 - 127.72: 1 127.72 - 159.65: 3 Dihedral angle restraints: 22650 sinusoidal: 8850 harmonic: 13800 Sorted by residual: dihedral pdb=" O2A ADP F 501 " pdb=" O3A ADP F 501 " pdb=" PA ADP F 501 " pdb=" PB ADP F 501 " ideal model delta sinusoidal sigma weight residual -60.00 99.65 -159.65 1 2.00e+01 2.50e-03 4.65e+01 dihedral pdb=" O1B ADP D 501 " pdb=" O3A ADP D 501 " pdb=" PB ADP D 501 " pdb=" PA ADP D 501 " ideal model delta sinusoidal sigma weight residual -60.00 87.69 -147.69 1 2.00e+01 2.50e-03 4.43e+01 dihedral pdb=" O1B ADP F 501 " pdb=" O3A ADP F 501 " pdb=" PB ADP F 501 " pdb=" PA ADP F 501 " ideal model delta sinusoidal sigma weight residual -60.00 82.20 -142.20 1 2.00e+01 2.50e-03 4.30e+01 ... (remaining 22647 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 4139 0.097 - 0.193: 1556 0.193 - 0.290: 192 0.290 - 0.387: 40 0.387 - 0.483: 9 Chirality restraints: 5936 Sorted by residual: chirality pdb=" CA GLU E 42 " pdb=" N GLU E 42 " pdb=" C GLU E 42 " pdb=" CB GLU E 42 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.84e+00 chirality pdb=" CA ARG B 279 " pdb=" N ARG B 279 " pdb=" C ARG B 279 " pdb=" CB ARG B 279 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.73e+00 chirality pdb=" CA ALA E 338 " pdb=" N ALA E 338 " pdb=" C ALA E 338 " pdb=" CB ALA E 338 " both_signs ideal model delta sigma weight residual False 2.48 2.02 0.46 2.00e-01 2.50e+01 5.31e+00 ... (remaining 5933 not shown) Planarity restraints: 6568 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA a 284 " -0.114 2.00e-02 2.50e+03 1.86e-01 3.46e+02 pdb=" C ALA a 284 " 0.322 2.00e-02 2.50e+03 pdb=" O ALA a 284 " -0.111 2.00e-02 2.50e+03 pdb=" N HIS a 285 " -0.097 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN P 82 " 0.082 2.00e-02 2.50e+03 1.64e-01 2.69e+02 pdb=" C GLN P 82 " -0.283 2.00e-02 2.50e+03 pdb=" O GLN P 82 " 0.119 2.00e-02 2.50e+03 pdb=" N ILE P 83 " 0.081 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY R 81 " 0.069 2.00e-02 2.50e+03 1.29e-01 1.67e+02 pdb=" C GLY R 81 " -0.223 2.00e-02 2.50e+03 pdb=" O GLY R 81 " 0.084 2.00e-02 2.50e+03 pdb=" N GLN R 82 " 0.070 2.00e-02 2.50e+03 ... (remaining 6565 not shown) Histogram of nonbonded interaction distances: 1.18 - 1.92: 5 1.92 - 2.67: 200 2.67 - 3.41: 48971 3.41 - 4.16: 88139 4.16 - 4.90: 159726 Nonbonded interactions: 297041 Sorted by model distance: nonbonded pdb=" OG1 THR E 161 " pdb="MG MG E 502 " model vdw 1.180 2.170 nonbonded pdb=" O1B ADP E 501 " pdb="MG MG E 502 " model vdw 1.516 2.170 nonbonded pdb=" O2G ATP B 600 " pdb="MG MG B 601 " model vdw 1.871 2.170 nonbonded pdb=" O2G ATP C 600 " pdb="MG MG C 601 " model vdw 1.895 2.170 nonbonded pdb=" O1G ATP A 600 " pdb="MG MG A 601 " model vdw 1.905 2.170 ... (remaining 297036 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' selection = (chain 'B' and resid 7 through 601) selection = (chain 'C' and resid 7 through 601) } ncs_group { reference = (chain 'D' and resid 8 through 501) selection = (chain 'E' and resid 8 through 501) selection = chain 'F' } ncs_group { reference = (chain 'I' and (resid 1 through 82 or (resid 83 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'J' and (resid 1 through 82 or (resid 83 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'L' and (resid 1 through 82 or (resid 83 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'M' and (resid 1 through 82 or (resid 83 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'N' and (resid 1 through 82 or (resid 83 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'O' and (resid 1 through 82 or (resid 83 and (name N or name CA or name C \ or name O or name CB )))) selection = chain 'P' selection = (chain 'Q' and (resid 1 through 82 or (resid 83 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'R' and (resid 1 through 82 or (resid 83 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'S' and (resid 1 through 82 or (resid 83 and (name N or name CA or name C \ or name O or name CB )))) } ncs_group { reference = chain 'X' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.680 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 40.200 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:9.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.142 37615 Z= 0.746 Angle : 1.838 32.710 50905 Z= 1.257 Chirality : 0.097 0.483 5936 Planarity : 0.014 0.198 6568 Dihedral : 13.167 159.646 13850 Min Nonbonded Distance : 1.180 Molprobity Statistics. All-atom Clashscore : 0.75 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.20 % Favored : 97.73 % Rotamer: Outliers : 0.68 % Allowed : 3.48 % Favored : 95.84 % Cbeta Deviations : 0.50 % 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: -0.57 (0.11), residues: 4854 helix: -0.35 (0.09), residues: 2640 sheet: 0.27 (0.20), residues: 503 loop : -0.34 (0.15), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.002 ARG E 221 TYR 0.133 0.016 TYR G 45 PHE 0.068 0.011 PHE N 75 TRP 0.082 0.021 TRP a 256 HIS 0.014 0.004 HIS a 186 Details of bonding type rmsd covalent geometry : bond 0.01207 (37614) covalent geometry : angle 1.83753 (50905) hydrogen bonds : bond 0.21705 ( 2365) hydrogen bonds : angle 7.29538 ( 6930) metal coordination : bond 0.08382 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 3823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 563 time to evaluate : 1.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 464 LYS cc_start: 0.8067 (mttt) cc_final: 0.7724 (tttt) outliers start: 26 outliers final: 7 residues processed: 582 average time/residue: 0.8193 time to fit residues: 556.9650 Evaluate side-chains 330 residues out of total 3823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 323 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain F residue 348 GLN Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain S residue 23 THR Chi-restraints excluded: chain Y residue 88 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 432 optimal weight: 6.9990 chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 1.9990 chunk 455 optimal weight: 6.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.0670 chunk 470 optimal weight: 10.0000 overall best weight: 1.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 GLN B 3 GLN B 5 ASN C 66 ASN C 458 GLN E 128 ASN F 358 HIS G 109 GLN G 201 HIS G 202 HIS L 41 GLN N 41 GLN N 82 GLN P 82 GLN Q 77 ASN R 49 GLN R 82 GLN S 82 GLN W 122 GLN Y 64 GLN Y 71 GLN Y 78 GLN Y 143 ASN a 11 GLN a 13 HIS a 24 ASN ** a 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 192 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.089979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.065740 restraints weight = 82494.446| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.12 r_work: 0.2974 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 37615 Z= 0.159 Angle : 0.623 9.938 50905 Z= 0.331 Chirality : 0.044 0.249 5936 Planarity : 0.004 0.073 6568 Dihedral : 7.457 162.451 5364 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.11 % Favored : 98.85 % Rotamer: Outliers : 2.20 % Allowed : 9.18 % Favored : 88.62 % 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: 1.33 (0.12), residues: 4854 helix: 1.54 (0.10), residues: 2688 sheet: 0.41 (0.19), residues: 568 loop : 0.08 (0.16), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG Y 91 TYR 0.028 0.002 TYR H 115 PHE 0.029 0.001 PHE Y 14 TRP 0.012 0.001 TRP F 112 HIS 0.007 0.001 HIS G 202 Details of bonding type rmsd covalent geometry : bond 0.00337 (37614) covalent geometry : angle 0.62341 (50905) hydrogen bonds : bond 0.06099 ( 2365) hydrogen bonds : angle 4.75736 ( 6930) metal coordination : bond 0.00406 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 353 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 LYS cc_start: 0.8981 (OUTLIER) cc_final: 0.8732 (tttm) REVERT: C 464 LYS cc_start: 0.8739 (mttt) cc_final: 0.7683 (tttt) REVERT: G 143 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.7818 (pp20) REVERT: H 121 ARG cc_start: 0.7307 (ttm-80) cc_final: 0.6943 (ttp-110) REVERT: I 60 ASP cc_start: 0.8260 (p0) cc_final: 0.7597 (t0) REVERT: I 64 MET cc_start: 0.8359 (mmt) cc_final: 0.7972 (mmm) REVERT: J 41 GLN cc_start: 0.8258 (OUTLIER) cc_final: 0.7972 (mt0) REVERT: J 44 MET cc_start: 0.8682 (mtt) cc_final: 0.8200 (mtp) REVERT: L 44 MET cc_start: 0.8126 (mmm) cc_final: 0.7838 (mmm) REVERT: Q 44 MET cc_start: 0.7500 (mmp) cc_final: 0.6914 (mmm) REVERT: Q 47 MET cc_start: 0.7104 (OUTLIER) cc_final: 0.6768 (tmm) REVERT: Q 83 ILE cc_start: 0.6468 (mt) cc_final: 0.6079 (mm) REVERT: X 66 ARG cc_start: 0.8071 (ptp-170) cc_final: 0.7601 (ptp-170) REVERT: X 69 LYS cc_start: 0.7059 (OUTLIER) cc_final: 0.6850 (mttp) REVERT: Y 36 ARG cc_start: 0.7638 (OUTLIER) cc_final: 0.7386 (tpp80) REVERT: Y 39 LYS cc_start: 0.7328 (mmtm) cc_final: 0.7116 (tppp) REVERT: Y 66 ARG cc_start: 0.7906 (mtt90) cc_final: 0.7640 (mmm160) REVERT: a 87 GLU cc_start: 0.8155 (tt0) cc_final: 0.7947 (pt0) REVERT: a 101 ASN cc_start: 0.6064 (t0) cc_final: 0.5770 (t0) REVERT: a 283 MET cc_start: 0.8356 (ptm) cc_final: 0.7890 (ttp) REVERT: a 286 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7966 (pm20) outliers start: 84 outliers final: 18 residues processed: 405 average time/residue: 0.7466 time to fit residues: 357.7506 Evaluate side-chains 313 residues out of total 3823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 288 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain F residue 348 GLN Chi-restraints excluded: chain F residue 381 ILE Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain H residue 66 SER Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 41 GLN Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain M residue 65 ILE Chi-restraints excluded: chain N residue 23 THR Chi-restraints excluded: chain N residue 60 ASP Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain Q residue 47 MET Chi-restraints excluded: chain S residue 16 ILE Chi-restraints excluded: chain X residue 69 LYS Chi-restraints excluded: chain Y residue 30 ILE Chi-restraints excluded: chain Y residue 36 ARG Chi-restraints excluded: chain Y residue 139 SER Chi-restraints excluded: chain a residue 59 PHE Chi-restraints excluded: chain a residue 96 THR Chi-restraints excluded: chain a residue 286 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 168 optimal weight: 9.9990 chunk 164 optimal weight: 0.7980 chunk 453 optimal weight: 9.9990 chunk 210 optimal weight: 6.9990 chunk 263 optimal weight: 5.9990 chunk 279 optimal weight: 7.9990 chunk 51 optimal weight: 6.9990 chunk 272 optimal weight: 6.9990 chunk 87 optimal weight: 9.9990 chunk 434 optimal weight: 10.0000 chunk 278 optimal weight: 0.8980 overall best weight: 4.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 HIS B 295 HIS E 175 HIS ** G 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 187 GLN G 202 HIS H 39 HIS H 128 GLN N 41 GLN O 49 GLN P 49 GLN Y 4 ASN a 24 ASN a 35 GLN a 74 GLN a 285 HIS a 289 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.085412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.060061 restraints weight = 79926.538| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.10 r_work: 0.2842 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 37615 Z= 0.234 Angle : 0.639 7.926 50905 Z= 0.334 Chirality : 0.046 0.173 5936 Planarity : 0.005 0.064 6568 Dihedral : 7.404 166.384 5359 Min Nonbonded Distance : 1.744 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.59 % Favored : 98.37 % Rotamer: Outliers : 2.64 % Allowed : 10.23 % Favored : 87.13 % 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: 1.35 (0.12), residues: 4854 helix: 1.69 (0.10), residues: 2703 sheet: 0.39 (0.20), residues: 549 loop : -0.21 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG X 95 TYR 0.033 0.002 TYR H 115 PHE 0.021 0.002 PHE X 20 TRP 0.008 0.001 TRP F 112 HIS 0.007 0.001 HIS a 13 Details of bonding type rmsd covalent geometry : bond 0.00568 (37614) covalent geometry : angle 0.63928 (50905) hydrogen bonds : bond 0.06467 ( 2365) hydrogen bonds : angle 4.60962 ( 6930) metal coordination : bond 0.00237 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 3823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 322 time to evaluate : 1.529 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 3 GLN cc_start: 0.8434 (mt0) cc_final: 0.8217 (pt0) REVERT: C 237 TYR cc_start: 0.9329 (OUTLIER) cc_final: 0.8967 (t80) REVERT: C 470 GLN cc_start: 0.8226 (mm-40) cc_final: 0.8017 (tp-100) REVERT: G 143 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.7789 (pp20) REVERT: G 148 ASP cc_start: 0.8354 (m-30) cc_final: 0.7987 (m-30) REVERT: H 91 ASP cc_start: 0.8452 (t0) cc_final: 0.8157 (t0) REVERT: H 121 ARG cc_start: 0.7116 (ttm-80) cc_final: 0.6805 (ttp-110) REVERT: I 60 ASP cc_start: 0.8010 (p0) cc_final: 0.7446 (t0) REVERT: I 64 MET cc_start: 0.8448 (mmt) cc_final: 0.7932 (mmm) REVERT: J 41 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.7971 (mt0) REVERT: J 44 MET cc_start: 0.8776 (mtt) cc_final: 0.8235 (mtm) REVERT: L 43 GLU cc_start: 0.8276 (pm20) cc_final: 0.7944 (pm20) REVERT: L 44 MET cc_start: 0.8301 (mmm) cc_final: 0.7871 (mmm) REVERT: O 80 VAL cc_start: 0.8769 (OUTLIER) cc_final: 0.8502 (m) REVERT: Q 1 MET cc_start: 0.7986 (tpp) cc_final: 0.7589 (tpt) REVERT: Q 44 MET cc_start: 0.7708 (mmp) cc_final: 0.7237 (mmm) REVERT: X 30 ILE cc_start: 0.7294 (OUTLIER) cc_final: 0.6894 (pp) REVERT: X 66 ARG cc_start: 0.7869 (ptp-170) cc_final: 0.7358 (ptp-170) REVERT: X 69 LYS cc_start: 0.6811 (OUTLIER) cc_final: 0.6540 (mttt) REVERT: X 86 ILE cc_start: 0.8292 (mt) cc_final: 0.8085 (mp) REVERT: Y 4 ASN cc_start: 0.7662 (OUTLIER) cc_final: 0.7347 (m-40) REVERT: Y 36 ARG cc_start: 0.7539 (OUTLIER) cc_final: 0.7261 (tpp80) REVERT: Y 38 LYS cc_start: 0.8380 (ttmm) cc_final: 0.8082 (ttpp) REVERT: Y 66 ARG cc_start: 0.7869 (mtt90) cc_final: 0.7582 (mmm160) REVERT: Y 69 LYS cc_start: 0.8062 (mmmt) cc_final: 0.7785 (mmmm) REVERT: a 24 ASN cc_start: 0.4134 (OUTLIER) cc_final: 0.3848 (m-40) REVERT: a 101 ASN cc_start: 0.5944 (t0) cc_final: 0.5701 (t0) REVERT: a 283 MET cc_start: 0.8186 (ptm) cc_final: 0.7866 (ttp) REVERT: a 286 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7988 (pm20) outliers start: 101 outliers final: 34 residues processed: 389 average time/residue: 0.8140 time to fit residues: 374.7669 Evaluate side-chains 323 residues out of total 3823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 279 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 427 ARG Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain C residue 237 TYR Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 198 MET Chi-restraints excluded: chain E residue 343 ASP Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 348 GLN Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain H residue 66 SER Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 41 GLN Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain M residue 65 ILE Chi-restraints excluded: chain N residue 23 THR Chi-restraints excluded: chain N residue 60 ASP Chi-restraints excluded: chain O residue 23 THR Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain Q residue 60 ASP Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain W residue 34 VAL Chi-restraints excluded: chain X residue 8 ILE Chi-restraints excluded: chain X residue 22 MET Chi-restraints excluded: chain X residue 25 VAL Chi-restraints excluded: chain X residue 30 ILE Chi-restraints excluded: chain X residue 69 LYS Chi-restraints excluded: chain X residue 87 VAL Chi-restraints excluded: chain Y residue 4 ASN Chi-restraints excluded: chain Y residue 36 ARG Chi-restraints excluded: chain Y residue 136 LEU Chi-restraints excluded: chain Y residue 139 SER Chi-restraints excluded: chain a residue 24 ASN Chi-restraints excluded: chain a residue 59 PHE Chi-restraints excluded: chain a residue 96 THR Chi-restraints excluded: chain a residue 262 HIS Chi-restraints excluded: chain a residue 286 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 5 optimal weight: 2.9990 chunk 147 optimal weight: 0.9990 chunk 277 optimal weight: 0.9990 chunk 129 optimal weight: 2.9990 chunk 204 optimal weight: 0.9980 chunk 384 optimal weight: 8.9990 chunk 296 optimal weight: 6.9990 chunk 292 optimal weight: 5.9990 chunk 385 optimal weight: 0.9980 chunk 217 optimal weight: 1.9990 chunk 312 optimal weight: 0.9980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 512 GLN B 424 HIS D 437 ASN G 202 HIS H 6 HIS H 128 GLN M 49 GLN N 41 GLN N 49 GLN R 49 GLN Y 4 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.088305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.064609 restraints weight = 82108.233| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.09 r_work: 0.2968 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 37615 Z= 0.120 Angle : 0.519 7.544 50905 Z= 0.271 Chirality : 0.041 0.149 5936 Planarity : 0.004 0.051 6568 Dihedral : 7.004 176.578 5359 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.19 % Favored : 98.76 % Rotamer: Outliers : 1.96 % Allowed : 11.98 % Favored : 86.05 % 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: 1.79 (0.12), residues: 4854 helix: 2.08 (0.10), residues: 2713 sheet: 0.43 (0.20), residues: 588 loop : -0.05 (0.16), residues: 1553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG Y 49 TYR 0.021 0.001 TYR H 115 PHE 0.014 0.001 PHE X 20 TRP 0.006 0.001 TRP X 26 HIS 0.006 0.001 HIS a 13 Details of bonding type rmsd covalent geometry : bond 0.00240 (37614) covalent geometry : angle 0.51950 (50905) hydrogen bonds : bond 0.05012 ( 2365) hydrogen bonds : angle 4.29844 ( 6930) metal coordination : bond 0.00085 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 3823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 309 time to evaluate : 1.473 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 141 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8577 (tttm) REVERT: B 505 ILE cc_start: 0.8419 (OUTLIER) cc_final: 0.8153 (mp) REVERT: C 366 ARG cc_start: 0.7473 (OUTLIER) cc_final: 0.6746 (mmt90) REVERT: C 419 ARG cc_start: 0.6899 (mtt90) cc_final: 0.6489 (mtt90) REVERT: F 11 ARG cc_start: 0.8289 (mtm110) cc_final: 0.7721 (mmm-85) REVERT: G 143 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.7744 (pp20) REVERT: H 91 ASP cc_start: 0.8284 (t0) cc_final: 0.8001 (t0) REVERT: H 121 ARG cc_start: 0.7170 (ttm-80) cc_final: 0.6842 (ttp-110) REVERT: I 41 GLN cc_start: 0.8280 (tp40) cc_final: 0.8065 (tp40) REVERT: I 60 ASP cc_start: 0.7794 (p0) cc_final: 0.7504 (t0) REVERT: I 64 MET cc_start: 0.8357 (mmt) cc_final: 0.7950 (mmm) REVERT: J 44 MET cc_start: 0.8737 (mtt) cc_final: 0.8475 (mtp) REVERT: L 36 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7935 (tt0) REVERT: L 43 GLU cc_start: 0.8196 (pm20) cc_final: 0.7898 (pm20) REVERT: L 44 MET cc_start: 0.8142 (mmm) cc_final: 0.7824 (mmm) REVERT: P 36 GLU cc_start: 0.8480 (tt0) cc_final: 0.8183 (tt0) REVERT: Q 1 MET cc_start: 0.7869 (tpp) cc_final: 0.7537 (tpt) REVERT: Q 44 MET cc_start: 0.7500 (mmp) cc_final: 0.7109 (mmm) REVERT: X 30 ILE cc_start: 0.7322 (OUTLIER) cc_final: 0.6966 (pp) REVERT: X 86 ILE cc_start: 0.8354 (OUTLIER) cc_final: 0.8071 (mp) REVERT: Y 38 LYS cc_start: 0.8408 (ttmm) cc_final: 0.8103 (ttpp) REVERT: Y 39 LYS cc_start: 0.7065 (tmtt) cc_final: 0.6646 (tppp) REVERT: Y 152 LEU cc_start: 0.8545 (mt) cc_final: 0.8243 (pp) REVERT: a 101 ASN cc_start: 0.5975 (t0) cc_final: 0.5600 (t0) REVERT: a 283 MET cc_start: 0.8085 (ptm) cc_final: 0.7807 (ttp) REVERT: a 286 GLU cc_start: 0.8247 (pt0) cc_final: 0.7618 (pp20) outliers start: 75 outliers final: 25 residues processed: 356 average time/residue: 0.7749 time to fit residues: 327.3841 Evaluate side-chains 310 residues out of total 3823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 278 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 427 ARG Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain C residue 366 ARG Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 343 ASP Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 348 GLN Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain H residue 66 SER Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 36 GLU Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain M residue 65 ILE Chi-restraints excluded: chain N residue 60 ASP Chi-restraints excluded: chain Q residue 60 ASP Chi-restraints excluded: chain S residue 65 ILE Chi-restraints excluded: chain X residue 8 ILE Chi-restraints excluded: chain X residue 30 ILE Chi-restraints excluded: chain X residue 86 ILE Chi-restraints excluded: chain X residue 113 LEU Chi-restraints excluded: chain Y residue 136 LEU Chi-restraints excluded: chain Y residue 139 SER Chi-restraints excluded: chain a residue 11 GLN Chi-restraints excluded: chain a residue 94 LYS Chi-restraints excluded: chain a residue 96 THR Chi-restraints excluded: chain a residue 262 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 435 optimal weight: 0.0870 chunk 242 optimal weight: 0.9990 chunk 470 optimal weight: 5.9990 chunk 167 optimal weight: 0.4980 chunk 400 optimal weight: 3.9990 chunk 116 optimal weight: 5.9990 chunk 182 optimal weight: 10.0000 chunk 211 optimal weight: 1.9990 chunk 402 optimal weight: 8.9990 chunk 390 optimal weight: 0.9990 chunk 50 optimal weight: 0.0570 overall best weight: 0.5280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 202 HIS H 73 GLN J 41 GLN N 41 GLN N 49 GLN Y 63 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.089663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.066179 restraints weight = 81904.782| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.07 r_work: 0.3005 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.124 37615 Z= 0.110 Angle : 0.496 7.901 50905 Z= 0.257 Chirality : 0.040 0.141 5936 Planarity : 0.003 0.046 6568 Dihedral : 6.557 166.079 5359 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.19 % Favored : 98.76 % Rotamer: Outliers : 1.86 % Allowed : 12.35 % Favored : 85.79 % 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: 2.07 (0.12), residues: 4854 helix: 2.32 (0.10), residues: 2710 sheet: 0.53 (0.20), residues: 588 loop : 0.07 (0.16), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG X 95 TYR 0.017 0.001 TYR F 367 PHE 0.014 0.001 PHE Y 24 TRP 0.006 0.001 TRP G 203 HIS 0.003 0.000 HIS Y 145 Details of bonding type rmsd covalent geometry : bond 0.00223 (37614) covalent geometry : angle 0.49601 (50905) hydrogen bonds : bond 0.04477 ( 2365) hydrogen bonds : angle 4.12555 ( 6930) metal coordination : bond 0.00071 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 3823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 308 time to evaluate : 1.584 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 505 ILE cc_start: 0.8320 (OUTLIER) cc_final: 0.8112 (mp) REVERT: C 366 ARG cc_start: 0.7428 (OUTLIER) cc_final: 0.6605 (mmt90) REVERT: F 11 ARG cc_start: 0.8270 (mtm110) cc_final: 0.7746 (mmm-85) REVERT: G 109 GLN cc_start: 0.7780 (tt0) cc_final: 0.7380 (mt0) REVERT: G 143 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.7697 (pp20) REVERT: H 91 ASP cc_start: 0.8212 (t0) cc_final: 0.7899 (t0) REVERT: H 121 ARG cc_start: 0.7152 (ttm-80) cc_final: 0.6862 (ttp-110) REVERT: I 54 ILE cc_start: 0.8831 (OUTLIER) cc_final: 0.8571 (mp) REVERT: I 64 MET cc_start: 0.8324 (mmt) cc_final: 0.8035 (mmm) REVERT: L 43 GLU cc_start: 0.8181 (pm20) cc_final: 0.7833 (pm20) REVERT: L 44 MET cc_start: 0.8077 (mmm) cc_final: 0.7798 (mmm) REVERT: Q 1 MET cc_start: 0.7827 (tpp) cc_final: 0.7531 (tpt) REVERT: Q 44 MET cc_start: 0.7384 (mmp) cc_final: 0.7149 (mmt) REVERT: X 66 ARG cc_start: 0.7927 (ptp-110) cc_final: 0.7590 (ptt180) REVERT: X 69 LYS cc_start: 0.6937 (OUTLIER) cc_final: 0.6629 (mttt) REVERT: X 86 ILE cc_start: 0.8253 (OUTLIER) cc_final: 0.7960 (mp) REVERT: Y 67 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7926 (mp0) REVERT: Y 152 LEU cc_start: 0.8558 (mt) cc_final: 0.8277 (pp) REVERT: a 13 HIS cc_start: 0.8799 (OUTLIER) cc_final: 0.8583 (m90) REVERT: a 95 ASP cc_start: 0.8329 (t0) cc_final: 0.8104 (t0) REVERT: a 101 ASN cc_start: 0.6058 (t0) cc_final: 0.5630 (t0) REVERT: a 286 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7644 (pp20) outliers start: 71 outliers final: 22 residues processed: 355 average time/residue: 0.8059 time to fit residues: 342.3558 Evaluate side-chains 310 residues out of total 3823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 279 time to evaluate : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain C residue 366 ARG Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 343 ASP Chi-restraints excluded: chain F residue 198 MET Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 348 GLN Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain G residue 276 ILE Chi-restraints excluded: chain H residue 66 SER Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain M residue 65 ILE Chi-restraints excluded: chain Q residue 60 ASP Chi-restraints excluded: chain S residue 16 ILE Chi-restraints excluded: chain W residue 34 VAL Chi-restraints excluded: chain X residue 69 LYS Chi-restraints excluded: chain X residue 86 ILE Chi-restraints excluded: chain Y residue 67 GLU Chi-restraints excluded: chain a residue 11 GLN Chi-restraints excluded: chain a residue 13 HIS Chi-restraints excluded: chain a residue 96 THR Chi-restraints excluded: chain a residue 262 HIS Chi-restraints excluded: chain a residue 286 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 41 optimal weight: 10.0000 chunk 477 optimal weight: 9.9990 chunk 471 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 416 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 245 optimal weight: 8.9990 chunk 26 optimal weight: 6.9990 chunk 390 optimal weight: 8.9990 chunk 451 optimal weight: 5.9990 chunk 259 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 88 ASN D 319 HIS ** G 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 202 HIS H 73 GLN N 41 GLN N 49 GLN a 288 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.085346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.061377 restraints weight = 82597.250| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.04 r_work: 0.2897 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 37615 Z= 0.272 Angle : 0.651 14.300 50905 Z= 0.333 Chirality : 0.046 0.178 5936 Planarity : 0.005 0.054 6568 Dihedral : 7.033 155.719 5358 Min Nonbonded Distance : 1.716 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.98 % Favored : 97.98 % Rotamer: Outliers : 2.38 % Allowed : 13.06 % Favored : 84.56 % 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: 4854 helix: 1.97 (0.10), residues: 2703 sheet: 0.34 (0.20), residues: 572 loop : -0.19 (0.15), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG Y 49 TYR 0.028 0.002 TYR H 115 PHE 0.038 0.002 PHE Y 14 TRP 0.009 0.001 TRP X 26 HIS 0.008 0.001 HIS A 480 Details of bonding type rmsd covalent geometry : bond 0.00666 (37614) covalent geometry : angle 0.65146 (50905) hydrogen bonds : bond 0.06246 ( 2365) hydrogen bonds : angle 4.45840 ( 6930) metal coordination : bond 0.00260 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 3823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 291 time to evaluate : 1.562 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 141 LYS cc_start: 0.9039 (OUTLIER) cc_final: 0.8816 (tttm) REVERT: B 3 GLN cc_start: 0.8388 (mt0) cc_final: 0.8156 (pt0) REVERT: B 505 ILE cc_start: 0.8392 (OUTLIER) cc_final: 0.8123 (mp) REVERT: C 449 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8626 (mp) REVERT: E 198 MET cc_start: 0.8367 (OUTLIER) cc_final: 0.7932 (mtp) REVERT: E 343 ASP cc_start: 0.8737 (OUTLIER) cc_final: 0.8446 (t70) REVERT: F 178 TYR cc_start: 0.9092 (m-80) cc_final: 0.8875 (m-80) REVERT: G 143 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.7740 (pp20) REVERT: H 30 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8219 (mt) REVERT: H 73 GLN cc_start: 0.7834 (OUTLIER) cc_final: 0.7576 (mt0) REVERT: H 91 ASP cc_start: 0.8256 (t0) cc_final: 0.7942 (t0) REVERT: H 121 ARG cc_start: 0.7212 (ttm-80) cc_final: 0.6884 (ttp-110) REVERT: I 41 GLN cc_start: 0.8373 (tp40) cc_final: 0.8173 (tp40) REVERT: I 60 ASP cc_start: 0.8045 (t0) cc_final: 0.7636 (t0) REVERT: I 64 MET cc_start: 0.8579 (mmt) cc_final: 0.8226 (mmm) REVERT: J 43 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.8034 (mp0) REVERT: L 43 GLU cc_start: 0.8364 (pm20) cc_final: 0.7906 (pm20) REVERT: L 44 MET cc_start: 0.8182 (mmm) cc_final: 0.7865 (mmm) REVERT: P 41 GLN cc_start: 0.7438 (mp10) cc_final: 0.7205 (mp10) REVERT: Q 44 MET cc_start: 0.7600 (mmp) cc_final: 0.7095 (tpp) REVERT: X 86 ILE cc_start: 0.8391 (OUTLIER) cc_final: 0.8189 (mp) REVERT: Y 36 ARG cc_start: 0.7136 (OUTLIER) cc_final: 0.5672 (tpp80) REVERT: Y 49 ARG cc_start: 0.7117 (mtm110) cc_final: 0.6830 (mmp80) REVERT: Y 67 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7924 (mp0) REVERT: a 27 TRP cc_start: -0.0221 (OUTLIER) cc_final: -0.0581 (p90) REVERT: a 95 ASP cc_start: 0.8397 (t0) cc_final: 0.8192 (t0) REVERT: a 101 ASN cc_start: 0.5865 (t0) cc_final: 0.5517 (t0) outliers start: 91 outliers final: 35 residues processed: 348 average time/residue: 0.8361 time to fit residues: 344.2094 Evaluate side-chains 320 residues out of total 3823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 272 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASP Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 445 MET Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain D residue 384 MET Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 198 MET Chi-restraints excluded: chain E residue 343 ASP Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 348 GLN Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain G residue 202 HIS Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 66 SER Chi-restraints excluded: chain H residue 73 GLN Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain I residue 43 GLU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 43 GLU Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 83 ILE Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain M residue 65 ILE Chi-restraints excluded: chain O residue 23 THR Chi-restraints excluded: chain P residue 59 LEU Chi-restraints excluded: chain Q residue 49 GLN Chi-restraints excluded: chain Q residue 60 ASP Chi-restraints excluded: chain S residue 16 ILE Chi-restraints excluded: chain W residue 34 VAL Chi-restraints excluded: chain X residue 8 ILE Chi-restraints excluded: chain X residue 86 ILE Chi-restraints excluded: chain X residue 87 VAL Chi-restraints excluded: chain X residue 113 LEU Chi-restraints excluded: chain Y residue 36 ARG Chi-restraints excluded: chain Y residue 67 GLU Chi-restraints excluded: chain Y residue 96 THR Chi-restraints excluded: chain a residue 11 GLN Chi-restraints excluded: chain a residue 27 TRP Chi-restraints excluded: chain a residue 96 THR Chi-restraints excluded: chain a residue 262 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 407 optimal weight: 3.9990 chunk 170 optimal weight: 7.9990 chunk 176 optimal weight: 0.9990 chunk 424 optimal weight: 7.9990 chunk 400 optimal weight: 3.9990 chunk 336 optimal weight: 5.9990 chunk 87 optimal weight: 10.0000 chunk 385 optimal weight: 8.9990 chunk 39 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 283 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 HIS B 400 GLN ** G 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 109 GLN G 202 HIS N 41 GLN N 49 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.086040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.062217 restraints weight = 82108.738| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.12 r_work: 0.2910 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 37615 Z= 0.193 Angle : 0.585 11.278 50905 Z= 0.301 Chirality : 0.043 0.158 5936 Planarity : 0.004 0.054 6568 Dihedral : 6.850 146.101 5357 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.55 % Favored : 98.41 % Rotamer: Outliers : 1.96 % Allowed : 14.15 % Favored : 83.88 % 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: 1.66 (0.12), residues: 4854 helix: 2.04 (0.10), residues: 2705 sheet: 0.26 (0.20), residues: 561 loop : -0.17 (0.15), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 347 TYR 0.026 0.001 TYR H 115 PHE 0.029 0.001 PHE Y 14 TRP 0.004 0.001 TRP Y 26 HIS 0.017 0.001 HIS G 202 Details of bonding type rmsd covalent geometry : bond 0.00463 (37614) covalent geometry : angle 0.58456 (50905) hydrogen bonds : bond 0.05628 ( 2365) hydrogen bonds : angle 4.36578 ( 6930) metal coordination : bond 0.00086 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 3823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 289 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 427 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.8175 (mtm-85) REVERT: B 3 GLN cc_start: 0.8387 (mt0) cc_final: 0.8167 (pt0) REVERT: B 95 ILE cc_start: 0.8853 (OUTLIER) cc_final: 0.7795 (pp) REVERT: B 505 ILE cc_start: 0.8358 (OUTLIER) cc_final: 0.8130 (mp) REVERT: E 86 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8640 (mptp) REVERT: E 198 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.7906 (mtp) REVERT: E 343 ASP cc_start: 0.8730 (OUTLIER) cc_final: 0.8456 (t70) REVERT: G 109 GLN cc_start: 0.7840 (tt0) cc_final: 0.7445 (mt0) REVERT: G 143 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.7748 (pp20) REVERT: H 91 ASP cc_start: 0.8190 (t0) cc_final: 0.7830 (t0) REVERT: H 121 ARG cc_start: 0.7234 (ttm-80) cc_final: 0.6883 (ttp-110) REVERT: I 2 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7416 (mt-10) REVERT: I 54 ILE cc_start: 0.8819 (OUTLIER) cc_final: 0.8596 (mp) REVERT: I 60 ASP cc_start: 0.8055 (t0) cc_final: 0.7706 (t0) REVERT: I 64 MET cc_start: 0.8522 (mmt) cc_final: 0.8238 (mmm) REVERT: J 43 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.8064 (mp0) REVERT: L 43 GLU cc_start: 0.8386 (pm20) cc_final: 0.7912 (pm20) REVERT: L 44 MET cc_start: 0.8163 (mmm) cc_final: 0.7829 (mmm) REVERT: L 64 MET cc_start: 0.8486 (OUTLIER) cc_final: 0.7630 (mpt) REVERT: P 41 GLN cc_start: 0.7397 (mp10) cc_final: 0.7182 (mp10) REVERT: Q 44 MET cc_start: 0.7561 (mmp) cc_final: 0.7065 (tpp) REVERT: S 1 MET cc_start: 0.6754 (mmp) cc_final: 0.6450 (mmp) REVERT: X 66 ARG cc_start: 0.7964 (ptp-170) cc_final: 0.7716 (ptp-170) REVERT: X 86 ILE cc_start: 0.8358 (OUTLIER) cc_final: 0.8141 (mp) REVERT: Y 36 ARG cc_start: 0.7053 (OUTLIER) cc_final: 0.5487 (tpp80) REVERT: Y 67 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7943 (mp0) REVERT: Y 139 SER cc_start: 0.7260 (OUTLIER) cc_final: 0.6902 (p) REVERT: a 27 TRP cc_start: -0.0267 (OUTLIER) cc_final: -0.0675 (p90) REVERT: a 95 ASP cc_start: 0.8356 (t0) cc_final: 0.8135 (t0) REVERT: a 101 ASN cc_start: 0.5871 (t0) cc_final: 0.5515 (t0) outliers start: 75 outliers final: 32 residues processed: 335 average time/residue: 0.7820 time to fit residues: 310.4607 Evaluate side-chains 321 residues out of total 3823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 274 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 427 ARG Chi-restraints excluded: chain A residue 445 MET Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain D residue 384 MET Chi-restraints excluded: chain E residue 86 LYS Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 198 MET Chi-restraints excluded: chain E residue 259 VAL Chi-restraints excluded: chain E residue 343 ASP Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 348 GLN Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain G residue 202 HIS Chi-restraints excluded: chain H residue 43 ILE Chi-restraints excluded: chain H residue 66 SER Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 43 GLU Chi-restraints excluded: chain J residue 83 ILE Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 64 MET Chi-restraints excluded: chain M residue 65 ILE Chi-restraints excluded: chain O residue 23 THR Chi-restraints excluded: chain P residue 59 LEU Chi-restraints excluded: chain Q residue 49 GLN Chi-restraints excluded: chain Q residue 60 ASP Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain S residue 16 ILE Chi-restraints excluded: chain W residue 34 VAL Chi-restraints excluded: chain X residue 8 ILE Chi-restraints excluded: chain X residue 86 ILE Chi-restraints excluded: chain X residue 113 LEU Chi-restraints excluded: chain Y residue 36 ARG Chi-restraints excluded: chain Y residue 67 GLU Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 139 SER Chi-restraints excluded: chain a residue 11 GLN Chi-restraints excluded: chain a residue 27 TRP Chi-restraints excluded: chain a residue 96 THR Chi-restraints excluded: chain a residue 262 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 201 optimal weight: 7.9990 chunk 221 optimal weight: 4.9990 chunk 148 optimal weight: 2.9990 chunk 207 optimal weight: 4.9990 chunk 370 optimal weight: 1.9990 chunk 161 optimal weight: 8.9990 chunk 387 optimal weight: 4.9990 chunk 346 optimal weight: 0.9980 chunk 373 optimal weight: 10.0000 chunk 85 optimal weight: 4.9990 chunk 80 optimal weight: 7.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 458 GLN ** G 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 202 HIS N 41 GLN N 49 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.086173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.062417 restraints weight = 81926.905| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 2.08 r_work: 0.2912 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 37615 Z= 0.186 Angle : 0.581 10.504 50905 Z= 0.298 Chirality : 0.043 0.154 5936 Planarity : 0.004 0.055 6568 Dihedral : 6.755 137.163 5357 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.57 % Favored : 98.39 % Rotamer: Outliers : 2.01 % Allowed : 14.31 % Favored : 83.67 % 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: 1.68 (0.12), residues: 4854 helix: 2.07 (0.10), residues: 2704 sheet: 0.26 (0.20), residues: 561 loop : -0.18 (0.15), residues: 1589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG Y 49 TYR 0.025 0.001 TYR H 115 PHE 0.026 0.001 PHE Y 14 TRP 0.004 0.001 TRP X 26 HIS 0.022 0.001 HIS G 202 Details of bonding type rmsd covalent geometry : bond 0.00443 (37614) covalent geometry : angle 0.58131 (50905) hydrogen bonds : bond 0.05513 ( 2365) hydrogen bonds : angle 4.33420 ( 6930) metal coordination : bond 0.00111 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 3823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 287 time to evaluate : 1.590 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 95 ILE cc_start: 0.8903 (OUTLIER) cc_final: 0.7904 (pp) REVERT: B 505 ILE cc_start: 0.8399 (OUTLIER) cc_final: 0.8176 (mp) REVERT: C 449 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8676 (mp) REVERT: E 198 MET cc_start: 0.8420 (OUTLIER) cc_final: 0.7993 (mtp) REVERT: E 343 ASP cc_start: 0.8705 (OUTLIER) cc_final: 0.8469 (t70) REVERT: G 109 GLN cc_start: 0.7859 (tt0) cc_final: 0.7436 (mt0) REVERT: G 143 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.7752 (pp20) REVERT: H 91 ASP cc_start: 0.8213 (t0) cc_final: 0.7842 (t0) REVERT: H 121 ARG cc_start: 0.7279 (ttm-80) cc_final: 0.7061 (mtp-110) REVERT: I 2 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7442 (mt-10) REVERT: I 54 ILE cc_start: 0.8871 (OUTLIER) cc_final: 0.8636 (mp) REVERT: I 60 ASP cc_start: 0.8117 (t0) cc_final: 0.7773 (t0) REVERT: I 64 MET cc_start: 0.8565 (mmt) cc_final: 0.8309 (mmm) REVERT: L 43 GLU cc_start: 0.8413 (pm20) cc_final: 0.7940 (pm20) REVERT: L 44 MET cc_start: 0.8174 (mmm) cc_final: 0.7880 (mmm) REVERT: L 64 MET cc_start: 0.8501 (OUTLIER) cc_final: 0.7625 (mpt) REVERT: O 60 ASP cc_start: 0.8915 (OUTLIER) cc_final: 0.8606 (m-30) REVERT: P 41 GLN cc_start: 0.7418 (mp10) cc_final: 0.7195 (mp10) REVERT: Q 1 MET cc_start: 0.7795 (tpp) cc_final: 0.7443 (tpt) REVERT: Q 44 MET cc_start: 0.7515 (mmp) cc_final: 0.7035 (tpp) REVERT: S 1 MET cc_start: 0.6757 (mmp) cc_final: 0.6471 (mmp) REVERT: X 86 ILE cc_start: 0.8441 (OUTLIER) cc_final: 0.8231 (mp) REVERT: Y 36 ARG cc_start: 0.7120 (OUTLIER) cc_final: 0.5650 (tpp80) REVERT: Y 67 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7903 (mp0) REVERT: Y 139 SER cc_start: 0.7281 (OUTLIER) cc_final: 0.6906 (p) REVERT: a 27 TRP cc_start: -0.0245 (OUTLIER) cc_final: -0.0675 (p90) REVERT: a 95 ASP cc_start: 0.8351 (t0) cc_final: 0.8147 (t0) REVERT: a 101 ASN cc_start: 0.5855 (t0) cc_final: 0.5467 (t0) outliers start: 77 outliers final: 39 residues processed: 340 average time/residue: 0.7801 time to fit residues: 314.2285 Evaluate side-chains 320 residues out of total 3823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 267 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASP Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 445 MET Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain D residue 384 MET Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 198 MET Chi-restraints excluded: chain E residue 259 VAL Chi-restraints excluded: chain E residue 343 ASP Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 348 GLN Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain G residue 202 HIS Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain H residue 43 ILE Chi-restraints excluded: chain H residue 66 SER Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 83 ILE Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 64 MET Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain M residue 65 ILE Chi-restraints excluded: chain O residue 23 THR Chi-restraints excluded: chain O residue 60 ASP Chi-restraints excluded: chain P residue 59 LEU Chi-restraints excluded: chain Q residue 60 ASP Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain S residue 16 ILE Chi-restraints excluded: chain W residue 34 VAL Chi-restraints excluded: chain X residue 8 ILE Chi-restraints excluded: chain X residue 86 ILE Chi-restraints excluded: chain X residue 87 VAL Chi-restraints excluded: chain X residue 113 LEU Chi-restraints excluded: chain Y residue 36 ARG Chi-restraints excluded: chain Y residue 67 GLU Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 135 ILE Chi-restraints excluded: chain Y residue 139 SER Chi-restraints excluded: chain a residue 11 GLN Chi-restraints excluded: chain a residue 27 TRP Chi-restraints excluded: chain a residue 96 THR Chi-restraints excluded: chain a residue 262 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 408 optimal weight: 0.3980 chunk 68 optimal weight: 4.9990 chunk 153 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 239 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 57 optimal weight: 7.9990 chunk 162 optimal weight: 0.0670 chunk 208 optimal weight: 7.9990 chunk 221 optimal weight: 3.9990 chunk 287 optimal weight: 2.9990 overall best weight: 2.0924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 458 GLN ** G 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 202 HIS N 41 GLN N 49 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.087723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.063839 restraints weight = 82606.882| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.11 r_work: 0.2926 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 37615 Z= 0.146 Angle : 0.560 10.397 50905 Z= 0.287 Chirality : 0.041 0.148 5936 Planarity : 0.004 0.059 6568 Dihedral : 6.553 126.448 5357 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.55 % Favored : 98.41 % Rotamer: Outliers : 1.54 % Allowed : 14.86 % Favored : 83.59 % 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: 1.84 (0.12), residues: 4854 helix: 2.20 (0.10), residues: 2706 sheet: 0.33 (0.20), residues: 568 loop : -0.11 (0.15), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG Y 49 TYR 0.021 0.001 TYR H 115 PHE 0.026 0.001 PHE Y 14 TRP 0.005 0.001 TRP G 203 HIS 0.021 0.001 HIS G 202 Details of bonding type rmsd covalent geometry : bond 0.00335 (37614) covalent geometry : angle 0.56030 (50905) hydrogen bonds : bond 0.05104 ( 2365) hydrogen bonds : angle 4.25359 ( 6930) metal coordination : bond 0.00027 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 3823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 277 time to evaluate : 1.551 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 95 ILE cc_start: 0.8797 (OUTLIER) cc_final: 0.7616 (pp) REVERT: B 505 ILE cc_start: 0.8358 (OUTLIER) cc_final: 0.8140 (mp) REVERT: C 419 ARG cc_start: 0.7137 (mtt-85) cc_final: 0.6929 (mtt-85) REVERT: E 343 ASP cc_start: 0.8693 (OUTLIER) cc_final: 0.8473 (t70) REVERT: F 11 ARG cc_start: 0.8436 (mtm110) cc_final: 0.7928 (mmm-85) REVERT: F 348 GLN cc_start: 0.8967 (OUTLIER) cc_final: 0.8199 (mm-40) REVERT: G 109 GLN cc_start: 0.7838 (tt0) cc_final: 0.7460 (mt0) REVERT: G 143 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.7781 (pp20) REVERT: H 91 ASP cc_start: 0.8160 (t0) cc_final: 0.7761 (t0) REVERT: H 121 ARG cc_start: 0.7275 (ttm-80) cc_final: 0.7070 (mtp-110) REVERT: I 2 GLU cc_start: 0.7722 (mt-10) cc_final: 0.7400 (mt-10) REVERT: I 54 ILE cc_start: 0.8830 (OUTLIER) cc_final: 0.8604 (mp) REVERT: I 60 ASP cc_start: 0.8128 (t0) cc_final: 0.7787 (t0) REVERT: I 64 MET cc_start: 0.8481 (mmt) cc_final: 0.8247 (mmm) REVERT: L 43 GLU cc_start: 0.8423 (pm20) cc_final: 0.7911 (pm20) REVERT: L 44 MET cc_start: 0.8106 (mmm) cc_final: 0.7809 (mmm) REVERT: L 60 ASP cc_start: 0.8155 (t0) cc_final: 0.6683 (t0) REVERT: L 64 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.7681 (mpt) REVERT: P 41 GLN cc_start: 0.7342 (mp10) cc_final: 0.7107 (mp10) REVERT: Q 1 MET cc_start: 0.7789 (tpp) cc_final: 0.7413 (tpt) REVERT: S 1 MET cc_start: 0.6704 (mmp) cc_final: 0.6415 (mmp) REVERT: X 86 ILE cc_start: 0.8397 (OUTLIER) cc_final: 0.8180 (mp) REVERT: Y 36 ARG cc_start: 0.7104 (OUTLIER) cc_final: 0.5644 (tpp80) REVERT: Y 67 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7885 (mp0) REVERT: Y 139 SER cc_start: 0.7240 (OUTLIER) cc_final: 0.6875 (p) REVERT: a 27 TRP cc_start: -0.0240 (OUTLIER) cc_final: -0.0725 (p90) REVERT: a 101 ASN cc_start: 0.5763 (t0) cc_final: 0.5382 (t0) outliers start: 59 outliers final: 37 residues processed: 318 average time/residue: 0.7976 time to fit residues: 302.1786 Evaluate side-chains 321 residues out of total 3823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 272 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASP Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 445 MET Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain D residue 384 MET Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 259 VAL Chi-restraints excluded: chain E residue 343 ASP Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 348 GLN Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain G residue 202 HIS Chi-restraints excluded: chain G residue 276 ILE Chi-restraints excluded: chain H residue 66 SER Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 47 MET Chi-restraints excluded: chain J residue 83 ILE Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 64 MET Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain M residue 65 ILE Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 23 THR Chi-restraints excluded: chain P residue 59 LEU Chi-restraints excluded: chain Q residue 60 ASP Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain S residue 16 ILE Chi-restraints excluded: chain S residue 47 MET Chi-restraints excluded: chain W residue 34 VAL Chi-restraints excluded: chain X residue 86 ILE Chi-restraints excluded: chain X residue 87 VAL Chi-restraints excluded: chain X residue 109 ILE Chi-restraints excluded: chain Y residue 36 ARG Chi-restraints excluded: chain Y residue 67 GLU Chi-restraints excluded: chain Y residue 139 SER Chi-restraints excluded: chain a residue 11 GLN Chi-restraints excluded: chain a residue 27 TRP Chi-restraints excluded: chain a residue 96 THR Chi-restraints excluded: chain a residue 262 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 306 optimal weight: 4.9990 chunk 410 optimal weight: 2.9990 chunk 89 optimal weight: 9.9990 chunk 199 optimal weight: 6.9990 chunk 424 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 chunk 364 optimal weight: 0.9990 chunk 133 optimal weight: 3.9990 chunk 332 optimal weight: 8.9990 chunk 282 optimal weight: 5.9990 chunk 313 optimal weight: 9.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 458 GLN ** G 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 202 HIS N 49 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.086434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.062716 restraints weight = 82143.103| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.07 r_work: 0.2923 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 37615 Z= 0.177 Angle : 0.583 10.764 50905 Z= 0.298 Chirality : 0.042 0.155 5936 Planarity : 0.004 0.064 6568 Dihedral : 6.560 118.654 5357 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.75 % Favored : 98.21 % Rotamer: Outliers : 1.60 % Allowed : 14.89 % Favored : 83.52 % 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: 1.80 (0.12), residues: 4854 helix: 2.17 (0.10), residues: 2705 sheet: 0.32 (0.20), residues: 568 loop : -0.14 (0.15), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 347 TYR 0.022 0.001 TYR H 115 PHE 0.024 0.001 PHE Y 14 TRP 0.005 0.001 TRP X 26 HIS 0.016 0.001 HIS G 202 Details of bonding type rmsd covalent geometry : bond 0.00421 (37614) covalent geometry : angle 0.58263 (50905) hydrogen bonds : bond 0.05318 ( 2365) hydrogen bonds : angle 4.28095 ( 6930) metal coordination : bond 0.00042 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 3823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 270 time to evaluate : 1.546 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 49 MET cc_start: 0.8968 (mtm) cc_final: 0.8676 (mtm) REVERT: B 95 ILE cc_start: 0.8750 (OUTLIER) cc_final: 0.7531 (pp) REVERT: B 505 ILE cc_start: 0.8355 (OUTLIER) cc_final: 0.8128 (mp) REVERT: C 419 ARG cc_start: 0.7128 (mtt-85) cc_final: 0.6927 (mtt-85) REVERT: E 343 ASP cc_start: 0.8739 (OUTLIER) cc_final: 0.8476 (t70) REVERT: F 348 GLN cc_start: 0.8934 (OUTLIER) cc_final: 0.8169 (mm-40) REVERT: G 109 GLN cc_start: 0.7781 (tt0) cc_final: 0.7423 (mt0) REVERT: G 143 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.7757 (pp20) REVERT: H 91 ASP cc_start: 0.8173 (t0) cc_final: 0.7773 (t0) REVERT: H 121 ARG cc_start: 0.7232 (ttm-80) cc_final: 0.7021 (mtp-110) REVERT: I 2 GLU cc_start: 0.7746 (mt-10) cc_final: 0.7404 (mt-10) REVERT: I 54 ILE cc_start: 0.8802 (OUTLIER) cc_final: 0.8580 (mp) REVERT: I 60 ASP cc_start: 0.8094 (t0) cc_final: 0.7737 (t0) REVERT: I 64 MET cc_start: 0.8505 (mmt) cc_final: 0.8245 (mmm) REVERT: L 43 GLU cc_start: 0.8425 (pm20) cc_final: 0.7907 (pm20) REVERT: L 44 MET cc_start: 0.8150 (mmm) cc_final: 0.7846 (mmm) REVERT: L 64 MET cc_start: 0.8457 (OUTLIER) cc_final: 0.7595 (mpt) REVERT: P 41 GLN cc_start: 0.7330 (mp10) cc_final: 0.7085 (mp10) REVERT: Q 1 MET cc_start: 0.7779 (tpp) cc_final: 0.7416 (tpt) REVERT: S 1 MET cc_start: 0.6632 (mmp) cc_final: 0.6335 (mmp) REVERT: X 86 ILE cc_start: 0.8341 (OUTLIER) cc_final: 0.8128 (mp) REVERT: Y 36 ARG cc_start: 0.7023 (OUTLIER) cc_final: 0.5648 (tpp80) REVERT: Y 67 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7831 (mp0) REVERT: Y 139 SER cc_start: 0.7223 (OUTLIER) cc_final: 0.6855 (p) REVERT: a 27 TRP cc_start: -0.0326 (OUTLIER) cc_final: -0.0836 (p90) REVERT: a 101 ASN cc_start: 0.5718 (t0) cc_final: 0.5335 (t0) outliers start: 61 outliers final: 38 residues processed: 315 average time/residue: 0.7268 time to fit residues: 273.2389 Evaluate side-chains 317 residues out of total 3823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 267 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASP Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 445 MET Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain D residue 384 MET Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 259 VAL Chi-restraints excluded: chain E residue 343 ASP Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 348 GLN Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain G residue 276 ILE Chi-restraints excluded: chain H residue 43 ILE Chi-restraints excluded: chain H residue 66 SER Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 47 MET Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 47 MET Chi-restraints excluded: chain L residue 64 MET Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain M residue 65 ILE Chi-restraints excluded: chain O residue 23 THR Chi-restraints excluded: chain P residue 59 LEU Chi-restraints excluded: chain Q residue 60 ASP Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain S residue 16 ILE Chi-restraints excluded: chain S residue 47 MET Chi-restraints excluded: chain W residue 34 VAL Chi-restraints excluded: chain X residue 86 ILE Chi-restraints excluded: chain X residue 87 VAL Chi-restraints excluded: chain X residue 109 ILE Chi-restraints excluded: chain X residue 113 LEU Chi-restraints excluded: chain Y residue 36 ARG Chi-restraints excluded: chain Y residue 67 GLU Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 139 SER Chi-restraints excluded: chain a residue 11 GLN Chi-restraints excluded: chain a residue 27 TRP Chi-restraints excluded: chain a residue 96 THR Chi-restraints excluded: chain a residue 262 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 378 optimal weight: 0.9980 chunk 141 optimal weight: 0.0030 chunk 302 optimal weight: 9.9990 chunk 309 optimal weight: 5.9990 chunk 134 optimal weight: 6.9990 chunk 186 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 chunk 163 optimal weight: 10.0000 chunk 56 optimal weight: 8.9990 chunk 114 optimal weight: 4.9990 chunk 418 optimal weight: 10.0000 overall best weight: 3.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 458 GLN ** G 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 202 HIS N 41 GLN N 49 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.086108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.062336 restraints weight = 82305.014| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.08 r_work: 0.2912 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 37615 Z= 0.194 Angle : 0.600 10.204 50905 Z= 0.307 Chirality : 0.043 0.156 5936 Planarity : 0.004 0.065 6568 Dihedral : 6.583 117.909 5357 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.69 % Favored : 98.27 % Rotamer: Outliers : 1.57 % Allowed : 14.94 % Favored : 83.49 % 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: 1.73 (0.12), residues: 4854 helix: 2.11 (0.10), residues: 2705 sheet: 0.27 (0.21), residues: 558 loop : -0.16 (0.15), residues: 1591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 347 TYR 0.025 0.001 TYR H 115 PHE 0.024 0.001 PHE Y 14 TRP 0.009 0.001 TRP G 203 HIS 0.008 0.001 HIS G 202 Details of bonding type rmsd covalent geometry : bond 0.00466 (37614) covalent geometry : angle 0.59973 (50905) hydrogen bonds : bond 0.05499 ( 2365) hydrogen bonds : angle 4.32184 ( 6930) metal coordination : bond 0.00052 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13916.81 seconds wall clock time: 237 minutes 9.24 seconds (14229.24 seconds total)