Starting phenix.real_space_refine (version: dev) on Tue May 17 05:08:53 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oqr_20167/05_2022/6oqr_20167_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oqr_20167/05_2022/6oqr_20167.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oqr_20167/05_2022/6oqr_20167.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oqr_20167/05_2022/6oqr_20167.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oqr_20167/05_2022/6oqr_20167_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oqr_20167/05_2022/6oqr_20167_neut_updated.pdb" } resolution = 3.1 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 ------------------------------------------------------------------------------- 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= -0.000 sd= 0.003 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "H TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 36951 Number of models: 1 Model: "" Number of chains: 28 Chain: "W" Number of atoms: 1320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1320 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 3, 'TRANS': 169} Chain: "C" Number of atoms: 3869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3869 Classifications: {'peptide': 512} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 17, 'TRANS': 493, 'PCIS': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 3851 Classifications: {'peptide': 511} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 17, 'TRANS': 492, 'PCIS': 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 3832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 3832 Classifications: {'peptide': 508} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 17, 'TRANS': 489, 'PCIS': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "X" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1210 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 153} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "H" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1034 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 4, 'TRANS': 131} Chain: "G" Number of atoms: 2186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2186 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 7, 'TRANS': 274, 'PCIS': 2} Chain: "F" Number of atoms: 3520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3520 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 19, 'TRANS': 437, 'PCIS': 1} Chain: "E" Number of atoms: 3533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3533 Classifications: {'peptide': 460} Link IDs: {'PTRANS': 19, 'TRANS': 439, 'PCIS': 1} Chain: "D" Number of atoms: 3533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3533 Classifications: {'peptide': 460} Link IDs: {'PTRANS': 19, 'TRANS': 439, 'PCIS': 1} Chain: "J" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "L" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "M" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "N" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "O" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "P" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "Q" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "R" Number of atoms: 552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 552 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "Y" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1210 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 153} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "a" Number of atoms: 2104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2104 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 14, 'TRANS': 250, 'PCIS': 1} Chain: "I" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "S" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} 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: "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: "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: "F" 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: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {'PO4': 1, ' MG': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 19.59, per 1000 atoms: 0.53 Number of scatterers: 36951 At special positions: 0 Unit cell: (178.035, 214.721, 135.954, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 180 16.00 P 16 15.00 Mg 5 11.99 O 6965 8.00 N 6314 7.00 C 23471 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 - 3.50 Amino acid : False - 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: 14.75 Conformation dependent library (CDL) restraints added in 5.7 seconds 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8814 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 181 helices and 26 sheets defined 56.4% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.34 Creating SS restraints... Processing helix chain 'W' and resid 4 through 20 removed outlier: 3.888A pdb=" N ARG W 8 " --> pdb=" O ILE W 4 " (cutoff:3.500A) Proline residue: W 9 - end of helix Processing helix chain 'W' and resid 24 through 39 removed outlier: 3.677A pdb=" N ASP W 29 " --> pdb=" O GLU W 25 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS W 39 " --> pdb=" O ALA W 35 " (cutoff:3.500A) Processing helix chain 'W' and resid 41 through 48 removed outlier: 3.647A pdb=" N GLU W 45 " --> pdb=" O GLU W 41 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU W 46 " --> pdb=" O GLN W 42 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER W 48 " --> pdb=" O ALA W 44 " (cutoff:3.500A) Processing helix chain 'W' and resid 53 through 63 removed outlier: 4.158A pdb=" N VAL W 63 " --> pdb=" O SER W 59 " (cutoff:3.500A) Processing helix chain 'W' and resid 71 through 82 removed outlier: 3.580A pdb=" N ILE W 76 " --> pdb=" O GLY W 72 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN W 82 " --> pdb=" O VAL W 78 " (cutoff:3.500A) Processing helix chain 'W' and resid 85 through 102 Proline residue: W 89 - end of helix removed outlier: 4.340A pdb=" N LEU W 92 " --> pdb=" O PRO W 89 " (cutoff:3.500A) Processing helix chain 'W' and resid 120 through 131 Processing helix chain 'W' and resid 163 through 173 removed outlier: 4.103A pdb=" N ASP W 172 " --> pdb=" O GLU W 168 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL W 173 " --> pdb=" O ARG W 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 17 Processing helix chain 'C' and resid 136 through 138 No H-bonds generated for 'chain 'C' and resid 136 through 138' Processing helix chain 'C' and resid 151 through 156 removed outlier: 3.782A pdb=" N MET C 156 " --> pdb=" O ALA C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 186 removed outlier: 4.026A pdb=" N GLN C 186 " --> pdb=" O ALA C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 214 removed outlier: 3.601A pdb=" N ASN C 207 " --> pdb=" O SER C 203 " (cutoff:3.500A) 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 252 Proline residue: C 239 - end of helix removed outlier: 3.902A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG C 252 " --> pdb=" O TYR C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 276 removed outlier: 3.959A pdb=" N VAL C 268 " --> pdb=" O SER C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 285 No H-bonds generated for 'chain 'C' and resid 283 through 285' Processing helix chain 'C' and resid 288 through 300 removed outlier: 4.325A pdb=" N PHE C 291 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N SER C 295 " --> pdb=" O TYR C 292 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ARG C 296 " --> pdb=" O LEU C 293 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLU C 299 " --> pdb=" O ARG C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 312 Processing helix chain 'C' and resid 333 through 335 No H-bonds generated for 'chain 'C' and resid 333 through 335' Processing helix chain 'C' and resid 340 through 348 removed outlier: 3.954A pdb=" N SER C 347 " --> pdb=" O THR C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 361 Processing helix chain 'C' and resid 378 through 381 Processing helix chain 'C' and resid 384 through 412 removed outlier: 3.777A pdb=" N GLY C 391 " --> pdb=" O LYS C 387 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N GLY C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ILE C 393 " --> pdb=" O LEU C 389 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N THR C 395 " --> pdb=" O GLY C 391 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N ALA C 405 " --> pdb=" O ARG C 401 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N PHE C 406 " --> pdb=" O GLU C 402 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N SER C 407 " --> pdb=" O LEU C 403 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N GLN C 408 " --> pdb=" O ALA C 404 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N PHE C 409 " --> pdb=" O ALA C 405 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N SER C 411 " --> pdb=" O SER C 407 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ASP C 412 " --> pdb=" O GLN C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 431 removed outlier: 3.509A pdb=" N LYS C 419 " --> pdb=" O ASP C 415 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLN C 420 " --> pdb=" O ALA C 416 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN C 425 " --> pdb=" O LEU C 421 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS C 426 " --> pdb=" O ASP C 422 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU C 431 " --> pdb=" O VAL C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 452 Processing helix chain 'C' and resid 455 through 457 No H-bonds generated for 'chain 'C' and resid 455 through 457' Processing helix chain 'C' and resid 461 through 478 removed outlier: 3.868A pdb=" N ILE C 464 " --> pdb=" O LEU C 461 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N GLY C 465 " --> pdb=" O SER C 462 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU C 472 " --> pdb=" O ALA C 469 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP C 478 " --> pdb=" O VAL C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 489 removed outlier: 3.548A pdb=" N GLU C 485 " --> pdb=" O PRO C 481 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN C 488 " --> pdb=" O GLN C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 510 Processing helix chain 'B' and resid 5 through 17 removed outlier: 3.562A pdb=" N ARG B 15 " --> pdb=" O LEU B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 156 Processing helix chain 'B' and resid 175 through 188 removed outlier: 3.571A pdb=" N GLN B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG B 187 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N ASP B 188 " --> pdb=" O ILE B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 214 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 251 Proline residue: B 239 - end of helix removed outlier: 3.504A pdb=" N MET B 245 " --> pdb=" O ALA B 241 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 275 Processing helix chain 'B' and resid 283 through 285 No H-bonds generated for 'chain 'B' and resid 283 through 285' Processing helix chain 'B' and resid 288 through 300 removed outlier: 4.550A pdb=" N PHE B 291 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU B 293 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG B 296 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU B 298 " --> pdb=" O SER B 295 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLU B 299 " --> pdb=" O ARG B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 312 Processing helix chain 'B' and resid 333 through 335 No H-bonds generated for 'chain 'B' and resid 333 through 335' Processing helix chain 'B' and resid 341 through 346 Processing helix chain 'B' and resid 357 through 361 Processing helix chain 'B' and resid 378 through 381 Processing helix chain 'B' and resid 384 through 390 Processing helix chain 'B' and resid 393 through 408 removed outlier: 3.960A pdb=" N ALA B 405 " --> pdb=" O ARG B 401 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLN B 408 " --> pdb=" O ALA B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 431 removed outlier: 3.691A pdb=" N HIS B 423 " --> pdb=" O LYS B 419 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN B 425 " --> pdb=" O LEU B 421 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N THR B 428 " --> pdb=" O GLY B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 452 removed outlier: 3.643A pdb=" N VAL B 447 " --> pdb=" O GLN B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 458 removed outlier: 3.801A pdb=" N ASP B 458 " --> pdb=" O TYR B 455 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 455 through 458' Processing helix chain 'B' and resid 461 through 477 removed outlier: 4.772A pdb=" N GLY B 465 " --> pdb=" O SER B 462 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU B 468 " --> pdb=" O GLY B 465 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LEU B 472 " --> pdb=" O ALA B 469 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL B 475 " --> pdb=" O LEU B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 488 removed outlier: 3.826A pdb=" N GLN B 484 " --> pdb=" O ALA B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 508 removed outlier: 3.507A pdb=" N LEU B 504 " --> pdb=" O LEU B 500 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER B 506 " --> pdb=" O GLY B 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 5 through 19 removed outlier: 3.795A pdb=" N SER A 9 " --> pdb=" O SER A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 103 No H-bonds generated for 'chain 'A' and resid 101 through 103' Processing helix chain 'A' and resid 136 through 138 No H-bonds generated for 'chain 'A' and resid 136 through 138' Processing helix chain 'A' and resid 151 through 156 removed outlier: 3.667A pdb=" N SER A 155 " --> pdb=" O LYS A 151 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N MET A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 151 through 156' Processing helix chain 'A' and resid 175 through 188 removed outlier: 4.132A pdb=" N GLN A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ARG A 187 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N ASP A 188 " --> pdb=" O ILE A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 214 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 251 Proline residue: A 239 - end of helix removed outlier: 3.774A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 277 removed outlier: 4.016A pdb=" N LEU A 277 " --> pdb=" O ILE A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 290 through 300 removed outlier: 3.517A pdb=" N HIS A 294 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ARG A 300 " --> pdb=" O ARG A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 312 Processing helix chain 'A' and resid 333 through 335 No H-bonds generated for 'chain 'A' and resid 333 through 335' Processing helix chain 'A' and resid 340 through 347 removed outlier: 3.557A pdb=" N SER A 347 " --> pdb=" O THR A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 361 Processing helix chain 'A' and resid 378 through 381 Processing helix chain 'A' and resid 384 through 390 Processing helix chain 'A' and resid 393 through 409 removed outlier: 3.677A pdb=" N ALA A 405 " --> pdb=" O ARG A 401 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLN A 408 " --> pdb=" O ALA A 404 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N PHE A 409 " --> pdb=" O ALA A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 431 removed outlier: 3.658A pdb=" N GLN A 420 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS A 426 " --> pdb=" O ASP A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 452 Processing helix chain 'A' and resid 461 through 478 removed outlier: 3.873A pdb=" N GLY A 465 " --> pdb=" O LEU A 461 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N SER A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA A 469 " --> pdb=" O GLY A 465 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP A 476 " --> pdb=" O LEU A 472 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG A 477 " --> pdb=" O ALA A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 489 Processing helix chain 'A' and resid 494 through 508 removed outlier: 3.692A pdb=" N LYS A 499 " --> pdb=" O GLU A 495 " (cutoff:3.500A) Processing helix chain 'X' and resid 5 through 24 removed outlier: 4.301A pdb=" N GLN X 10 " --> pdb=" O ILE X 7 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA X 11 " --> pdb=" O LEU X 8 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N MET X 22 " --> pdb=" O LEU X 19 " (cutoff:3.500A) Processing helix chain 'X' and resid 26 through 135 removed outlier: 4.046A pdb=" N ARG X 36 " --> pdb=" O ALA X 32 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE X 40 " --> pdb=" O ARG X 36 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY X 43 " --> pdb=" O GLU X 39 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR X 62 " --> pdb=" O LYS X 58 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN X 64 " --> pdb=" O SER X 60 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU X 65 " --> pdb=" O ALA X 61 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA X 70 " --> pdb=" O LYS X 66 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE X 75 " --> pdb=" O GLU X 71 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLN X 96 " --> pdb=" O ALA X 92 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU X 97 " --> pdb=" O GLU X 93 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA X 107 " --> pdb=" O ALA X 103 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N LYS X 122 " --> pdb=" O GLU X 118 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLN X 123 " --> pdb=" O GLU X 119 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ALA X 125 " --> pdb=" O ARG X 121 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ILE X 126 " --> pdb=" O LYS X 122 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL X 129 " --> pdb=" O ALA X 125 " (cutoff:3.500A) Processing helix chain 'X' and resid 143 through 154 removed outlier: 5.990A pdb=" N ASP X 147 " --> pdb=" O ALA X 144 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASP X 150 " --> pdb=" O ASP X 147 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL X 153 " --> pdb=" O ASP X 150 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 102 removed outlier: 3.732A pdb=" N GLU H 91 " --> pdb=" O GLN H 87 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA H 92 " --> pdb=" O ASP H 88 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA H 101 " --> pdb=" O ALA H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 112 through 124 removed outlier: 3.522A pdb=" N ALA H 119 " --> pdb=" O ALA H 115 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 133 No H-bonds generated for 'chain 'H' and resid 130 through 133' Processing helix chain 'G' and resid 3 through 57 removed outlier: 3.862A pdb=" N ARG G 32 " --> pdb=" O ALA G 28 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N SER G 41 " --> pdb=" O ARG G 37 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ARG G 42 " --> pdb=" O MET G 38 " (cutoff:3.500A) Proline residue: G 43 - end of helix Processing helix chain 'G' and resid 65 through 67 No H-bonds generated for 'chain 'G' and resid 65 through 67' Processing helix chain 'G' and resid 88 through 107 removed outlier: 4.482A pdb=" N ASN G 91 " --> pdb=" O GLY G 88 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASN G 93 " --> pdb=" O LEU G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 128 Processing helix chain 'G' and resid 145 through 160 removed outlier: 5.054A pdb=" N GLY G 150 " --> pdb=" O SER G 146 " (cutoff:3.500A) Proline residue: G 151 - end of helix Processing helix chain 'G' and resid 197 through 202 removed outlier: 3.639A pdb=" N LYS G 201 " --> pdb=" O LEU G 198 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER G 202 " --> pdb=" O LYS G 199 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 280 removed outlier: 3.909A pdb=" N ASP G 216 " --> pdb=" O LYS G 212 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR G 217 " --> pdb=" O ALA G 213 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS G 258 " --> pdb=" O GLY G 254 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLU G 259 " --> pdb=" O SER G 255 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU G 262 " --> pdb=" O LYS G 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 83 No H-bonds generated for 'chain 'F' and resid 81 through 83' Processing helix chain 'F' and resid 116 through 118 No H-bonds generated for 'chain 'F' and resid 116 through 118' Processing helix chain 'F' and resid 131 through 136 Processing helix chain 'F' and resid 157 through 167 Processing helix chain 'F' and resid 183 through 196 removed outlier: 3.608A pdb=" N SER F 196 " --> pdb=" O GLU F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 201 No H-bonds generated for 'chain 'F' and resid 199 through 201' Processing helix chain 'F' and resid 213 through 232 removed outlier: 4.972A pdb=" N ALA F 220 " --> pdb=" O ARG F 216 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N LEU F 221 " --> pdb=" O LEU F 217 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR F 222 " --> pdb=" O ARG F 218 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY F 223 " --> pdb=" O VAL F 219 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 255 removed outlier: 3.915A pdb=" N LEU F 249 " --> pdb=" O ARG F 246 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ALA F 250 " --> pdb=" O TYR F 247 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU F 253 " --> pdb=" O ALA F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 279 removed outlier: 3.711A pdb=" N LEU F 278 " --> pdb=" O GLU F 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 301 No H-bonds generated for 'chain 'F' and resid 299 through 301' Processing helix chain 'F' and resid 306 through 309 No H-bonds generated for 'chain 'F' and resid 306 through 309' Processing helix chain 'F' and resid 312 through 314 No H-bonds generated for 'chain 'F' and resid 312 through 314' Processing helix chain 'F' and resid 323 through 328 removed outlier: 4.763A pdb=" N LEU F 328 " --> pdb=" O GLN F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 346 through 349 No H-bonds generated for 'chain 'F' and resid 346 through 349' Processing helix chain 'F' and resid 351 through 377 removed outlier: 3.599A pdb=" N LYS F 371 " --> pdb=" O TYR F 367 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ASP F 372 " --> pdb=" O GLN F 368 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N ILE F 373 " --> pdb=" O GLU F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 379 through 381 No H-bonds generated for 'chain 'F' and resid 379 through 381' Processing helix chain 'F' and resid 386 through 399 Processing helix chain 'F' and resid 408 through 411 No H-bonds generated for 'chain 'F' and resid 408 through 411' Processing helix chain 'F' and resid 420 through 432 removed outlier: 3.725A pdb=" N ARG F 425 " --> pdb=" O LYS F 421 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLY F 426 " --> pdb=" O ASP F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 440 through 443 Processing helix chain 'F' and resid 449 through 457 removed outlier: 4.086A pdb=" N LYS F 457 " --> pdb=" O VAL F 453 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 83 No H-bonds generated for 'chain 'E' and resid 81 through 83' Processing helix chain 'E' and resid 116 through 118 No H-bonds generated for 'chain 'E' and resid 116 through 118' Processing helix chain 'E' and resid 131 through 136 Processing helix chain 'E' and resid 155 through 168 removed outlier: 3.625A pdb=" N ALA E 167 " --> pdb=" O ILE E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 194 Processing helix chain 'E' and resid 198 through 201 Processing helix chain 'E' and resid 213 through 232 removed outlier: 3.501A pdb=" N ARG E 218 " --> pdb=" O GLY E 214 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N ALA E 220 " --> pdb=" O ARG E 216 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N LEU E 221 " --> pdb=" O LEU E 217 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS E 229 " --> pdb=" O THR E 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 258 Processing helix chain 'E' and resid 271 through 279 removed outlier: 3.808A pdb=" N LEU E 278 " --> pdb=" O GLU E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 301 No H-bonds generated for 'chain 'E' and resid 299 through 301' Processing helix chain 'E' and resid 306 through 312 Processing helix chain 'E' and resid 323 through 327 Processing helix chain 'E' and resid 346 through 349 No H-bonds generated for 'chain 'E' and resid 346 through 349' Processing helix chain 'E' and resid 351 through 377 removed outlier: 3.756A pdb=" N GLU E 369 " --> pdb=" O GLN E 365 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA E 375 " --> pdb=" O LYS E 371 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE E 376 " --> pdb=" O ASP E 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 379 through 381 No H-bonds generated for 'chain 'E' and resid 379 through 381' Processing helix chain 'E' and resid 384 through 399 removed outlier: 3.567A pdb=" N LYS E 395 " --> pdb=" O ALA E 391 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 411 removed outlier: 3.728A pdb=" N GLU E 408 " --> pdb=" O PHE E 405 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N VAL E 409 " --> pdb=" O VAL E 406 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR E 411 " --> pdb=" O GLU E 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 420 through 431 Processing helix chain 'E' and resid 440 through 443 Processing helix chain 'E' and resid 449 through 458 removed outlier: 4.407A pdb=" N GLU E 454 " --> pdb=" O GLU E 450 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS E 458 " --> pdb=" O GLU E 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 83 No H-bonds generated for 'chain 'D' and resid 81 through 83' Processing helix chain 'D' and resid 131 through 136 Processing helix chain 'D' and resid 155 through 169 Processing helix chain 'D' and resid 183 through 195 Processing helix chain 'D' and resid 199 through 201 No H-bonds generated for 'chain 'D' and resid 199 through 201' Processing helix chain 'D' and resid 213 through 232 removed outlier: 5.054A pdb=" N ALA D 220 " --> pdb=" O ARG D 216 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N LEU D 221 " --> pdb=" O LEU D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 257 Processing helix chain 'D' and resid 271 through 279 Processing helix chain 'D' and resid 299 through 301 No H-bonds generated for 'chain 'D' and resid 299 through 301' Processing helix chain 'D' and resid 306 through 314 removed outlier: 3.792A pdb=" N THR D 311 " --> pdb=" O SER D 307 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ALA D 313 " --> pdb=" O ALA D 309 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N HIS D 314 " --> pdb=" O THR D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 327 Processing helix chain 'D' and resid 346 through 377 removed outlier: 7.670A pdb=" N GLN D 351 " --> pdb=" O LEU D 347 " (cutoff:3.500A) removed outlier: 9.111A pdb=" N GLU D 352 " --> pdb=" O VAL D 348 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N HIS D 353 " --> pdb=" O VAL D 349 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ASP D 372 " --> pdb=" O GLN D 368 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE D 373 " --> pdb=" O GLU D 369 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE D 376 " --> pdb=" O ASP D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 381 No H-bonds generated for 'chain 'D' and resid 379 through 381' Processing helix chain 'D' and resid 384 through 399 removed outlier: 3.607A pdb=" N LEU D 388 " --> pdb=" O GLU D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 411 removed outlier: 3.963A pdb=" N VAL D 409 " --> pdb=" O VAL D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 432 removed outlier: 3.521A pdb=" N GLU D 432 " --> pdb=" O LYS D 428 " (cutoff:3.500A) Processing helix chain 'D' and resid 440 through 443 Processing helix chain 'D' and resid 449 through 458 removed outlier: 3.829A pdb=" N VAL D 453 " --> pdb=" O GLU D 450 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU D 454 " --> pdb=" O GLU D 451 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 41 removed outlier: 4.441A pdb=" N LEU J 9 " --> pdb=" O MET J 6 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N TYR J 10 " --> pdb=" O ASP J 7 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ALA J 13 " --> pdb=" O TYR J 10 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LEU J 19 " --> pdb=" O MET J 16 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS J 34 " --> pdb=" O LEU J 31 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 75 removed outlier: 4.112A pdb=" N LEU J 59 " --> pdb=" O ILE J 55 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ALA J 62 " --> pdb=" O GLY J 58 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N ILE J 63 " --> pdb=" O LEU J 59 " (cutoff:3.500A) Proline residue: J 64 - end of helix Processing helix chain 'L' and resid 4 through 41 removed outlier: 3.501A pdb=" N LEU L 8 " --> pdb=" O LEU L 4 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU L 9 " --> pdb=" O ASN L 5 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA L 14 " --> pdb=" O TYR L 10 " (cutoff:3.500A) Processing helix chain 'L' and resid 43 through 76 Proline residue: L 47 - end of helix removed outlier: 3.722A pdb=" N MET L 57 " --> pdb=" O PHE L 54 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLY L 58 " --> pdb=" O ILE L 55 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASP L 61 " --> pdb=" O GLY L 58 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ILE L 63 " --> pdb=" O VAL L 60 " (cutoff:3.500A) Proline residue: L 64 - end of helix removed outlier: 3.511A pdb=" N LEU L 70 " --> pdb=" O ALA L 67 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LEU L 72 " --> pdb=" O GLY L 69 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 41 removed outlier: 5.021A pdb=" N LEU M 9 " --> pdb=" O ASN M 5 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR M 10 " --> pdb=" O MET M 6 " (cutoff:3.500A) Processing helix chain 'M' and resid 43 through 76 Proline residue: M 47 - end of helix removed outlier: 3.757A pdb=" N GLY M 58 " --> pdb=" O ILE M 55 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ILE M 63 " --> pdb=" O VAL M 60 " (cutoff:3.500A) Proline residue: M 64 - end of helix removed outlier: 3.910A pdb=" N VAL M 68 " --> pdb=" O MET M 65 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE M 76 " --> pdb=" O TYR M 73 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 41 removed outlier: 4.464A pdb=" N LEU N 9 " --> pdb=" O ASN N 5 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N TYR N 10 " --> pdb=" O MET N 6 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N MET N 11 " --> pdb=" O ASP N 7 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N LEU N 19 " --> pdb=" O VAL N 15 " (cutoff:3.500A) Processing helix chain 'N' and resid 43 through 76 Proline residue: N 47 - end of helix removed outlier: 3.770A pdb=" N THR N 51 " --> pdb=" O LEU N 48 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY N 58 " --> pdb=" O ILE N 55 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASP N 61 " --> pdb=" O GLY N 58 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ILE N 63 " --> pdb=" O VAL N 60 " (cutoff:3.500A) Proline residue: N 64 - end of helix Processing helix chain 'O' and resid 6 through 41 Processing helix chain 'O' and resid 43 through 62 Proline residue: O 47 - end of helix removed outlier: 3.532A pdb=" N THR O 51 " --> pdb=" O LEU O 48 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL O 56 " --> pdb=" O PHE O 53 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N MET O 57 " --> pdb=" O PHE O 54 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA O 62 " --> pdb=" O LEU O 59 " (cutoff:3.500A) Processing helix chain 'O' and resid 64 through 76 Processing helix chain 'P' and resid 8 through 41 removed outlier: 3.779A pdb=" N ALA P 21 " --> pdb=" O MET P 17 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU P 31 " --> pdb=" O GLY P 27 " (cutoff:3.500A) Processing helix chain 'P' and resid 46 through 77 removed outlier: 4.925A pdb=" N ILE P 63 " --> pdb=" O LEU P 59 " (cutoff:3.500A) Proline residue: P 64 - end of helix removed outlier: 4.053A pdb=" N ALA P 67 " --> pdb=" O ILE P 63 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU P 72 " --> pdb=" O VAL P 68 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 41 removed outlier: 3.643A pdb=" N LEU Q 8 " --> pdb=" O ASN Q 5 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LEU Q 9 " --> pdb=" O MET Q 6 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU Q 19 " --> pdb=" O MET Q 16 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE Q 28 " --> pdb=" O ALA Q 25 " (cutoff:3.500A) Processing helix chain 'Q' and resid 43 through 76 Proline residue: Q 47 - end of helix removed outlier: 3.873A pdb=" N GLY Q 58 " --> pdb=" O ILE Q 55 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ILE Q 63 " --> pdb=" O VAL Q 60 " (cutoff:3.500A) Proline residue: Q 64 - end of helix removed outlier: 3.560A pdb=" N LEU Q 70 " --> pdb=" O ALA Q 67 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TYR Q 73 " --> pdb=" O LEU Q 70 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 41 removed outlier: 3.526A pdb=" N LEU R 8 " --> pdb=" O LEU R 4 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LEU R 9 " --> pdb=" O ASN R 5 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N TYR R 10 " --> pdb=" O MET R 6 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N MET R 16 " --> pdb=" O ALA R 12 " (cutoff:3.500A) Processing helix chain 'R' and resid 43 through 59 Proline residue: R 47 - end of helix removed outlier: 3.582A pdb=" N PHE R 54 " --> pdb=" O THR R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 61 through 76 Processing helix chain 'Y' and resid 4 through 24 removed outlier: 3.540A pdb=" N LEU Y 16 " --> pdb=" O ILE Y 12 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE Y 20 " --> pdb=" O LEU Y 16 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N CYS Y 21 " --> pdb=" O PHE Y 17 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS Y 23 " --> pdb=" O LEU Y 19 " (cutoff:3.500A) Processing helix chain 'Y' and resid 26 through 139 removed outlier: 3.862A pdb=" N ALA Y 47 " --> pdb=" O GLY Y 43 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ALA Y 50 " --> pdb=" O SER Y 46 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASP Y 53 " --> pdb=" O ARG Y 49 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASP Y 55 " --> pdb=" O HIS Y 51 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU Y 56 " --> pdb=" O LYS Y 52 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU Y 65 " --> pdb=" O ALA Y 61 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN Y 73 " --> pdb=" O LYS Y 69 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ILE Y 76 " --> pdb=" O ALA Y 72 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS Y 91 " --> pdb=" O LEU Y 87 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN Y 96 " --> pdb=" O ALA Y 92 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N THR Y 99 " --> pdb=" O GLU Y 95 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS Y 100 " --> pdb=" O GLN Y 96 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU Y 112 " --> pdb=" O GLU Y 108 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL Y 124 " --> pdb=" O LEU Y 120 " (cutoff:3.500A) Processing helix chain 'Y' and resid 142 through 155 removed outlier: 3.926A pdb=" N ALA Y 154 " --> pdb=" O ASP Y 150 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU Y 155 " --> pdb=" O LYS Y 151 " (cutoff:3.500A) Processing helix chain 'a' and resid 8 through 16 removed outlier: 3.693A pdb=" N GLY a 13 " --> pdb=" O GLN a 9 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS a 15 " --> pdb=" O TYR a 11 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N LEU a 16 " --> pdb=" O ILE a 12 " (cutoff:3.500A) Processing helix chain 'a' and resid 47 through 64 removed outlier: 3.718A pdb=" N LEU a 52 " --> pdb=" O PHE a 48 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU a 57 " --> pdb=" O GLY a 53 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU a 59 " --> pdb=" O LEU a 55 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N SER a 62 " --> pdb=" O VAL a 58 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N VAL a 63 " --> pdb=" O LEU a 59 " (cutoff:3.500A) Processing helix chain 'a' and resid 74 through 92 removed outlier: 3.951A pdb=" N ASP a 92 " --> pdb=" O GLY a 88 " (cutoff:3.500A) Processing helix chain 'a' and resid 99 through 120 Proline residue: a 103 - end of helix removed outlier: 3.748A pdb=" N LEU a 106 " --> pdb=" O ALA a 102 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N MET a 118 " --> pdb=" O LEU a 114 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ASP a 119 " --> pdb=" O MET a 115 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LEU a 120 " --> pdb=" O ASN a 116 " (cutoff:3.500A) Processing helix chain 'a' and resid 123 through 132 Proline residue: a 127 - end of helix Processing helix chain 'a' and resid 143 through 145 No H-bonds generated for 'chain 'a' and resid 143 through 145' Processing helix chain 'a' and resid 147 through 180 removed outlier: 7.620A pdb=" N ILE a 171 " --> pdb=" O LYS a 167 " (cutoff:3.500A) removed outlier: 9.401A pdb=" N GLY a 172 " --> pdb=" O MET a 168 " (cutoff:3.500A) Processing helix chain 'a' and resid 186 through 228 Proline residue: a 190 - end of helix removed outlier: 4.314A pdb=" N LEU a 193 " --> pdb=" O PRO a 190 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLU a 196 " --> pdb=" O LEU a 193 " (cutoff:3.500A) Proline residue: a 204 - end of helix removed outlier: 4.076A pdb=" N ARG a 210 " --> pdb=" O LEU a 207 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE a 221 " --> pdb=" O GLY a 218 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE a 225 " --> pdb=" O PHE a 222 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA a 226 " --> pdb=" O ILE a 223 " (cutoff:3.500A) Processing helix chain 'a' and resid 231 through 268 removed outlier: 3.569A pdb=" N GLN a 234 " --> pdb=" O TRP a 231 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N TRP a 235 " --> pdb=" O TRP a 232 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N VAL a 239 " --> pdb=" O ILE a 236 " (cutoff:3.500A) Proline residue: a 240 - end of helix removed outlier: 3.925A pdb=" N ILE a 246 " --> pdb=" O ILE a 243 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR a 250 " --> pdb=" O LEU a 247 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN a 252 " --> pdb=" O ILE a 249 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 41 removed outlier: 3.855A pdb=" N TYR I 10 " --> pdb=" O MET I 6 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N MET I 11 " --> pdb=" O ASP I 7 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA I 12 " --> pdb=" O LEU I 8 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA I 20 " --> pdb=" O MET I 16 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE I 22 " --> pdb=" O GLY I 18 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU I 37 " --> pdb=" O GLY I 33 " (cutoff:3.500A) Processing helix chain 'I' and resid 43 through 76 removed outlier: 3.884A pdb=" N ILE I 46 " --> pdb=" O PRO I 43 " (cutoff:3.500A) Proline residue: I 47 - end of helix removed outlier: 3.570A pdb=" N ARG I 50 " --> pdb=" O PRO I 47 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL I 60 " --> pdb=" O MET I 57 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ILE I 63 " --> pdb=" O VAL I 60 " (cutoff:3.500A) Proline residue: I 64 - end of helix removed outlier: 3.764A pdb=" N LEU I 70 " --> pdb=" O ALA I 67 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE I 76 " --> pdb=" O TYR I 73 " (cutoff:3.500A) Processing helix chain 'S' and resid 4 through 41 removed outlier: 4.905A pdb=" N LEU S 8 " --> pdb=" O LEU S 4 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N LEU S 9 " --> pdb=" O ASN S 5 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TYR S 10 " --> pdb=" O MET S 6 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N MET S 11 " --> pdb=" O ASP S 7 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG S 41 " --> pdb=" O GLU S 37 " (cutoff:3.500A) Processing helix chain 'S' and resid 43 through 76 removed outlier: 3.558A pdb=" N ILE S 46 " --> pdb=" O PRO S 43 " (cutoff:3.500A) Proline residue: S 47 - end of helix removed outlier: 3.567A pdb=" N THR S 51 " --> pdb=" O LEU S 48 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N PHE S 54 " --> pdb=" O THR S 51 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL S 56 " --> pdb=" O PHE S 53 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N MET S 57 " --> pdb=" O PHE S 54 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL S 60 " --> pdb=" O MET S 57 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASP S 61 " --> pdb=" O GLY S 58 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE S 63 " --> pdb=" O VAL S 60 " (cutoff:3.500A) Proline residue: S 64 - end of helix removed outlier: 3.998A pdb=" N LEU S 70 " --> pdb=" O ALA S 67 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'W' and resid 135 through 142 removed outlier: 3.783A pdb=" N VAL W 110 " --> pdb=" O ASN W 139 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 87 through 89 removed outlier: 6.438A pdb=" N ARG C 40 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N VAL C 34 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER C 70 " --> pdb=" O GLU C 67 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N VAL C 74 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ALA C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ARG C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 96 through 98 Processing sheet with id= D, first strand: chain 'C' and resid 107 through 109 removed outlier: 8.349A pdb=" N VAL C 108 " --> pdb=" O THR C 221 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N VAL C 223 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 8.723A pdb=" N ILE C 222 " --> pdb=" O ILE C 191 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N CYS C 193 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N VAL C 224 " --> pdb=" O CYS C 193 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N TYR C 195 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N ALA C 226 " --> pdb=" O TYR C 195 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ALA C 197 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ASP C 255 " --> pdb=" O LYS C 192 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N ILE C 194 " --> pdb=" O ASP C 255 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU C 257 " --> pdb=" O ILE C 194 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N VAL C 196 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ILE C 259 " --> pdb=" O VAL C 196 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ILE C 198 " --> pdb=" O ILE C 259 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ASP C 261 " --> pdb=" O ILE C 198 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N SER C 323 " --> pdb=" O ALA C 256 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N ILE C 258 " --> pdb=" O SER C 323 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N THR C 325 " --> pdb=" O ILE C 258 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N TYR C 260 " --> pdb=" O THR C 325 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'C' and resid 351 through 355 removed outlier: 3.551A pdb=" N LEU C 166 " --> pdb=" O GLY C 351 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 87 through 90 removed outlier: 4.482A pdb=" N ASN B 27 " --> pdb=" O CYS B 90 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ARG B 40 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL B 34 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL B 74 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ALA B 63 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ARG B 59 " --> pdb=" O LEU B 55 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 96 through 98 Processing sheet with id= H, first strand: chain 'B' and resid 107 through 109 removed outlier: 8.234A pdb=" N VAL B 108 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N VAL B 223 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N CYS B 193 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N VAL B 224 " --> pdb=" O CYS B 193 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N TYR B 195 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N ALA B 226 " --> pdb=" O TYR B 195 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ALA B 197 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N SER B 323 " --> pdb=" O ALA B 256 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N ILE B 258 " --> pdb=" O SER B 323 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N THR B 325 " --> pdb=" O ILE B 258 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N TYR B 260 " --> pdb=" O THR B 325 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 352 through 355 removed outlier: 6.626A pdb=" N LEU B 166 " --> pdb=" O ILE B 353 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N LEU B 355 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ILE B 168 " --> pdb=" O LEU B 355 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 87 through 89 removed outlier: 6.534A pdb=" N ARG A 40 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N VAL A 34 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N VAL A 74 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N ALA A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 96 through 98 Processing sheet with id= L, first strand: chain 'A' and resid 107 through 109 removed outlier: 8.194A pdb=" N VAL A 108 " --> pdb=" O THR A 221 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N VAL A 223 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N CYS A 193 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N VAL A 224 " --> pdb=" O CYS A 193 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N TYR A 195 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ALA A 226 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ALA A 197 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N SER A 323 " --> pdb=" O ALA A 256 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N ILE A 258 " --> pdb=" O SER A 323 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N THR A 325 " --> pdb=" O ILE A 258 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N TYR A 260 " --> pdb=" O THR A 325 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LEU A 327 " --> pdb=" O TYR A 260 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 352 through 355 removed outlier: 6.563A pdb=" N LEU A 166 " --> pdb=" O ILE A 353 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N LEU A 355 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ILE A 168 " --> pdb=" O LEU A 355 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'H' and resid 41 through 44 removed outlier: 6.336A pdb=" N HIS H 5 " --> pdb=" O VAL H 76 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N VAL H 78 " --> pdb=" O HIS H 5 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASP H 7 " --> pdb=" O VAL H 78 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N VAL H 53 " --> pdb=" O GLU H 21 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ILE H 23 " --> pdb=" O ARG H 51 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ARG H 51 " --> pdb=" O ILE H 23 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N VAL H 25 " --> pdb=" O MET H 49 " (cutoff:3.500A) removed outlier: 9.115A pdb=" N MET H 49 " --> pdb=" O VAL H 25 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'H' and resid 22 through 26 Processing sheet with id= P, first strand: chain 'G' and resid 181 through 188 removed outlier: 6.710A pdb=" N LEU G 167 " --> pdb=" O LEU G 187 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS G 166 " --> pdb=" O ARG G 74 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N ASN G 172 " --> pdb=" O VAL G 80 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N GLN G 111 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N TYR G 77 " --> pdb=" O GLN G 111 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ASP G 113 " --> pdb=" O TYR G 77 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N VAL G 79 " --> pdb=" O ASP G 113 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ALA G 115 " --> pdb=" O VAL G 79 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N MET G 116 " --> pdb=" O VAL G 133 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLN G 135 " --> pdb=" O MET G 116 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 4 through 9 removed outlier: 6.516A pdb=" N ASP F 14 " --> pdb=" O VAL F 6 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N VAL F 8 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL F 12 " --> pdb=" O VAL F 8 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ILE F 54 " --> pdb=" O VAL F 42 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N VAL F 42 " --> pdb=" O ILE F 54 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ASP F 27 " --> pdb=" O VAL F 42 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N HIS F 73 " --> pdb=" O ALA F 28 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N GLU F 30 " --> pdb=" O LEU F 71 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LEU F 71 " --> pdb=" O GLU F 30 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 76 through 79 removed outlier: 4.729A pdb=" N GLU F 105 " --> pdb=" O VAL F 79 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 317 through 320 removed outlier: 8.014A pdb=" N VAL F 145 " --> pdb=" O ILE F 290 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N SER F 292 " --> pdb=" O VAL F 145 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N LEU F 147 " --> pdb=" O SER F 292 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N GLN F 294 " --> pdb=" O LEU F 147 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N GLY F 149 " --> pdb=" O GLN F 294 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N VAL F 296 " --> pdb=" O GLY F 149 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 4 through 9 removed outlier: 6.556A pdb=" N ASP E 14 " --> pdb=" O VAL E 6 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N VAL E 8 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL E 12 " --> pdb=" O VAL E 8 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ILE E 54 " --> pdb=" O VAL E 42 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N VAL E 42 " --> pdb=" O ILE E 54 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU E 36 " --> pdb=" O ASN E 33 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 76 through 78 Processing sheet with id= V, first strand: chain 'E' and resid 317 through 319 removed outlier: 8.462A pdb=" N VAL E 145 " --> pdb=" O ILE E 290 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N SER E 292 " --> pdb=" O VAL E 145 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N LEU E 147 " --> pdb=" O SER E 292 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLN E 294 " --> pdb=" O LEU E 147 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N TYR E 173 " --> pdb=" O LEU E 238 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N PHE E 240 " --> pdb=" O TYR E 173 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL E 175 " --> pdb=" O PHE E 240 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N SER E 203 " --> pdb=" O PHE E 176 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N GLY E 178 " --> pdb=" O SER E 203 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N VAL E 205 " --> pdb=" O GLY E 178 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 4 through 9 removed outlier: 6.570A pdb=" N ASP D 14 " --> pdb=" O VAL D 6 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N VAL D 8 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL D 12 " --> pdb=" O VAL D 8 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE D 54 " --> pdb=" O VAL D 42 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N VAL D 42 " --> pdb=" O ILE D 54 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ASP D 27 " --> pdb=" O VAL D 42 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N HIS D 73 " --> pdb=" O ALA D 28 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N GLU D 30 " --> pdb=" O LEU D 71 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LEU D 71 " --> pdb=" O GLU D 30 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N GLN D 32 " --> pdb=" O LYS D 69 " (cutoff:3.500A) removed outlier: 9.733A pdb=" N LYS D 69 " --> pdb=" O GLN D 32 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 76 through 79 removed outlier: 4.589A pdb=" N GLU D 105 " --> pdb=" O VAL D 79 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 317 through 321 removed outlier: 8.804A pdb=" N VAL D 145 " --> pdb=" O ILE D 290 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N SER D 292 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N LEU D 147 " --> pdb=" O SER D 292 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLN D 294 " --> pdb=" O LEU D 147 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N GLY D 149 " --> pdb=" O GLN D 294 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N VAL D 296 " --> pdb=" O GLY D 149 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL D 175 " --> pdb=" O PHE D 240 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'a' and resid 20 through 22 removed outlier: 3.550A pdb=" N ILE a 41 " --> pdb=" O LEU a 21 " (cutoff:3.500A) 1901 hydrogen bonds defined for protein. 4596 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: 14.54 Time building geometry restraints manager: 16.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 6329 1.28 - 1.42: 8549 1.42 - 1.55: 22243 1.55 - 1.68: 25 1.68 - 1.81: 360 Bond restraints: 37506 Sorted by residual: bond pdb=" C4 ATP B 600 " pdb=" C5 ATP B 600 " ideal model delta sigma weight residual 1.388 1.457 -0.069 1.00e-02 1.00e+04 4.75e+01 bond pdb=" C4 ATP A 600 " pdb=" C5 ATP A 600 " ideal model delta sigma weight residual 1.388 1.456 -0.068 1.00e-02 1.00e+04 4.68e+01 bond pdb=" C PRO C 342 " pdb=" O PRO C 342 " ideal model delta sigma weight residual 1.238 1.153 0.085 1.24e-02 6.50e+03 4.68e+01 bond pdb=" C4 ATP C 600 " pdb=" C5 ATP C 600 " ideal model delta sigma weight residual 1.388 1.454 -0.066 1.00e-02 1.00e+04 4.37e+01 bond pdb=" C5 ATP B 600 " pdb=" C6 ATP B 600 " ideal model delta sigma weight residual 1.409 1.467 -0.058 1.00e-02 1.00e+04 3.36e+01 ... (remaining 37501 not shown) Histogram of bond angle deviations from ideal: 98.26 - 105.80: 848 105.80 - 113.35: 21178 113.35 - 120.90: 18635 120.90 - 128.44: 9886 128.44 - 135.99: 219 Bond angle restraints: 50766 Sorted by residual: angle pdb=" PB ATP B 600 " pdb=" O3B ATP B 600 " pdb=" PG ATP B 600 " ideal model delta sigma weight residual 139.87 116.08 23.79 1.00e+00 1.00e+00 5.66e+02 angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 116.84 23.03 1.00e+00 1.00e+00 5.30e+02 angle pdb=" PB ATP C 600 " pdb=" O3B ATP C 600 " pdb=" PG ATP C 600 " ideal model delta sigma weight residual 139.87 117.61 22.26 1.00e+00 1.00e+00 4.95e+02 angle pdb=" PA ATP A 600 " pdb=" O3A ATP A 600 " pdb=" PB ATP A 600 " ideal model delta sigma weight residual 136.83 116.86 19.97 1.00e+00 1.00e+00 3.99e+02 angle pdb=" PA ATP B 600 " pdb=" O3A ATP B 600 " pdb=" PB ATP B 600 " ideal model delta sigma weight residual 136.83 118.52 18.31 1.00e+00 1.00e+00 3.35e+02 ... (remaining 50761 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.35: 21859 28.35 - 56.71: 721 56.71 - 85.06: 95 85.06 - 113.42: 12 113.42 - 141.77: 5 Dihedral angle restraints: 22692 sinusoidal: 8914 harmonic: 13778 Sorted by residual: dihedral pdb=" O1B ADP D 500 " pdb=" O3A ADP D 500 " pdb=" PB ADP D 500 " pdb=" PA ADP D 500 " ideal model delta sinusoidal sigma weight residual 300.00 158.22 141.77 1 2.00e+01 2.50e-03 4.29e+01 dihedral pdb=" O2A ADP F 500 " pdb=" O3A ADP F 500 " pdb=" PA ADP F 500 " pdb=" PB ADP F 500 " ideal model delta sinusoidal sigma weight residual -60.00 80.10 -140.09 1 2.00e+01 2.50e-03 4.24e+01 dihedral pdb=" C5' ADP E 500 " pdb=" O5' ADP E 500 " pdb=" PA ADP E 500 " pdb=" O2A ADP E 500 " ideal model delta sinusoidal sigma weight residual 300.00 170.76 129.24 1 2.00e+01 2.50e-03 3.92e+01 ... (remaining 22689 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 5338 0.083 - 0.166: 548 0.166 - 0.249: 24 0.249 - 0.332: 5 0.332 - 0.415: 3 Chirality restraints: 5918 Sorted by residual: chirality pdb=" CA LEU a 178 " pdb=" N LEU a 178 " pdb=" C LEU a 178 " pdb=" CB LEU a 178 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.30e+00 chirality pdb=" CA SER a 202 " pdb=" N SER a 202 " pdb=" C SER a 202 " pdb=" CB SER a 202 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" CA ASP L 7 " pdb=" N ASP L 7 " pdb=" C ASP L 7 " pdb=" CB ASP L 7 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.93e+00 ... (remaining 5915 not shown) Planarity restraints: 6547 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA D 264 " 0.020 2.00e-02 2.50e+03 4.22e-02 1.78e+01 pdb=" C ALA D 264 " -0.073 2.00e-02 2.50e+03 pdb=" O ALA D 264 " 0.027 2.00e-02 2.50e+03 pdb=" N VAL D 265 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 414 " -0.017 2.00e-02 2.50e+03 3.61e-02 1.30e+01 pdb=" C ASP B 414 " 0.062 2.00e-02 2.50e+03 pdb=" O ASP B 414 " -0.023 2.00e-02 2.50e+03 pdb=" N ASP B 415 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 338 " 0.017 2.00e-02 2.50e+03 3.59e-02 1.29e+01 pdb=" C SER C 338 " -0.062 2.00e-02 2.50e+03 pdb=" O SER C 338 " 0.023 2.00e-02 2.50e+03 pdb=" N ALA C 339 " 0.022 2.00e-02 2.50e+03 ... (remaining 6544 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 51 2.38 - 3.01: 23648 3.01 - 3.64: 53165 3.64 - 4.27: 84692 4.27 - 4.90: 143337 Nonbonded interactions: 304893 Sorted by model distance: nonbonded pdb=" O2B ATP A 600 " pdb="MG MG A 601 " model vdw 1.753 2.170 nonbonded pdb=" O2G ATP C 600 " pdb="MG MG C 601 " model vdw 1.849 2.170 nonbonded pdb=" OG1 THR C 176 " pdb="MG MG C 601 " model vdw 1.851 2.170 nonbonded pdb=" O3 PO4 D 501 " pdb="MG MG D 502 " model vdw 1.851 2.170 nonbonded pdb=" O2B ATP C 600 " pdb="MG MG C 601 " model vdw 1.892 2.170 ... (remaining 304888 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 408 or (resid 409 through 410 and (name N or nam \ e CA or name C or name O or name CB )) or resid 411 through 511 or resid 600 thr \ ough 601)) selection = (chain 'B' and (resid 4 through 511 or resid 600 through 601)) selection = (chain 'C' and (resid 4 through 408 or (resid 409 through 410 and (name N or nam \ e CA or name C or name O or name CB )) or resid 411 through 511 or resid 600 thr \ ough 601)) } ncs_group { reference = (chain 'D' and (resid 2 through 459 or resid 500)) selection = (chain 'E' and (resid 2 through 459 or resid 500)) selection = (chain 'F' and (resid 2 through 459 or resid 500)) } ncs_group { reference = (chain 'I' and resid 3 through 78) selection = (chain 'J' and resid 3 through 78) selection = (chain 'L' and resid 3 through 78) selection = (chain 'M' and resid 3 through 78) selection = (chain 'N' and resid 3 through 78) selection = (chain 'O' and resid 3 through 78) selection = (chain 'P' and resid 3 through 78) selection = (chain 'Q' and resid 3 through 78) selection = chain 'R' selection = (chain 'S' and resid 3 through 78) } ncs_group { reference = chain 'X' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 16 5.49 5 Mg 5 5.21 5 S 180 5.16 5 C 23471 2.51 5 N 6314 2.21 5 O 6965 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 2.510 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: 12.320 Check model and map are aligned: 0.530 Convert atoms to be neutral: 0.300 Process input model: 92.210 Find NCS groups from input model: 2.880 Set up NCS constraints: 0.330 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 114.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 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 : 0.010 0.112 37506 Z= 0.627 Angle : 0.900 23.786 50766 Z= 0.586 Chirality : 0.051 0.415 5918 Planarity : 0.005 0.055 6547 Dihedral : 14.745 141.774 13878 Min Nonbonded Distance : 1.753 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer Outliers : 2.50 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 5.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.10), residues: 4805 helix: -1.67 (0.09), residues: 2555 sheet: -1.11 (0.19), residues: 545 loop : -1.43 (0.14), residues: 1705 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 869 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 773 time to evaluate : 4.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 96 outliers final: 52 residues processed: 851 average time/residue: 0.5119 time to fit residues: 693.3856 Evaluate side-chains 648 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 596 time to evaluate : 4.359 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 0 residues processed: 52 average time/residue: 0.3381 time to fit residues: 38.3902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 399 optimal weight: 0.9990 chunk 358 optimal weight: 0.9990 chunk 198 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 241 optimal weight: 0.9990 chunk 191 optimal weight: 2.9990 chunk 370 optimal weight: 3.9990 chunk 143 optimal weight: 0.7980 chunk 225 optimal weight: 3.9990 chunk 275 optimal weight: 0.3980 chunk 429 optimal weight: 2.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 71 ASN C 333 GLN C 511 GLN ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 GLN B 423 HIS ** B 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 20 ASN A 65 ASN A 344 ASN H 14 GLN ** H 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 142 ASN G 180 GLN ** G 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 GLN F 353 HIS F 437 HIS J 42 GLN L 5 ASN L 52 GLN M 5 ASN N 3 ASN O 3 ASN Q 3 ASN Q 5 ASN Q 42 GLN Q 52 GLN R 52 GLN a 32 GLN a 76 GLN a 132 HIS ** a 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 52 GLN S 5 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.073 37506 Z= 0.199 Angle : 0.628 7.896 50766 Z= 0.328 Chirality : 0.043 0.258 5918 Planarity : 0.005 0.051 6547 Dihedral : 6.762 129.979 5246 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer Outliers : 1.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.11), residues: 4805 helix: -0.12 (0.10), residues: 2573 sheet: -0.59 (0.20), residues: 534 loop : -0.74 (0.14), residues: 1698 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 737 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 674 time to evaluate : 4.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 63 outliers final: 26 residues processed: 710 average time/residue: 0.5184 time to fit residues: 599.0007 Evaluate side-chains 616 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 590 time to evaluate : 4.690 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.3399 time to fit residues: 22.9341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 238 optimal weight: 5.9990 chunk 133 optimal weight: 3.9990 chunk 357 optimal weight: 3.9990 chunk 292 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 430 optimal weight: 0.7980 chunk 464 optimal weight: 2.9990 chunk 383 optimal weight: 10.0000 chunk 426 optimal weight: 7.9990 chunk 146 optimal weight: 4.9990 chunk 345 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 399 GLN A 147 GLN H 127 GLN ** G 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 HIS D 121 ASN O 52 GLN Q 3 ASN Q 42 GLN Y 64 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 37506 Z= 0.283 Angle : 0.605 7.591 50766 Z= 0.314 Chirality : 0.043 0.241 5918 Planarity : 0.005 0.052 6547 Dihedral : 6.303 116.742 5246 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer Outliers : 1.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.12), residues: 4805 helix: 0.21 (0.10), residues: 2578 sheet: -0.45 (0.21), residues: 532 loop : -0.61 (0.15), residues: 1695 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 615 time to evaluate : 4.237 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 69 outliers final: 34 residues processed: 658 average time/residue: 0.4977 time to fit residues: 533.7103 Evaluate side-chains 609 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 575 time to evaluate : 4.270 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.3453 time to fit residues: 28.2019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 425 optimal weight: 4.9990 chunk 323 optimal weight: 0.5980 chunk 223 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 205 optimal weight: 0.0570 chunk 288 optimal weight: 8.9990 chunk 431 optimal weight: 9.9990 chunk 457 optimal weight: 5.9990 chunk 225 optimal weight: 3.9990 chunk 409 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 overall best weight: 2.1304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 399 GLN ** H 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 64 HIS ** G 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 368 GLN ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 3 ASN Q 42 GLN Y 64 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 37506 Z= 0.275 Angle : 0.596 9.283 50766 Z= 0.307 Chirality : 0.043 0.217 5918 Planarity : 0.005 0.084 6547 Dihedral : 6.059 119.230 5246 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer Outliers : 1.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.12), residues: 4805 helix: 0.42 (0.10), residues: 2566 sheet: -0.40 (0.21), residues: 532 loop : -0.54 (0.15), residues: 1707 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 593 time to evaluate : 4.706 Fit side-chains revert: symmetry clash outliers start: 55 outliers final: 29 residues processed: 626 average time/residue: 0.4991 time to fit residues: 506.4046 Evaluate side-chains 599 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 570 time to evaluate : 4.511 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.3355 time to fit residues: 24.6310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 380 optimal weight: 2.9990 chunk 259 optimal weight: 4.9990 chunk 6 optimal weight: 0.1980 chunk 340 optimal weight: 3.9990 chunk 188 optimal weight: 7.9990 chunk 390 optimal weight: 20.0000 chunk 316 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 233 optimal weight: 2.9990 chunk 410 optimal weight: 4.9990 chunk 115 optimal weight: 0.6980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 399 GLN H 127 GLN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 43 GLN ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 3 ASN Q 42 GLN ** Q 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 64 GLN ** a 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 252 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.086 37506 Z= 0.221 Angle : 0.572 9.326 50766 Z= 0.292 Chirality : 0.042 0.224 5918 Planarity : 0.004 0.072 6547 Dihedral : 5.838 120.408 5246 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer Outliers : 1.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.12), residues: 4805 helix: 0.61 (0.10), residues: 2567 sheet: -0.30 (0.22), residues: 522 loop : -0.51 (0.15), residues: 1716 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 603 time to evaluate : 4.303 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 22 residues processed: 627 average time/residue: 0.5027 time to fit residues: 511.0982 Evaluate side-chains 591 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 569 time to evaluate : 4.433 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.3443 time to fit residues: 20.3609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 153 optimal weight: 0.9990 chunk 411 optimal weight: 8.9990 chunk 90 optimal weight: 0.7980 chunk 268 optimal weight: 0.9980 chunk 112 optimal weight: 6.9990 chunk 457 optimal weight: 0.9990 chunk 379 optimal weight: 2.9990 chunk 211 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 151 optimal weight: 4.9990 chunk 240 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 55 GLN H 127 GLN G 59 ASN F 324 GLN ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 64 GLN a 184 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.070 37506 Z= 0.211 Angle : 0.581 9.958 50766 Z= 0.293 Chirality : 0.042 0.337 5918 Planarity : 0.005 0.089 6547 Dihedral : 5.699 121.620 5246 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer Outliers : 0.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.12), residues: 4805 helix: 0.74 (0.10), residues: 2572 sheet: -0.26 (0.22), residues: 529 loop : -0.46 (0.15), residues: 1704 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 592 time to evaluate : 4.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 17 residues processed: 611 average time/residue: 0.5320 time to fit residues: 527.3871 Evaluate side-chains 575 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 558 time to evaluate : 4.349 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.3439 time to fit residues: 17.0409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 441 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 260 optimal weight: 0.9980 chunk 334 optimal weight: 4.9990 chunk 258 optimal weight: 0.3980 chunk 385 optimal weight: 0.6980 chunk 255 optimal weight: 4.9990 chunk 455 optimal weight: 6.9990 chunk 285 optimal weight: 1.9990 chunk 277 optimal weight: 0.5980 chunk 210 optimal weight: 10.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 55 GLN H 127 GLN ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 64 GLN ** a 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.062 37506 Z= 0.182 Angle : 0.571 11.767 50766 Z= 0.288 Chirality : 0.042 0.246 5918 Planarity : 0.004 0.072 6547 Dihedral : 5.510 121.819 5246 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.12), residues: 4805 helix: 0.83 (0.11), residues: 2581 sheet: -0.17 (0.22), residues: 530 loop : -0.40 (0.15), residues: 1694 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 615 time to evaluate : 4.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 14 residues processed: 622 average time/residue: 0.5274 time to fit residues: 534.0480 Evaluate side-chains 587 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 573 time to evaluate : 4.369 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.3417 time to fit residues: 14.9579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 282 optimal weight: 6.9990 chunk 182 optimal weight: 6.9990 chunk 272 optimal weight: 5.9990 chunk 137 optimal weight: 0.3980 chunk 89 optimal weight: 6.9990 chunk 88 optimal weight: 0.9990 chunk 289 optimal weight: 2.9990 chunk 310 optimal weight: 0.6980 chunk 225 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 358 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 67 GLN B 14 GLN ** B 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 55 GLN F 324 GLN D 121 ASN ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 64 GLN ** a 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 37506 Z= 0.168 Angle : 0.585 10.960 50766 Z= 0.293 Chirality : 0.041 0.229 5918 Planarity : 0.004 0.070 6547 Dihedral : 5.302 122.130 5246 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer Outliers : 0.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.12), residues: 4805 helix: 0.89 (0.11), residues: 2616 sheet: -0.05 (0.22), residues: 537 loop : -0.37 (0.15), residues: 1652 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 605 time to evaluate : 4.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 18 residues processed: 621 average time/residue: 0.5182 time to fit residues: 523.6431 Evaluate side-chains 587 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 569 time to evaluate : 4.283 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.3359 time to fit residues: 17.1691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 414 optimal weight: 7.9990 chunk 436 optimal weight: 0.1980 chunk 398 optimal weight: 0.9980 chunk 424 optimal weight: 3.9990 chunk 255 optimal weight: 0.0770 chunk 185 optimal weight: 7.9990 chunk 333 optimal weight: 10.0000 chunk 130 optimal weight: 0.8980 chunk 383 optimal weight: 2.9990 chunk 401 optimal weight: 6.9990 chunk 423 optimal weight: 4.9990 overall best weight: 1.0340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 73 GLN ** B 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 55 GLN H 72 GLN F 7 GLN D 121 ASN J 52 GLN ** O 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 64 GLN ** a 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 37506 Z= 0.191 Angle : 0.602 12.509 50766 Z= 0.301 Chirality : 0.042 0.268 5918 Planarity : 0.004 0.075 6547 Dihedral : 5.220 123.944 5246 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.12), residues: 4805 helix: 0.93 (0.11), residues: 2610 sheet: 0.05 (0.22), residues: 537 loop : -0.35 (0.15), residues: 1658 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 600 time to evaluate : 4.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 603 average time/residue: 0.5664 time to fit residues: 564.3135 Evaluate side-chains 584 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 578 time to evaluate : 4.342 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.4180 time to fit residues: 10.0248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 278 optimal weight: 3.9990 chunk 449 optimal weight: 5.9990 chunk 274 optimal weight: 1.9990 chunk 213 optimal weight: 0.9980 chunk 312 optimal weight: 2.9990 chunk 471 optimal weight: 3.9990 chunk 433 optimal weight: 20.0000 chunk 375 optimal weight: 0.0470 chunk 38 optimal weight: 3.9990 chunk 289 optimal weight: 0.7980 chunk 230 optimal weight: 4.9990 overall best weight: 1.3682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 333 GLN ** B 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 7 GLN D 121 ASN Y 64 GLN ** a 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.122 37506 Z= 0.225 Angle : 0.624 12.553 50766 Z= 0.314 Chirality : 0.044 0.664 5918 Planarity : 0.005 0.138 6547 Dihedral : 5.240 125.399 5246 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.12), residues: 4805 helix: 0.92 (0.11), residues: 2599 sheet: 0.04 (0.22), residues: 537 loop : -0.36 (0.15), residues: 1669 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 585 time to evaluate : 5.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 8 residues processed: 590 average time/residue: 0.5173 time to fit residues: 500.7248 Evaluate side-chains 584 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 576 time to evaluate : 4.229 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.3418 time to fit residues: 10.9142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 298 optimal weight: 0.9990 chunk 399 optimal weight: 0.8980 chunk 114 optimal weight: 0.8980 chunk 345 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 375 optimal weight: 2.9990 chunk 157 optimal weight: 7.9990 chunk 385 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 7 GLN D 121 ASN ** J 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 GLN Y 64 GLN ** a 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 252 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.100728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.067290 restraints weight = 75858.548| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 2.07 r_work: 0.2880 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 1.86 restraints_weight: 0.2500 r_work: 0.2857 rms_B_bonded: 1.88 restraints_weight: 0.1250 r_work: 0.2846 rms_B_bonded: 1.95 restraints_weight: 0.0625 r_work: 0.2833 rms_B_bonded: 2.05 restraints_weight: 0.0312 r_work: 0.2820 rms_B_bonded: 2.17 restraints_weight: 0.0156 r_work: 0.2805 rms_B_bonded: 2.33 restraints_weight: 0.0078 r_work: 0.2790 rms_B_bonded: 2.51 restraints_weight: 0.0039 r_work: 0.2774 rms_B_bonded: 2.73 restraints_weight: 0.0020 r_work: 0.2756 rms_B_bonded: 2.99 restraints_weight: 0.0010 r_work: 0.2737 rms_B_bonded: 3.28 restraints_weight: 0.0005 r_work: 0.2717 rms_B_bonded: 3.62 restraints_weight: 0.0002 r_work: 0.2695 rms_B_bonded: 4.00 restraints_weight: 0.0001 r_work: 0.2671 rms_B_bonded: 4.43 restraints_weight: 0.0001 r_work: 0.2645 rms_B_bonded: 4.93 restraints_weight: 0.0000 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.107 37506 Z= 0.194 Angle : 0.622 11.951 50766 Z= 0.309 Chirality : 0.043 0.560 5918 Planarity : 0.005 0.105 6547 Dihedral : 5.168 124.754 5246 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.12), residues: 4805 helix: 0.94 (0.11), residues: 2608 sheet: 0.11 (0.22), residues: 530 loop : -0.33 (0.15), residues: 1667 =============================================================================== Job complete usr+sys time: 9500.53 seconds wall clock time: 171 minutes 7.70 seconds (10267.70 seconds total)