Starting phenix.real_space_refine on Fri Feb 23 04:40:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbs_27304/02_2024/8dbs_27304_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbs_27304/02_2024/8dbs_27304.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbs_27304/02_2024/8dbs_27304.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbs_27304/02_2024/8dbs_27304.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbs_27304/02_2024/8dbs_27304_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbs_27304/02_2024/8dbs_27304_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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 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 179 5.16 5 C 23302 2.51 5 N 6263 2.21 5 O 6913 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 280": "OE1" <-> "OE2" Residue "D TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 146": "OD1" <-> "OD2" Residue "a PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 36678 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 3826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 3826 Classifications: {'peptide': 508} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 489} Chain: "B" Number of atoms: 3877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 3877 Classifications: {'peptide': 513} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 494} Chain: "C" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 3849 Classifications: {'peptide': 510} Link IDs: {'PTRANS': 18, 'TRANS': 491} Chain: "D" Number of atoms: 3520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3520 Classifications: {'peptide': 458} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 437} Chain: "E" Number of atoms: 3533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3533 Classifications: {'peptide': 460} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 439} Chain: "F" Number of atoms: 3533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3533 Classifications: {'peptide': 460} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 439} Chain: "G" Number of atoms: 2186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2186 Classifications: {'peptide': 284} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 274} Chain: "H" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 772 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} 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: "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: "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: "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: "X" Number of atoms: 1200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1200 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 153} Chain: "Y" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1210 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 153} Chain: "a" Number of atoms: 2104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2104 Classifications: {'peptide': 266} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 250} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 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: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 18.61, per 1000 atoms: 0.51 Number of scatterers: 36678 At special positions: 0 Unit cell: (185.588, 215.8, 134.875, 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 179 16.00 P 16 15.00 Mg 5 11.99 O 6913 8.00 N 6263 7.00 C 23302 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: 16.01 Conformation dependent library (CDL) restraints added in 7.1 seconds 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8746 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 178 helices and 26 sheets defined 56.6% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.57 Creating SS restraints... Processing helix chain 'A' and resid 5 through 19 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 151 through 156 Processing helix chain 'A' and resid 175 through 188 removed outlier: 3.675A pdb=" N ARG A 187 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 5.097A 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 234 through 252 Proline residue: A 239 - end of helix removed outlier: 3.829A pdb=" N ALA A 243 " --> pdb=" O PRO A 239 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 277 removed outlier: 3.560A pdb=" N ALA A 269 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 300 removed outlier: 3.851A pdb=" N PHE A 291 " --> pdb=" O GLY A 288 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG A 296 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A 298 " --> pdb=" O SER A 295 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLU A 299 " --> pdb=" O ARG A 296 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG A 300 " --> pdb=" O LEU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 313 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 346 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 407 removed outlier: 3.612A pdb=" N GLU A 402 " --> pdb=" O ALA A 398 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA A 405 " --> pdb=" O ARG A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 431 Processing helix chain 'A' and resid 441 through 452 Processing helix chain 'A' and resid 461 through 478 removed outlier: 5.481A pdb=" N GLY A 465 " --> pdb=" O SER A 462 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASP A 478 " --> pdb=" O VAL A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 488 Processing helix chain 'A' and resid 494 through 509 Processing helix chain 'B' and resid 3 through 18 removed outlier: 4.217A pdb=" N ILE B 8 " --> pdb=" O SER B 5 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN B 14 " --> pdb=" O LEU B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 103 No H-bonds generated for 'chain 'B' and resid 101 through 103' Processing helix chain 'B' and resid 136 through 138 No H-bonds generated for 'chain 'B' and resid 136 through 138' Processing helix chain 'B' and resid 151 through 156 Processing helix chain 'B' and resid 175 through 188 removed outlier: 3.679A pdb=" N GLN B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ARG B 187 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 5.426A 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 252 Proline residue: B 239 - end of helix removed outlier: 3.971A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG B 252 " --> pdb=" O TYR B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 276 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: 4.113A pdb=" N PHE B 291 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER B 295 " --> pdb=" O TYR B 292 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU B 299 " --> pdb=" O ARG B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 313 Processing helix chain 'B' and resid 340 through 348 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 409 removed outlier: 4.853A pdb=" N GLY B 392 " --> pdb=" O LYS B 388 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE B 393 " --> pdb=" O LEU B 389 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N THR B 395 " --> pdb=" O GLY B 391 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN B 408 " --> pdb=" O ALA B 404 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N PHE B 409 " --> pdb=" O ALA B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 430 Processing helix chain 'B' and resid 441 through 452 Processing helix chain 'B' and resid 462 through 478 removed outlier: 3.883A pdb=" N GLY B 465 " --> pdb=" O SER B 462 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP B 478 " --> pdb=" O VAL B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 489 Processing helix chain 'B' and resid 494 through 510 Processing helix chain 'C' and resid 9 through 17 Processing helix chain 'C' and resid 21 through 23 No H-bonds generated for 'chain 'C' and resid 21 through 23' Processing helix chain 'C' and resid 101 through 103 No H-bonds generated for 'chain 'C' and resid 101 through 103' Processing helix chain 'C' and resid 151 through 156 Processing helix chain 'C' and resid 175 through 187 removed outlier: 3.689A pdb=" N GLN C 186 " --> pdb=" O ALA C 182 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ARG C 187 " --> pdb=" O ILE C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 214 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: 4.199A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG C 252 " --> pdb=" O TYR C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 276 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: 4.556A pdb=" N PHE C 291 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARG C 296 " --> pdb=" O LEU C 293 " (cutoff:3.500A) removed outlier: 3.964A 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 340 through 348 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 409 removed outlier: 4.240A pdb=" N GLY C 391 " --> pdb=" O LYS C 387 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N GLY C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE C 393 " --> pdb=" O LEU C 389 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLU C 402 " --> pdb=" O ALA C 398 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU C 403 " --> pdb=" O GLN C 399 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ALA C 405 " --> pdb=" O ARG C 401 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N PHE C 406 " --> pdb=" O GLU C 402 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N GLN C 408 " --> pdb=" O ALA C 404 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N PHE C 409 " --> pdb=" O ALA C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 431 removed outlier: 3.593A pdb=" N LYS C 426 " --> pdb=" O ASP C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 452 Processing helix chain 'C' and resid 461 through 478 removed outlier: 3.649A pdb=" N ILE C 464 " --> pdb=" O LEU C 461 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N GLY C 465 " --> pdb=" O SER C 462 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASP C 478 " --> pdb=" O VAL C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 489 Processing helix chain 'C' and resid 494 through 508 removed outlier: 3.630A pdb=" N LYS C 499 " --> pdb=" O GLU C 495 " (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 116 through 118 No H-bonds generated for 'chain 'D' and resid 116 through 118' Processing helix chain 'D' and resid 131 through 136 Processing helix chain 'D' and resid 155 through 169 removed outlier: 3.899A pdb=" N ILE D 168 " --> pdb=" O ARG D 164 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLU D 169 " --> pdb=" O ASN D 165 " (cutoff:3.500A) 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: 4.768A pdb=" N ALA D 220 " --> pdb=" O ARG D 216 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N LEU D 221 " --> pdb=" O LEU D 217 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR D 222 " --> pdb=" O ARG D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 255 Processing helix chain 'D' and resid 271 through 281 removed outlier: 3.635A pdb=" N LEU D 278 " --> pdb=" O GLU D 274 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ARG D 281 " --> pdb=" O VAL D 277 " (cutoff:3.500A) 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: 4.408A pdb=" N ALA D 313 " --> pdb=" O ALA D 309 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N HIS D 314 " --> pdb=" O THR D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 328 Processing helix chain 'D' and resid 346 through 349 No H-bonds generated for 'chain 'D' and resid 346 through 349' Processing helix chain 'D' and resid 351 through 377 removed outlier: 4.243A pdb=" N ASP D 372 " --> pdb=" O GLN D 368 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ILE D 373 " --> pdb=" O GLU D 369 " (cutoff:3.500A) removed outlier: 3.695A 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 Processing helix chain 'D' and resid 406 through 411 removed outlier: 4.268A pdb=" N VAL D 409 " --> pdb=" O VAL D 406 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N THR D 411 " --> pdb=" O GLU D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 432 Processing helix chain 'D' and resid 440 through 443 Processing helix chain 'D' and resid 449 through 458 removed outlier: 3.982A pdb=" N LYS D 458 " --> pdb=" O GLU D 454 " (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 170 removed outlier: 4.309A pdb=" N ILE E 168 " --> pdb=" O ARG E 164 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU E 169 " --> pdb=" O ASN E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 195 Processing helix chain 'E' and resid 199 through 201 No H-bonds generated for 'chain 'E' and resid 199 through 201' Processing helix chain 'E' and resid 213 through 232 removed outlier: 4.763A pdb=" N ALA E 220 " --> pdb=" O ARG E 216 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N LEU E 221 " --> pdb=" O LEU E 217 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR E 222 " --> pdb=" O ARG E 218 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 257 removed outlier: 4.010A pdb=" N ALA E 256 " --> pdb=" O THR E 252 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N LEU E 257 " --> pdb=" O GLU E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 281 removed outlier: 4.113A pdb=" N ARG E 281 " --> pdb=" O VAL E 277 " (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 314 removed outlier: 3.625A pdb=" N THR E 311 " --> pdb=" O SER E 307 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE E 312 " --> pdb=" O PRO E 308 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ALA E 313 " --> pdb=" O ALA E 309 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N HIS E 314 " --> pdb=" O THR E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 328 removed outlier: 3.973A pdb=" N LEU E 328 " --> pdb=" O GLN E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 346 through 377 removed outlier: 7.441A pdb=" N GLN E 351 " --> pdb=" O LEU E 347 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N GLU E 352 " --> pdb=" O VAL E 348 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N HIS E 353 " --> pdb=" O VAL E 349 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASP E 372 " --> pdb=" O GLN E 368 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE E 373 " --> pdb=" O GLU E 369 " (cutoff:3.500A) removed outlier: 3.830A 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: 3.552A pdb=" N ARG E 398 " --> pdb=" O ARG E 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 411 No H-bonds generated for 'chain 'E' and resid 408 through 411' Processing helix chain 'E' and resid 420 through 431 Processing helix chain 'E' and resid 433 through 435 No H-bonds generated for 'chain 'E' and resid 433 through 435' Processing helix chain 'E' and resid 441 through 443 No H-bonds generated for 'chain 'E' and resid 441 through 443' Processing helix chain 'E' and resid 449 through 458 removed outlier: 3.997A pdb=" N VAL E 453 " --> pdb=" O ILE E 449 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N GLU E 454 " --> pdb=" O GLU E 450 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 49 No H-bonds generated for 'chain 'F' and resid 47 through 49' 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 131 through 136 Processing helix chain 'F' and resid 155 through 168 Processing helix chain 'F' and resid 183 through 196 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: 4.811A pdb=" N ALA F 220 " --> pdb=" O ARG F 216 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N LEU F 221 " --> pdb=" O LEU F 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 258 Processing helix chain 'F' and resid 264 through 266 No H-bonds generated for 'chain 'F' and resid 264 through 266' Processing helix chain 'F' and resid 271 through 281 removed outlier: 3.601A pdb=" N LEU F 278 " --> pdb=" O GLU F 274 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ARG F 281 " --> pdb=" O VAL F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 312 Processing helix chain 'F' and resid 323 through 328 removed outlier: 3.692A 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: 3.966A pdb=" N ASP F 372 " --> pdb=" O GLN F 368 " (cutoff:3.500A) removed outlier: 3.683A 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 384 through 399 Processing helix chain 'F' and resid 405 through 411 removed outlier: 3.734A pdb=" N GLU F 408 " --> pdb=" O PHE F 405 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N VAL F 409 " --> pdb=" O VAL F 406 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR F 411 " --> pdb=" O GLU F 408 " (cutoff:3.500A) Processing helix chain 'F' and resid 420 through 432 Processing helix chain 'F' and resid 440 through 442 No H-bonds generated for 'chain 'F' and resid 440 through 442' Processing helix chain 'F' and resid 449 through 458 removed outlier: 3.702A pdb=" N GLU F 454 " --> pdb=" O GLU F 450 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS F 458 " --> pdb=" O GLU F 454 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 56 removed outlier: 3.703A pdb=" N MET G 25 " --> pdb=" O LYS G 21 " (cutoff:3.500A) removed outlier: 3.692A 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 90 through 107 Processing helix chain 'G' and resid 119 through 128 Processing helix chain 'G' and resid 145 through 160 removed outlier: 4.664A 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 199 through 202 No H-bonds generated for 'chain 'G' and resid 199 through 202' Processing helix chain 'G' and resid 211 through 282 removed outlier: 3.852A pdb=" N LYS G 258 " --> pdb=" O GLY G 254 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU G 259 " --> pdb=" O SER G 255 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 57 No H-bonds generated for 'chain 'H' and resid 55 through 57' Processing helix chain 'H' and resid 89 through 102 removed outlier: 3.778A pdb=" N GLU H 96 " --> pdb=" O ARG H 93 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA H 97 " --> pdb=" O ALA H 94 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LYS H 100 " --> pdb=" O ALA H 97 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 41 removed outlier: 3.915A pdb=" N LEU I 9 " --> pdb=" O ASN I 5 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR I 10 " --> pdb=" O MET I 6 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N MET I 11 " --> pdb=" O ASP I 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 43 through 76 removed outlier: 3.525A pdb=" N ILE I 46 " --> pdb=" O PRO I 43 " (cutoff:3.500A) Proline residue: I 47 - end of helix removed outlier: 3.712A pdb=" N ARG I 50 " --> pdb=" O PRO I 47 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY I 58 " --> pdb=" O ILE I 55 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ASP I 61 " --> pdb=" O GLY I 58 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA I 62 " --> pdb=" O LEU I 59 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILE I 63 " --> pdb=" O VAL I 60 " (cutoff:3.500A) Proline residue: I 64 - end of helix Processing helix chain 'J' and resid 4 through 41 removed outlier: 3.775A pdb=" N LEU J 8 " --> pdb=" O LEU J 4 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 77 removed outlier: 3.556A pdb=" N LEU J 59 " --> pdb=" O ILE J 55 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA J 62 " --> pdb=" O GLY J 58 " (cutoff:3.500A) removed outlier: 5.148A 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: 3.713A pdb=" N LEU L 8 " --> pdb=" O ASN L 5 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL L 15 " --> pdb=" O ALA L 12 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA L 24 " --> pdb=" O ALA L 21 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE L 26 " --> pdb=" O GLY L 23 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY L 27 " --> pdb=" O ALA L 24 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE L 28 " --> pdb=" O ALA L 25 " (cutoff:3.500A) Processing helix chain 'L' and resid 43 through 76 removed outlier: 3.652A pdb=" N ILE L 46 " --> pdb=" O PRO L 43 " (cutoff:3.500A) Proline residue: L 47 - end of helix removed outlier: 3.749A pdb=" N ARG L 50 " --> pdb=" O PRO L 47 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ASP L 61 " --> pdb=" O GLY L 58 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ILE L 63 " --> pdb=" O VAL L 60 " (cutoff:3.500A) Proline residue: L 64 - end of helix Processing helix chain 'M' and resid 4 through 41 removed outlier: 3.637A pdb=" N MET M 11 " --> pdb=" O ASP M 7 " (cutoff:3.500A) Processing helix chain 'M' and resid 43 through 76 Proline residue: M 47 - end of helix removed outlier: 3.543A pdb=" N PHE M 53 " --> pdb=" O ARG M 50 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASP M 61 " --> pdb=" O GLY M 58 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ILE M 63 " --> pdb=" O VAL M 60 " (cutoff:3.500A) Proline residue: M 64 - end of helix Processing helix chain 'N' and resid 4 through 41 removed outlier: 4.410A pdb=" N LEU N 9 " --> pdb=" O ASN N 5 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N TYR N 10 " --> pdb=" O MET N 6 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N MET N 11 " --> pdb=" O ASP N 7 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N MET N 16 " --> pdb=" O ALA N 12 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA N 21 " --> pdb=" O MET N 17 " (cutoff:3.500A) Processing helix chain 'N' and resid 43 through 76 removed outlier: 3.564A pdb=" N ILE N 46 " --> pdb=" O PRO N 43 " (cutoff:3.500A) Proline residue: N 47 - end of helix removed outlier: 3.897A pdb=" N ARG N 50 " --> pdb=" O PRO N 47 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N MET N 57 " --> pdb=" O PHE N 54 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLY N 58 " --> pdb=" O ILE N 55 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASP N 61 " --> pdb=" O GLY N 58 " (cutoff:3.500A) removed outlier: 4.219A 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 4 through 41 removed outlier: 3.515A pdb=" N GLY O 23 " --> pdb=" O ALA O 20 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLY O 27 " --> pdb=" O ALA O 24 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE O 28 " --> pdb=" O ALA O 25 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA O 40 " --> pdb=" O GLU O 37 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG O 41 " --> pdb=" O GLY O 38 " (cutoff:3.500A) Processing helix chain 'O' and resid 43 through 60 removed outlier: 3.922A pdb=" N ILE O 46 " --> pdb=" O PRO O 43 " (cutoff:3.500A) Proline residue: O 47 - end of helix removed outlier: 3.881A pdb=" N ARG O 50 " --> pdb=" O PRO O 47 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE O 53 " --> pdb=" O ARG O 50 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY O 58 " --> pdb=" O ILE O 55 " (cutoff:3.500A) Processing helix chain 'O' and resid 62 through 76 Processing helix chain 'P' and resid 4 through 41 removed outlier: 3.952A pdb=" N LEU P 8 " --> pdb=" O LEU P 4 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU P 9 " --> pdb=" O ASN P 5 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA P 21 " --> pdb=" O MET P 17 " (cutoff:3.500A) Processing helix chain 'P' and resid 45 through 76 removed outlier: 3.639A pdb=" N ALA P 62 " --> pdb=" O LEU P 59 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE P 63 " --> pdb=" O VAL P 60 " (cutoff:3.500A) Proline residue: P 64 - end of helix Processing helix chain 'Q' and resid 4 through 41 Processing helix chain 'Q' and resid 43 through 76 Proline residue: Q 47 - end of helix removed outlier: 4.203A pdb=" N ARG Q 50 " --> pdb=" O PRO Q 47 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE Q 54 " --> pdb=" O THR Q 51 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ILE Q 63 " --> pdb=" O VAL Q 60 " (cutoff:3.500A) Proline residue: Q 64 - end of helix removed outlier: 3.526A pdb=" N PHE Q 76 " --> pdb=" O TYR Q 73 " (cutoff:3.500A) Processing helix chain 'R' and resid 6 through 41 removed outlier: 3.807A pdb=" N ILE R 28 " --> pdb=" O ALA R 24 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS R 34 " --> pdb=" O ILE R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 46 through 76 removed outlier: 3.622A pdb=" N GLN R 52 " --> pdb=" O LEU R 48 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU R 59 " --> pdb=" O ILE R 55 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA R 62 " --> pdb=" O GLY R 58 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ILE R 63 " --> pdb=" O LEU R 59 " (cutoff:3.500A) Proline residue: R 64 - end of helix Processing helix chain 'S' and resid 6 through 41 removed outlier: 4.663A pdb=" N TYR S 10 " --> pdb=" O ASP S 7 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL S 15 " --> pdb=" O ALA S 12 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU S 19 " --> pdb=" O MET S 16 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA S 20 " --> pdb=" O MET S 17 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY S 23 " --> pdb=" O ALA S 20 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA S 24 " --> pdb=" O ALA S 21 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE S 28 " --> pdb=" O ALA S 25 " (cutoff:3.500A) Processing helix chain 'S' and resid 43 through 60 Proline residue: S 47 - end of helix removed outlier: 3.717A pdb=" N MET S 57 " --> pdb=" O PHE S 54 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY S 58 " --> pdb=" O ILE S 55 " (cutoff:3.500A) Processing helix chain 'S' and resid 62 through 77 Processing helix chain 'W' and resid 4 through 21 removed outlier: 3.717A 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: 3.505A pdb=" N THR W 38 " --> pdb=" O ALA W 34 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS W 39 " --> pdb=" O ALA W 35 " (cutoff:3.500A) Processing helix chain 'W' and resid 41 through 48 Processing helix chain 'W' and resid 53 through 63 removed outlier: 3.648A pdb=" N VAL W 63 " --> pdb=" O SER W 59 " (cutoff:3.500A) Processing helix chain 'W' and resid 69 through 82 removed outlier: 4.224A pdb=" N ASN W 74 " --> pdb=" O GLU W 70 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASN W 82 " --> pdb=" O VAL W 78 " (cutoff:3.500A) Processing helix chain 'W' and resid 84 through 102 Proline residue: W 89 - end of helix removed outlier: 3.808A pdb=" N LEU W 92 " --> pdb=" O PRO W 89 " (cutoff:3.500A) Processing helix chain 'W' and resid 118 through 132 Processing helix chain 'W' and resid 163 through 173 removed outlier: 4.044A pdb=" N VAL W 173 " --> pdb=" O ARG W 169 " (cutoff:3.500A) Processing helix chain 'X' and resid 5 through 28 removed outlier: 3.568A pdb=" N GLY X 9 " --> pdb=" O THR X 6 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLN X 10 " --> pdb=" O ILE X 7 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE X 14 " --> pdb=" O ALA X 11 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS X 23 " --> pdb=" O PHE X 20 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR X 24 " --> pdb=" O ALA X 21 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N VAL X 25 " --> pdb=" O MET X 22 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N TRP X 26 " --> pdb=" O LYS X 23 " (cutoff:3.500A) Proline residue: X 27 - end of helix Processing helix chain 'X' and resid 31 through 62 removed outlier: 3.788A pdb=" N LEU X 56 " --> pdb=" O LYS X 52 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA X 57 " --> pdb=" O ASP X 53 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N LYS X 58 " --> pdb=" O LEU X 54 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ALA X 59 " --> pdb=" O ASP X 55 " (cutoff:3.500A) Processing helix chain 'X' and resid 65 through 125 removed outlier: 3.646A pdb=" N GLN X 73 " --> pdb=" O LYS X 69 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL X 74 " --> pdb=" O ALA X 70 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN X 96 " --> pdb=" O ALA X 92 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA X 111 " --> pdb=" O ALA X 107 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS X 114 " --> pdb=" O GLU X 110 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLU X 118 " --> pdb=" O LYS X 114 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLU X 119 " --> pdb=" O ARG X 115 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ALA X 125 " --> pdb=" O ARG X 121 " (cutoff:3.500A) Processing helix chain 'X' and resid 128 through 135 removed outlier: 4.384A pdb=" N LYS X 134 " --> pdb=" O ALA X 130 " (cutoff:3.500A) Processing helix chain 'X' and resid 147 through 155 Processing helix chain 'Y' and resid 3 through 24 Processing helix chain 'Y' and resid 27 through 139 removed outlier: 3.549A pdb=" N ASP Y 42 " --> pdb=" O GLU Y 39 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA Y 45 " --> pdb=" O ASP Y 42 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA Y 72 " --> pdb=" O LYS Y 69 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA Y 94 " --> pdb=" O LYS Y 91 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL Y 102 " --> pdb=" O THR Y 99 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA Y 125 " --> pdb=" O LYS Y 122 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE Y 126 " --> pdb=" O GLN Y 123 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU Y 127 " --> pdb=" O VAL Y 124 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU Y 133 " --> pdb=" O ALA Y 130 " (cutoff:3.500A) Processing helix chain 'Y' and resid 142 through 153 Processing helix chain 'a' and resid 8 through 15 Processing helix chain 'a' and resid 43 through 64 Processing helix chain 'a' and resid 74 through 93 removed outlier: 4.272A pdb=" N ALA a 78 " --> pdb=" O LYS a 74 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ILE a 79 " --> pdb=" O PHE a 75 " (cutoff:3.500A) Processing helix chain 'a' and resid 100 through 120 removed outlier: 3.690A pdb=" N MET a 118 " --> pdb=" O LEU a 114 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ASP a 119 " --> pdb=" O MET a 115 " (cutoff:3.500A) removed outlier: 4.399A 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 147 through 167 Processing helix chain 'a' and resid 171 through 179 removed outlier: 3.616A pdb=" N GLU a 177 " --> pdb=" O GLY a 173 " (cutoff:3.500A) Processing helix chain 'a' and resid 186 through 228 Proline residue: a 190 - end of helix Proline residue: a 204 - end of helix removed outlier: 3.833A pdb=" N ILE a 221 " --> pdb=" O ALA a 217 " (cutoff:3.500A) Processing helix chain 'a' and resid 231 through 268 removed outlier: 4.561A pdb=" N TRP a 235 " --> pdb=" O TRP a 231 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N ILE a 236 " --> pdb=" O TRP a 232 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LEU a 237 " --> pdb=" O SER a 233 " (cutoff:3.500A) Proline residue: a 240 - end of helix removed outlier: 3.687A pdb=" N PHE a 244 " --> pdb=" O PRO a 240 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU a 247 " --> pdb=" O ILE a 243 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 87 through 89 removed outlier: 6.681A pdb=" N ARG A 40 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N VAL A 34 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N VAL A 74 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N ALA A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 96 through 98 Processing sheet with id= C, first strand: chain 'A' and resid 107 through 109 removed outlier: 8.264A pdb=" N VAL A 108 " --> pdb=" O THR A 221 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N VAL A 223 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ALA A 193 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N VAL A 224 " --> pdb=" O ALA A 193 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N TYR A 195 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N ALA A 226 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ALA A 197 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A 196 " --> pdb=" O ILE A 259 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N SER A 323 " --> pdb=" O ALA A 256 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N ILE A 258 " --> pdb=" O SER A 323 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N THR A 325 " --> pdb=" O ILE A 258 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N TYR A 260 " --> pdb=" O THR A 325 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 352 through 355 removed outlier: 6.692A pdb=" N LEU A 166 " --> pdb=" O ILE A 353 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N LEU A 355 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE A 168 " --> pdb=" O LEU A 355 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 87 through 90 removed outlier: 4.200A pdb=" N ASN B 27 " --> pdb=" O ALA B 90 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ARG B 40 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N VAL B 34 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER B 70 " --> pdb=" O GLU B 67 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL B 74 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N ALA B 63 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ARG B 59 " --> pdb=" O LEU B 55 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 96 through 98 Processing sheet with id= G, first strand: chain 'B' and resid 107 through 109 removed outlier: 8.556A pdb=" N VAL B 108 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N VAL B 223 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ALA B 193 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N VAL B 224 " --> pdb=" O ALA B 193 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N TYR B 195 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ALA B 226 " --> pdb=" O TYR B 195 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ALA B 197 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE B 198 " --> pdb=" O ASP B 261 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N SER B 323 " --> pdb=" O ALA B 256 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N ILE B 258 " --> pdb=" O SER B 323 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N THR B 325 " --> pdb=" O ILE B 258 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N TYR B 260 " --> pdb=" O THR B 325 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 352 through 355 removed outlier: 6.786A pdb=" N LEU B 166 " --> pdb=" O ILE B 353 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N LEU B 355 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ILE B 168 " --> pdb=" O LEU B 355 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 87 through 89 removed outlier: 6.421A pdb=" N ARG C 40 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL C 34 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N VAL C 74 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ALA C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 96 through 98 Processing sheet with id= K, first strand: chain 'C' and resid 107 through 109 removed outlier: 8.357A pdb=" N VAL C 108 " --> pdb=" O THR C 221 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N VAL C 223 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ALA C 193 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N VAL C 224 " --> pdb=" O ALA C 193 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N TYR C 195 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N ALA C 226 " --> pdb=" O TYR C 195 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ALA C 197 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE C 198 " --> pdb=" O ASP C 261 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N SER C 323 " --> pdb=" O ALA C 256 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ILE C 258 " --> pdb=" O SER C 323 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N THR C 325 " --> pdb=" O ILE C 258 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N TYR C 260 " --> pdb=" O THR C 325 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 352 through 355 removed outlier: 6.863A pdb=" N LEU C 166 " --> pdb=" O ILE C 353 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N LEU C 355 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE C 168 " --> pdb=" O LEU C 355 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 4 through 9 removed outlier: 6.597A pdb=" N ASP D 14 " --> pdb=" O VAL D 6 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N VAL D 8 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL D 12 " --> pdb=" O VAL D 8 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ILE D 54 " --> pdb=" O VAL D 42 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N VAL D 42 " --> pdb=" O ILE D 54 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 76 through 79 removed outlier: 4.671A pdb=" N GLU D 105 " --> pdb=" O VAL D 79 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 317 through 320 removed outlier: 8.071A pdb=" N VAL D 145 " --> pdb=" O ILE D 290 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N SER D 292 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N LEU D 147 " --> pdb=" O SER D 292 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLN D 294 " --> pdb=" O LEU D 147 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N GLY D 149 " --> pdb=" O GLN D 294 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N VAL D 296 " --> pdb=" O GLY D 149 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 50 through 54 removed outlier: 3.530A pdb=" N GLN E 7 " --> pdb=" O ASP E 14 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N GLU E 16 " --> pdb=" O ILE E 5 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ILE E 5 " --> pdb=" O GLU E 16 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL E 68 " --> pdb=" O THR E 2 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ASP E 67 " --> pdb=" O GLN E 32 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N GLN E 32 " --> pdb=" O ASP E 67 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA E 28 " --> pdb=" O LEU E 71 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU E 36 " --> pdb=" O ASN E 33 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ARG E 52 " --> pdb=" O GLN E 43 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N GLN E 45 " --> pdb=" O ILE E 50 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N ILE E 50 " --> pdb=" O GLN E 45 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 76 through 79 removed outlier: 4.746A pdb=" N GLU E 105 " --> pdb=" O VAL E 79 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 317 through 320 removed outlier: 7.929A pdb=" N VAL E 145 " --> pdb=" O ILE E 290 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N SER E 292 " --> pdb=" O VAL E 145 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N LEU E 147 " --> pdb=" O SER E 292 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N GLN E 294 " --> pdb=" O LEU E 147 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N GLY E 149 " --> pdb=" O GLN E 294 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N VAL E 296 " --> pdb=" O GLY E 149 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 4 through 9 removed outlier: 6.625A pdb=" N ASP F 14 " --> pdb=" O VAL F 6 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N VAL F 8 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL F 12 " --> pdb=" O VAL F 8 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ILE F 54 " --> pdb=" O VAL F 42 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N VAL F 42 " --> pdb=" O ILE F 54 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ASP F 27 " --> pdb=" O VAL F 42 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA F 28 " --> pdb=" O HIS F 73 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N HIS F 73 " --> pdb=" O ALA F 28 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N GLU F 30 " --> pdb=" O LEU F 71 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LEU F 71 " --> pdb=" O GLU F 30 " (cutoff:3.500A) removed outlier: 8.566A pdb=" N GLN F 32 " --> pdb=" O LYS F 69 " (cutoff:3.500A) removed outlier: 9.654A pdb=" N LYS F 69 " --> pdb=" O GLN F 32 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 76 through 79 removed outlier: 4.566A pdb=" N GLU F 105 " --> pdb=" O VAL F 79 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 317 through 319 removed outlier: 8.582A pdb=" N VAL F 145 " --> pdb=" O ILE F 290 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N SER F 292 " --> pdb=" O VAL F 145 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N LEU F 147 " --> pdb=" O SER F 292 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N GLN F 294 " --> pdb=" O LEU F 147 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N TYR F 173 " --> pdb=" O LEU F 238 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N PHE F 240 " --> pdb=" O TYR F 173 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL F 175 " --> pdb=" O PHE F 240 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'G' and resid 180 through 188 removed outlier: 6.434A pdb=" N LEU G 167 " --> pdb=" O LEU G 187 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS G 166 " --> pdb=" O ARG G 74 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ASN G 172 " --> pdb=" O VAL G 80 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N GLN G 111 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N TYR G 77 " --> pdb=" O GLN G 111 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ASP G 113 " --> pdb=" O TYR G 77 " (cutoff:3.500A) removed outlier: 7.819A 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: 7.166A pdb=" N MET G 116 " --> pdb=" O VAL G 133 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLN G 135 " --> pdb=" O MET G 116 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'H' and resid 41 through 45 removed outlier: 3.550A pdb=" N LEU H 41 " --> pdb=" O VAL H 71 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY H 67 " --> pdb=" O ILE H 45 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N HIS H 5 " --> pdb=" O VAL H 76 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N VAL H 78 " --> pdb=" O HIS H 5 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ASP H 7 " --> pdb=" O VAL H 78 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ALA H 80 " --> pdb=" O ASP H 7 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL H 9 " --> pdb=" O ALA H 80 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR H 4 " --> pdb=" O VAL H 20 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N VAL H 53 " --> pdb=" O GLU H 21 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ILE H 23 " --> pdb=" O ARG H 51 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ARG H 51 " --> pdb=" O ILE H 23 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'H' and resid 22 through 26 Processing sheet with id= Y, first strand: chain 'W' and resid 135 through 140 Processing sheet with id= Z, first strand: chain 'a' and resid 20 through 22 2001 hydrogen bonds defined for protein. 4629 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: 14.25 Time building geometry restraints manager: 16.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 6284 1.31 - 1.43: 8700 1.43 - 1.56: 21863 1.56 - 1.68: 26 1.68 - 1.81: 358 Bond restraints: 37231 Sorted by residual: bond pdb=" N VAL a 142 " pdb=" CA VAL a 142 " ideal model delta sigma weight residual 1.460 1.493 -0.033 7.50e-03 1.78e+04 1.97e+01 bond pdb=" C PRO A 239 " pdb=" O PRO A 239 " ideal model delta sigma weight residual 1.236 1.183 0.053 1.23e-02 6.61e+03 1.88e+01 bond pdb=" CA SER A 274 " pdb=" CB SER A 274 " ideal model delta sigma weight residual 1.529 1.464 0.065 1.58e-02 4.01e+03 1.68e+01 bond pdb=" CA SER A 155 " pdb=" CB SER A 155 " ideal model delta sigma weight residual 1.533 1.476 0.057 1.58e-02 4.01e+03 1.31e+01 bond pdb=" C PRO A 287 " pdb=" O PRO A 287 " ideal model delta sigma weight residual 1.232 1.190 0.042 1.20e-02 6.94e+03 1.25e+01 ... (remaining 37226 not shown) Histogram of bond angle deviations from ideal: 99.01 - 107.15: 1105 107.15 - 115.29: 22909 115.29 - 123.43: 25490 123.43 - 131.57: 861 131.57 - 139.71: 34 Bond angle restraints: 50399 Sorted by residual: angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 123.76 16.11 1.00e+00 1.00e+00 2.60e+02 angle pdb=" PA ATP A 600 " pdb=" O3A ATP A 600 " pdb=" PB ATP A 600 " ideal model delta sigma weight residual 136.83 124.91 11.92 1.00e+00 1.00e+00 1.42e+02 angle pdb=" C VAL a 141 " pdb=" N VAL a 142 " pdb=" CA VAL a 142 " ideal model delta sigma weight residual 122.59 115.34 7.25 7.20e-01 1.93e+00 1.01e+02 angle pdb=" N VAL E 406 " pdb=" CA VAL E 406 " pdb=" C VAL E 406 " ideal model delta sigma weight residual 113.20 105.41 7.79 9.60e-01 1.09e+00 6.59e+01 angle pdb=" N TYR A 240 " pdb=" CA TYR A 240 " pdb=" C TYR A 240 " ideal model delta sigma weight residual 113.55 104.05 9.50 1.26e+00 6.30e-01 5.68e+01 ... (remaining 50394 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.61: 21729 23.61 - 47.23: 750 47.23 - 70.84: 125 70.84 - 94.46: 25 94.46 - 118.07: 5 Dihedral angle restraints: 22634 sinusoidal: 8960 harmonic: 13674 Sorted by residual: dihedral pdb=" O1B ADP F 500 " pdb=" O3A ADP F 500 " pdb=" PB ADP F 500 " pdb=" PA ADP F 500 " ideal model delta sinusoidal sigma weight residual -60.00 -178.07 118.07 1 2.00e+01 2.50e-03 3.53e+01 dihedral pdb=" C5' ADP F 500 " pdb=" O5' ADP F 500 " pdb=" PA ADP F 500 " pdb=" O2A ADP F 500 " ideal model delta sinusoidal sigma weight residual -60.00 50.06 -110.05 1 2.00e+01 2.50e-03 3.22e+01 dihedral pdb=" C5' ADP E 501 " pdb=" O5' ADP E 501 " pdb=" PA ADP E 501 " pdb=" O2A ADP E 501 " ideal model delta sinusoidal sigma weight residual -60.00 -165.07 105.07 1 2.00e+01 2.50e-03 3.02e+01 ... (remaining 22631 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 5501 0.091 - 0.182: 349 0.182 - 0.273: 20 0.273 - 0.364: 3 0.364 - 0.455: 2 Chirality restraints: 5875 Sorted by residual: chirality pdb=" CA ASP A 262 " pdb=" N ASP A 262 " pdb=" C ASP A 262 " pdb=" CB ASP A 262 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.17e+00 chirality pdb=" CA VAL A 146 " pdb=" N VAL A 146 " pdb=" C VAL A 146 " pdb=" CB VAL A 146 " both_signs ideal model delta sigma weight residual False 2.44 2.83 -0.39 2.00e-01 2.50e+01 3.87e+00 chirality pdb=" CA GLN A 266 " pdb=" N GLN A 266 " pdb=" C GLN A 266 " pdb=" CB GLN A 266 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.67e+00 ... (remaining 5872 not shown) Planarity restraints: 6501 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 236 " 0.049 2.00e-02 2.50e+03 2.76e-02 1.52e+01 pdb=" CG TYR A 236 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 TYR A 236 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR A 236 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR A 236 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 236 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 236 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 236 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 266 " 0.013 2.00e-02 2.50e+03 2.66e-02 7.09e+00 pdb=" C GLN A 266 " -0.046 2.00e-02 2.50e+03 pdb=" O GLN A 266 " 0.017 2.00e-02 2.50e+03 pdb=" N ALA A 267 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 234 " 0.012 2.00e-02 2.50e+03 2.49e-02 6.22e+00 pdb=" C LEU A 234 " -0.043 2.00e-02 2.50e+03 pdb=" O LEU A 234 " 0.017 2.00e-02 2.50e+03 pdb=" N GLN A 235 " 0.014 2.00e-02 2.50e+03 ... (remaining 6498 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.31: 39 2.31 - 2.96: 17866 2.96 - 3.61: 54967 3.61 - 4.25: 84669 4.25 - 4.90: 143814 Nonbonded interactions: 301355 Sorted by model distance: nonbonded pdb=" OG1 THR A 176 " pdb="MG MG A 601 " model vdw 1.666 2.170 nonbonded pdb=" N THR E 156 " pdb="MG MG E 502 " model vdw 1.786 2.250 nonbonded pdb=" CB THR E 156 " pdb="MG MG E 502 " model vdw 1.836 2.600 nonbonded pdb=" O2A ADP E 501 " pdb="MG MG E 502 " model vdw 1.884 2.170 nonbonded pdb=" O2G ATP B 600 " pdb="MG MG B 601 " model vdw 1.918 2.170 ... (remaining 301350 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 410 through 511 or resid 600 throug \ h 601)) selection = (chain 'B' and (resid 4 through 408 or resid 410 through 511 or resid 600 throug \ h 601)) selection = (chain 'C' and (resid 4 through 408 or resid 410 through 511 or resid 600 throug \ h 601)) } ncs_group { reference = (chain 'D' and resid 2 through 459) selection = (chain 'E' and resid 2 through 459) selection = (chain 'F' and resid 2 through 459) } 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' and (resid 1 through 80 or resid 83 through 156)) selection = (chain 'Y' and (resid 1 through 80 or resid 83 through 156)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 11.410 Check model and map are aligned: 0.530 Set scattering table: 0.330 Process input model: 101.340 Find NCS groups from input model: 2.810 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 121.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 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 : 0.004 0.065 37231 Z= 0.259 Angle : 0.637 16.114 50399 Z= 0.394 Chirality : 0.046 0.455 5875 Planarity : 0.004 0.048 6501 Dihedral : 12.596 118.071 13888 Min Nonbonded Distance : 1.666 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.53 % Favored : 98.43 % Rotamer: Outliers : 1.94 % Allowed : 5.12 % Favored : 92.93 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 4.47 % 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: 1.03 (0.12), residues: 4770 helix: 1.28 (0.10), residues: 2516 sheet: 0.57 (0.21), residues: 548 loop : -0.03 (0.15), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 105 HIS 0.006 0.001 HIS a 185 PHE 0.016 0.001 PHE a 48 TYR 0.056 0.001 TYR A 236 ARG 0.004 0.000 ARG H 93 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 691 residues out of total 3805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 617 time to evaluate : 4.041 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 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 revert: symmetry clash REVERT: B 1 MET cc_start: 0.4397 (tpt) cc_final: 0.1863 (mtm) REVERT: B 394 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.8272 (tmt170) REVERT: C 236 TYR cc_start: 0.9384 (OUTLIER) cc_final: 0.8855 (t80) REVERT: D 226 MET cc_start: 0.8546 (mtt) cc_final: 0.8254 (mtt) REVERT: D 340 THR cc_start: 0.8568 (m) cc_final: 0.8287 (p) REVERT: D 445 MET cc_start: 0.8669 (mmt) cc_final: 0.8426 (mpp) REVERT: E 265 VAL cc_start: 0.9497 (OUTLIER) cc_final: 0.9258 (t) REVERT: F 373 ILE cc_start: 0.9075 (OUTLIER) cc_final: 0.8874 (mt) REVERT: G 60 LEU cc_start: 0.6306 (tt) cc_final: 0.5303 (mt) REVERT: H 50 ILE cc_start: 0.9100 (OUTLIER) cc_final: 0.8576 (mp) REVERT: H 54 LYS cc_start: 0.8493 (mtmm) cc_final: 0.8274 (tptm) REVERT: I 11 MET cc_start: 0.7660 (tpp) cc_final: 0.6581 (mpp) REVERT: I 75 MET cc_start: 0.4979 (ttp) cc_final: 0.4774 (ttp) REVERT: J 10 TYR cc_start: 0.6983 (m-80) cc_final: 0.6722 (m-80) REVERT: L 6 MET cc_start: 0.5881 (ttp) cc_final: 0.5548 (ptt) REVERT: L 11 MET cc_start: 0.5056 (tpt) cc_final: 0.4604 (mtm) REVERT: L 16 MET cc_start: 0.7804 (ttm) cc_final: 0.7244 (mtp) REVERT: L 26 ILE cc_start: 0.7600 (mt) cc_final: 0.7306 (mm) REVERT: L 34 LYS cc_start: 0.7043 (mmtm) cc_final: 0.6619 (mmtt) REVERT: M 11 MET cc_start: 0.7848 (tpt) cc_final: 0.7580 (mtm) REVERT: M 68 VAL cc_start: 0.6994 (t) cc_final: 0.6743 (t) REVERT: M 76 PHE cc_start: 0.2853 (m-80) cc_final: 0.2596 (m-10) REVERT: N 16 MET cc_start: 0.6731 (mtp) cc_final: 0.5542 (mmm) REVERT: N 34 LYS cc_start: 0.7516 (mmtm) cc_final: 0.6708 (mmmt) REVERT: N 44 ASP cc_start: 0.7451 (m-30) cc_final: 0.6785 (p0) REVERT: P 11 MET cc_start: 0.6641 (tpp) cc_final: 0.6378 (mmm) REVERT: P 22 ILE cc_start: 0.8161 (mm) cc_final: 0.7891 (mm) REVERT: P 44 ASP cc_start: 0.8456 (m-30) cc_final: 0.8179 (p0) REVERT: P 49 LEU cc_start: 0.8899 (mt) cc_final: 0.8029 (tp) REVERT: P 54 PHE cc_start: 0.6580 (m-10) cc_final: 0.6279 (m-80) REVERT: Q 5 ASN cc_start: 0.2774 (t0) cc_final: 0.2324 (t0) REVERT: Q 37 GLU cc_start: 0.8584 (tp30) cc_final: 0.8384 (pt0) REVERT: Q 76 PHE cc_start: 0.5997 (m-10) cc_final: 0.5377 (t80) REVERT: R 22 ILE cc_start: 0.7844 (mm) cc_final: 0.7609 (mm) REVERT: S 11 MET cc_start: 0.6960 (tpp) cc_final: 0.6318 (mpp) REVERT: S 54 PHE cc_start: 0.6346 (m-80) cc_final: 0.6032 (t80) REVERT: S 73 TYR cc_start: 0.5716 (t80) cc_final: 0.4536 (m-10) REVERT: W 137 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.7837 (tmmm) REVERT: X 136 ILE cc_start: 0.6869 (OUTLIER) cc_final: 0.6648 (tt) REVERT: Y 44 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7775 (pp) REVERT: a 42 ASN cc_start: 0.6810 (OUTLIER) cc_final: 0.5942 (m110) REVERT: a 61 ARG cc_start: 0.6366 (tpt170) cc_final: 0.5363 (mmp-170) REVERT: a 66 LYS cc_start: 0.5292 (mtpt) cc_final: 0.4942 (ttpt) REVERT: a 91 LYS cc_start: 0.9092 (ttpp) cc_final: 0.8870 (ttpp) REVERT: a 118 MET cc_start: 0.7857 (mmp) cc_final: 0.7504 (mtp) REVERT: a 168 MET cc_start: 0.7826 (mmt) cc_final: 0.7101 (mtt) REVERT: a 215 MET cc_start: 0.7763 (mmt) cc_final: 0.6608 (tpt) REVERT: a 266 MET cc_start: 0.7903 (ttm) cc_final: 0.7697 (ptm) outliers start: 74 outliers final: 18 residues processed: 678 average time/residue: 0.5349 time to fit residues: 573.4048 Evaluate side-chains 378 residues out of total 3805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 351 time to evaluate : 4.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 394 ARG Chi-restraints excluded: chain B residue 513 TRP Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 409 PHE Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 373 ILE Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 203 TRP Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain O residue 46 ILE Chi-restraints excluded: chain W residue 137 LYS Chi-restraints excluded: chain X residue 136 ILE Chi-restraints excluded: chain X residue 140 VAL Chi-restraints excluded: chain Y residue 44 LEU Chi-restraints excluded: chain a residue 42 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 396 optimal weight: 6.9990 chunk 356 optimal weight: 6.9990 chunk 197 optimal weight: 1.9990 chunk 121 optimal weight: 6.9990 chunk 240 optimal weight: 1.9990 chunk 190 optimal weight: 4.9990 chunk 368 optimal weight: 20.0000 chunk 142 optimal weight: 3.9990 chunk 224 optimal weight: 2.9990 chunk 274 optimal weight: 2.9990 chunk 426 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 215 HIS C 425 GLN ** C 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 ASN G 54 HIS G 131 ASN G 142 ASN O 52 GLN a 17 ASN a 245 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 37231 Z= 0.228 Angle : 0.592 9.262 50399 Z= 0.316 Chirality : 0.042 0.250 5875 Planarity : 0.006 0.051 6501 Dihedral : 7.476 115.048 5371 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.10 % Favored : 97.88 % Rotamer: Outliers : 2.23 % Allowed : 9.91 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.47 % 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: 0.96 (0.12), residues: 4770 helix: 1.14 (0.10), residues: 2554 sheet: 0.62 (0.21), residues: 530 loop : 0.02 (0.16), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP a 235 HIS 0.007 0.001 HIS a 14 PHE 0.025 0.002 PHE I 53 TYR 0.036 0.001 TYR A 236 ARG 0.007 0.000 ARG X 117 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 3805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 368 time to evaluate : 4.482 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 477 ARG cc_start: 0.8366 (ttp-110) cc_final: 0.8033 (mtm110) REVERT: B 504 LEU cc_start: 0.9428 (OUTLIER) cc_final: 0.9203 (mm) REVERT: C 236 TYR cc_start: 0.9404 (OUTLIER) cc_final: 0.8655 (t80) REVERT: D 445 MET cc_start: 0.8638 (mmt) cc_final: 0.8420 (mpp) REVERT: F 445 MET cc_start: 0.8194 (mmm) cc_final: 0.7832 (mmm) REVERT: G 60 LEU cc_start: 0.6017 (tt) cc_final: 0.5249 (mt) REVERT: H 24 GLN cc_start: 0.8563 (tp40) cc_final: 0.8324 (mm110) REVERT: H 31 GLU cc_start: 0.6817 (pm20) cc_final: 0.6609 (pm20) REVERT: I 37 GLU cc_start: 0.7957 (tp30) cc_final: 0.7584 (pp20) REVERT: I 57 MET cc_start: 0.6692 (tmm) cc_final: 0.6399 (tpp) REVERT: J 6 MET cc_start: 0.6683 (mtp) cc_final: 0.6174 (ppp) REVERT: L 11 MET cc_start: 0.4877 (tpt) cc_final: 0.4409 (mtm) REVERT: M 11 MET cc_start: 0.7847 (tpt) cc_final: 0.7604 (mtp) REVERT: M 17 MET cc_start: 0.6523 (tpt) cc_final: 0.6014 (tpt) REVERT: N 16 MET cc_start: 0.6826 (mtp) cc_final: 0.5981 (mmm) REVERT: N 44 ASP cc_start: 0.7254 (m-30) cc_final: 0.6459 (p0) REVERT: N 54 PHE cc_start: 0.7569 (m-80) cc_final: 0.7248 (m-80) REVERT: O 11 MET cc_start: 0.2225 (tpp) cc_final: 0.0475 (ttt) REVERT: O 17 MET cc_start: 0.5979 (ttm) cc_final: 0.5726 (ptm) REVERT: O 28 ILE cc_start: 0.8075 (tt) cc_final: 0.7818 (pt) REVERT: O 53 PHE cc_start: 0.6590 (t80) cc_final: 0.5893 (t80) REVERT: P 35 PHE cc_start: 0.7567 (t80) cc_final: 0.7322 (t80) REVERT: P 44 ASP cc_start: 0.8454 (m-30) cc_final: 0.8187 (p0) REVERT: P 49 LEU cc_start: 0.8898 (mt) cc_final: 0.8624 (mp) REVERT: Q 75 MET cc_start: 0.7568 (mtm) cc_final: 0.7341 (mmm) REVERT: Q 76 PHE cc_start: 0.6013 (m-80) cc_final: 0.5218 (t80) REVERT: S 11 MET cc_start: 0.7057 (tpp) cc_final: 0.6545 (mpp) REVERT: S 54 PHE cc_start: 0.6594 (m-80) cc_final: 0.6104 (t80) REVERT: S 73 TYR cc_start: 0.5781 (t80) cc_final: 0.4630 (m-10) REVERT: W 137 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8188 (tmmm) REVERT: X 98 ARG cc_start: 0.9240 (ttp80) cc_final: 0.8791 (ttp80) REVERT: X 136 ILE cc_start: 0.6944 (OUTLIER) cc_final: 0.6723 (tt) REVERT: Y 30 MET cc_start: 0.6016 (mtm) cc_final: 0.5531 (ppp) REVERT: a 61 ARG cc_start: 0.6330 (tpt170) cc_final: 0.5259 (mmp-170) REVERT: a 66 LYS cc_start: 0.5167 (mtpt) cc_final: 0.4850 (ttpt) REVERT: a 168 MET cc_start: 0.7497 (mmt) cc_final: 0.7133 (mtt) REVERT: a 266 MET cc_start: 0.7987 (ttm) cc_final: 0.7605 (ptm) outliers start: 85 outliers final: 43 residues processed: 433 average time/residue: 0.4961 time to fit residues: 352.7536 Evaluate side-chains 374 residues out of total 3805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 327 time to evaluate : 4.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 406 PHE Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain B residue 15 ARG Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 513 TRP Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 409 PHE Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain F residue 285 THR Chi-restraints excluded: chain F residue 423 THR Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 203 TRP Chi-restraints excluded: chain G residue 276 LEU Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain I residue 6 MET Chi-restraints excluded: chain J residue 63 ILE Chi-restraints excluded: chain M residue 16 MET Chi-restraints excluded: chain M residue 53 PHE Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain O residue 57 MET Chi-restraints excluded: chain S residue 22 ILE Chi-restraints excluded: chain W residue 137 LYS Chi-restraints excluded: chain W residue 173 VAL Chi-restraints excluded: chain X residue 136 ILE Chi-restraints excluded: chain X residue 140 VAL Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 60 PHE Chi-restraints excluded: chain a residue 93 MET Chi-restraints excluded: chain a residue 247 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 237 optimal weight: 0.0980 chunk 132 optimal weight: 5.9990 chunk 355 optimal weight: 0.4980 chunk 290 optimal weight: 3.9990 chunk 117 optimal weight: 6.9990 chunk 427 optimal weight: 8.9990 chunk 461 optimal weight: 10.0000 chunk 380 optimal weight: 1.9990 chunk 424 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 chunk 343 optimal weight: 0.0570 overall best weight: 1.1302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN C 294 HIS ** C 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 314 HIS H 75 ASN L 42 GLN M 52 GLN Q 5 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 37231 Z= 0.170 Angle : 0.539 8.634 50399 Z= 0.284 Chirality : 0.041 0.228 5875 Planarity : 0.005 0.053 6501 Dihedral : 7.063 114.863 5354 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.01 % Favored : 97.97 % Rotamer: Outliers : 2.21 % Allowed : 10.25 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.47 % 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: 0.80 (0.12), residues: 4770 helix: 0.98 (0.10), residues: 2562 sheet: 0.73 (0.21), residues: 529 loop : -0.06 (0.15), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP a 235 HIS 0.005 0.001 HIS a 14 PHE 0.031 0.001 PHE P 54 TYR 0.025 0.001 TYR A 236 ARG 0.007 0.000 ARG X 83 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 3805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 354 time to evaluate : 4.232 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 revert: symmetry clash REVERT: B 504 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.9179 (mm) REVERT: C 236 TYR cc_start: 0.9376 (OUTLIER) cc_final: 0.8588 (t80) REVERT: E 56 MET cc_start: 0.9053 (mmm) cc_final: 0.8411 (mmt) REVERT: G 48 MET cc_start: 0.8511 (ttm) cc_final: 0.8206 (ttm) REVERT: G 60 LEU cc_start: 0.5961 (tt) cc_final: 0.5262 (mt) REVERT: H 24 GLN cc_start: 0.8520 (tp40) cc_final: 0.8236 (mm110) REVERT: I 11 MET cc_start: 0.7053 (mmm) cc_final: 0.6794 (mmm) REVERT: I 57 MET cc_start: 0.6754 (tmm) cc_final: 0.6553 (tpp) REVERT: J 6 MET cc_start: 0.6820 (mtp) cc_final: 0.6139 (ppp) REVERT: L 11 MET cc_start: 0.4952 (tpt) cc_final: 0.4593 (mtm) REVERT: L 28 ILE cc_start: 0.6782 (pt) cc_final: 0.6498 (mm) REVERT: M 6 MET cc_start: 0.6276 (mpp) cc_final: 0.5896 (mpp) REVERT: M 11 MET cc_start: 0.8013 (tpt) cc_final: 0.7593 (mtp) REVERT: N 16 MET cc_start: 0.6911 (mtp) cc_final: 0.6372 (mmm) REVERT: O 6 MET cc_start: 0.1995 (ppp) cc_final: 0.1595 (ppp) REVERT: O 11 MET cc_start: 0.2719 (tpp) cc_final: 0.1369 (ttt) REVERT: O 41 ARG cc_start: 0.7004 (mmm160) cc_final: 0.6435 (ttp80) REVERT: P 11 MET cc_start: 0.6147 (mmm) cc_final: 0.5663 (mmp) REVERT: P 35 PHE cc_start: 0.7824 (t80) cc_final: 0.7512 (t80) REVERT: P 44 ASP cc_start: 0.8478 (m-30) cc_final: 0.8175 (p0) REVERT: P 49 LEU cc_start: 0.8878 (mt) cc_final: 0.8672 (mt) REVERT: Q 37 GLU cc_start: 0.8495 (tm-30) cc_final: 0.8274 (tm-30) REVERT: Q 76 PHE cc_start: 0.5912 (m-80) cc_final: 0.5014 (t80) REVERT: R 17 MET cc_start: 0.7882 (tpp) cc_final: 0.7681 (tpt) REVERT: R 57 MET cc_start: 0.5611 (mmm) cc_final: 0.5294 (mmt) REVERT: S 11 MET cc_start: 0.7086 (tpp) cc_final: 0.6643 (mmt) REVERT: S 73 TYR cc_start: 0.5623 (t80) cc_final: 0.4548 (m-10) REVERT: W 69 ASP cc_start: 0.7468 (m-30) cc_final: 0.6980 (t0) REVERT: W 137 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8120 (tmmm) REVERT: X 1 MET cc_start: 0.1184 (mmp) cc_final: 0.0522 (ttt) REVERT: X 98 ARG cc_start: 0.9134 (ttp80) cc_final: 0.8812 (ttp80) REVERT: Y 30 MET cc_start: 0.6149 (mtm) cc_final: 0.5878 (ppp) REVERT: Y 82 ARG cc_start: 0.8645 (mmm-85) cc_final: 0.8433 (mmm160) REVERT: a 61 ARG cc_start: 0.6288 (tpt170) cc_final: 0.5249 (mmp-170) REVERT: a 66 LYS cc_start: 0.5107 (mtpt) cc_final: 0.4781 (ttpt) REVERT: a 92 ASP cc_start: 0.8328 (m-30) cc_final: 0.7968 (m-30) REVERT: a 118 MET cc_start: 0.8021 (tpp) cc_final: 0.7720 (tpt) REVERT: a 169 LYS cc_start: 0.2951 (tptt) cc_final: 0.2327 (tppt) REVERT: a 266 MET cc_start: 0.7954 (ttm) cc_final: 0.7598 (ptm) outliers start: 84 outliers final: 45 residues processed: 411 average time/residue: 0.4893 time to fit residues: 330.3197 Evaluate side-chains 369 residues out of total 3805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 321 time to evaluate : 4.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain B residue 15 ARG Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 513 TRP Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 409 PHE Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 285 THR Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 203 TRP Chi-restraints excluded: chain G residue 276 LEU Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain I residue 6 MET Chi-restraints excluded: chain I residue 46 ILE Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 17 MET Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 16 MET Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain O residue 3 ASN Chi-restraints excluded: chain O residue 57 MET Chi-restraints excluded: chain P residue 6 MET Chi-restraints excluded: chain W residue 137 LYS Chi-restraints excluded: chain X residue 140 VAL Chi-restraints excluded: chain Y residue 60 SER Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 60 PHE Chi-restraints excluded: chain a residue 93 MET Chi-restraints excluded: chain a residue 247 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 422 optimal weight: 5.9990 chunk 321 optimal weight: 30.0000 chunk 221 optimal weight: 6.9990 chunk 47 optimal weight: 8.9990 chunk 204 optimal weight: 3.9990 chunk 287 optimal weight: 7.9990 chunk 429 optimal weight: 10.0000 chunk 454 optimal weight: 6.9990 chunk 224 optimal weight: 7.9990 chunk 406 optimal weight: 7.9990 chunk 122 optimal weight: 8.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN C 420 GLN ** C 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 73 HIS F 361 GLN ** G 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 42 GLN S 52 GLN W 67 GLN Y 51 HIS ** a 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.121 37231 Z= 0.471 Angle : 0.659 9.617 50399 Z= 0.344 Chirality : 0.045 0.238 5875 Planarity : 0.005 0.054 6501 Dihedral : 7.299 120.704 5347 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.87 % Favored : 97.11 % Rotamer: Outliers : 2.94 % Allowed : 11.48 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.47 % 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: 0.57 (0.12), residues: 4770 helix: 0.77 (0.10), residues: 2606 sheet: 0.50 (0.21), residues: 549 loop : -0.10 (0.16), residues: 1615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP a 235 HIS 0.005 0.001 HIS A 479 PHE 0.023 0.002 PHE L 76 TYR 0.039 0.002 TYR A 236 ARG 0.007 0.001 ARG I 50 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 3805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 320 time to evaluate : 4.320 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 revert: symmetry clash REVERT: B 504 LEU cc_start: 0.9443 (OUTLIER) cc_final: 0.9240 (mm) REVERT: C 236 TYR cc_start: 0.9444 (OUTLIER) cc_final: 0.8696 (t80) REVERT: H 24 GLN cc_start: 0.8478 (tp40) cc_final: 0.8257 (mm110) REVERT: I 11 MET cc_start: 0.7345 (mmm) cc_final: 0.7016 (mmm) REVERT: J 16 MET cc_start: 0.5988 (tpt) cc_final: 0.5745 (tpt) REVERT: L 11 MET cc_start: 0.4814 (tpt) cc_final: 0.4336 (mtm) REVERT: L 28 ILE cc_start: 0.6786 (pt) cc_final: 0.6432 (mm) REVERT: M 11 MET cc_start: 0.8229 (tpt) cc_final: 0.7749 (mtp) REVERT: N 16 MET cc_start: 0.6546 (mtp) cc_final: 0.6245 (mmm) REVERT: O 6 MET cc_start: 0.2091 (ppp) cc_final: 0.1715 (ppp) REVERT: P 11 MET cc_start: 0.6319 (mmm) cc_final: 0.5732 (mmt) REVERT: P 35 PHE cc_start: 0.8067 (t80) cc_final: 0.7615 (t80) REVERT: P 44 ASP cc_start: 0.8653 (m-30) cc_final: 0.8294 (p0) REVERT: Q 37 GLU cc_start: 0.8369 (tm-30) cc_final: 0.8169 (tm-30) REVERT: Q 76 PHE cc_start: 0.5825 (m-10) cc_final: 0.5106 (t80) REVERT: R 17 MET cc_start: 0.7723 (tpp) cc_final: 0.7454 (tpp) REVERT: S 11 MET cc_start: 0.7128 (tpp) cc_final: 0.6591 (mmt) REVERT: S 73 TYR cc_start: 0.5558 (t80) cc_final: 0.4527 (m-10) REVERT: W 137 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.8150 (tmmm) REVERT: X 1 MET cc_start: 0.1177 (mmp) cc_final: 0.0817 (ttp) REVERT: Y 30 MET cc_start: 0.6232 (mtm) cc_final: 0.5960 (ppp) REVERT: a 66 LYS cc_start: 0.5364 (mtpt) cc_final: 0.4900 (ttpt) REVERT: a 118 MET cc_start: 0.8088 (tpp) cc_final: 0.7777 (tpt) REVERT: a 169 LYS cc_start: 0.3077 (tptt) cc_final: 0.2425 (tppt) REVERT: a 257 MET cc_start: 0.9045 (ppp) cc_final: 0.8603 (ppp) REVERT: a 266 MET cc_start: 0.7748 (ttm) cc_final: 0.7512 (ptt) outliers start: 112 outliers final: 72 residues processed: 402 average time/residue: 0.4552 time to fit residues: 308.9444 Evaluate side-chains 382 residues out of total 3805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 307 time to evaluate : 4.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain B residue 15 ARG Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 513 TRP Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 159 MET Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain E residue 390 VAL Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 285 THR Chi-restraints excluded: chain F residue 411 THR Chi-restraints excluded: chain F residue 423 THR Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 178 MET Chi-restraints excluded: chain G residue 203 TRP Chi-restraints excluded: chain G residue 276 LEU Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain I residue 6 MET Chi-restraints excluded: chain J residue 63 ILE Chi-restraints excluded: chain L residue 44 ASP Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 16 MET Chi-restraints excluded: chain N residue 22 ILE Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain O residue 57 MET Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain O residue 75 MET Chi-restraints excluded: chain P residue 7 ASP Chi-restraints excluded: chain Q residue 53 PHE Chi-restraints excluded: chain R residue 26 ILE Chi-restraints excluded: chain S residue 22 ILE Chi-restraints excluded: chain W residue 31 LEU Chi-restraints excluded: chain W residue 102 SER Chi-restraints excluded: chain W residue 137 LYS Chi-restraints excluded: chain W residue 173 VAL Chi-restraints excluded: chain X residue 30 MET Chi-restraints excluded: chain X residue 136 ILE Chi-restraints excluded: chain X residue 140 VAL Chi-restraints excluded: chain Y residue 60 SER Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 60 PHE Chi-restraints excluded: chain a residue 93 MET Chi-restraints excluded: chain a residue 247 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 378 optimal weight: 1.9990 chunk 257 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 338 optimal weight: 20.0000 chunk 187 optimal weight: 3.9990 chunk 387 optimal weight: 0.9980 chunk 314 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 231 optimal weight: 3.9990 chunk 407 optimal weight: 20.0000 chunk 114 optimal weight: 5.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 GLN B 27 ASN C 420 GLN ** C 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 5 ASN L 42 GLN N 42 GLN W 73 GLN ** a 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 37231 Z= 0.198 Angle : 0.547 9.611 50399 Z= 0.285 Chirality : 0.041 0.191 5875 Planarity : 0.004 0.055 6501 Dihedral : 6.839 119.710 5345 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.66 % Favored : 97.32 % Rotamer: Outliers : 2.37 % Allowed : 12.75 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.47 % 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 (0.12), residues: 4770 helix: 0.92 (0.10), residues: 2588 sheet: 0.61 (0.21), residues: 530 loop : -0.13 (0.16), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP a 235 HIS 0.004 0.001 HIS a 14 PHE 0.023 0.001 PHE a 56 TYR 0.029 0.001 TYR A 236 ARG 0.007 0.000 ARG Y 49 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 3805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 337 time to evaluate : 4.142 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 REVERT: D 84 LEU cc_start: 0.9489 (OUTLIER) cc_final: 0.9253 (mp) REVERT: H 24 GLN cc_start: 0.8389 (tp40) cc_final: 0.8158 (mm110) REVERT: I 16 MET cc_start: 0.7701 (tpt) cc_final: 0.7460 (tpt) REVERT: L 11 MET cc_start: 0.4637 (tpt) cc_final: 0.4335 (mtm) REVERT: L 28 ILE cc_start: 0.6859 (pt) cc_final: 0.6506 (mm) REVERT: M 11 MET cc_start: 0.8056 (tpt) cc_final: 0.7579 (mtm) REVERT: M 76 PHE cc_start: 0.2815 (m-10) cc_final: 0.1589 (t80) REVERT: N 16 MET cc_start: 0.6874 (mtp) cc_final: 0.6314 (mmm) REVERT: O 6 MET cc_start: 0.2458 (ppp) cc_final: 0.2227 (ppp) REVERT: O 11 MET cc_start: 0.2705 (OUTLIER) cc_final: 0.1304 (ttt) REVERT: P 11 MET cc_start: 0.6237 (mmm) cc_final: 0.5777 (mmt) REVERT: P 35 PHE cc_start: 0.8098 (t80) cc_final: 0.7732 (t80) REVERT: P 44 ASP cc_start: 0.8660 (m-30) cc_final: 0.8232 (p0) REVERT: Q 37 GLU cc_start: 0.8424 (tm-30) cc_final: 0.8213 (tm-30) REVERT: Q 76 PHE cc_start: 0.5787 (m-10) cc_final: 0.5073 (t80) REVERT: R 11 MET cc_start: 0.6220 (tpp) cc_final: 0.5050 (mmt) REVERT: R 17 MET cc_start: 0.7491 (tpp) cc_final: 0.7095 (tpp) REVERT: S 11 MET cc_start: 0.6988 (tpp) cc_final: 0.6465 (mmt) REVERT: S 73 TYR cc_start: 0.5417 (t80) cc_final: 0.4367 (m-10) REVERT: W 69 ASP cc_start: 0.7519 (m-30) cc_final: 0.7077 (t0) REVERT: W 137 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8051 (tmmm) REVERT: X 1 MET cc_start: 0.1186 (mmp) cc_final: 0.0791 (ttp) REVERT: X 136 ILE cc_start: 0.7049 (OUTLIER) cc_final: 0.6581 (tp) REVERT: Y 30 MET cc_start: 0.6244 (mtm) cc_final: 0.5903 (ppp) REVERT: a 61 ARG cc_start: 0.6358 (tpt170) cc_final: 0.5212 (mmp-170) REVERT: a 118 MET cc_start: 0.8045 (tpp) cc_final: 0.7675 (tpt) REVERT: a 169 LYS cc_start: 0.3240 (tptt) cc_final: 0.2564 (tppt) REVERT: a 215 MET cc_start: 0.7284 (mmt) cc_final: 0.6360 (tpt) REVERT: a 257 MET cc_start: 0.9103 (ppp) cc_final: 0.8662 (ppp) REVERT: a 266 MET cc_start: 0.7740 (ttm) cc_final: 0.7510 (ptt) outliers start: 90 outliers final: 57 residues processed: 401 average time/residue: 0.4902 time to fit residues: 329.7664 Evaluate side-chains 367 residues out of total 3805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 306 time to evaluate : 4.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain B residue 15 ARG Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 513 TRP Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 200 ASP Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 285 THR Chi-restraints excluded: chain F residue 372 ASP Chi-restraints excluded: chain F residue 423 THR Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 203 TRP Chi-restraints excluded: chain G residue 276 LEU Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain I residue 6 MET Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 16 MET Chi-restraints excluded: chain N residue 22 ILE Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain O residue 11 MET Chi-restraints excluded: chain O residue 57 MET Chi-restraints excluded: chain Q residue 53 PHE Chi-restraints excluded: chain R residue 16 MET Chi-restraints excluded: chain W residue 31 LEU Chi-restraints excluded: chain W residue 137 LYS Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain W residue 173 VAL Chi-restraints excluded: chain X residue 136 ILE Chi-restraints excluded: chain X residue 140 VAL Chi-restraints excluded: chain Y residue 8 LEU Chi-restraints excluded: chain Y residue 60 SER Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 60 PHE Chi-restraints excluded: chain a residue 93 MET Chi-restraints excluded: chain a residue 247 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 152 optimal weight: 0.0370 chunk 409 optimal weight: 6.9990 chunk 89 optimal weight: 9.9990 chunk 266 optimal weight: 0.0270 chunk 112 optimal weight: 7.9990 chunk 454 optimal weight: 6.9990 chunk 377 optimal weight: 40.0000 chunk 210 optimal weight: 9.9990 chunk 37 optimal weight: 9.9990 chunk 150 optimal weight: 4.9990 chunk 238 optimal weight: 1.9990 overall best weight: 2.8122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 ASN ** C 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 GLN ** G 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 37231 Z= 0.247 Angle : 0.554 8.232 50399 Z= 0.289 Chirality : 0.041 0.232 5875 Planarity : 0.005 0.058 6501 Dihedral : 6.610 117.973 5343 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.47 % Allowed : 13.30 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.47 % 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: 0.72 (0.12), residues: 4770 helix: 0.96 (0.10), residues: 2592 sheet: 0.58 (0.21), residues: 546 loop : -0.18 (0.16), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP a 241 HIS 0.004 0.001 HIS A 479 PHE 0.021 0.001 PHE a 56 TYR 0.033 0.001 TYR A 236 ARG 0.007 0.000 ARG S 50 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 3805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 311 time to evaluate : 4.669 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: D 84 LEU cc_start: 0.9493 (OUTLIER) cc_final: 0.9289 (mp) REVERT: E 431 MET cc_start: 0.8038 (ppp) cc_final: 0.7765 (ppp) REVERT: H 24 GLN cc_start: 0.8370 (tp40) cc_final: 0.8130 (mm110) REVERT: L 28 ILE cc_start: 0.6905 (pt) cc_final: 0.6546 (mm) REVERT: M 11 MET cc_start: 0.7948 (tpt) cc_final: 0.7450 (mtp) REVERT: M 76 PHE cc_start: 0.3224 (m-10) cc_final: 0.2026 (t80) REVERT: N 16 MET cc_start: 0.6943 (mtp) cc_final: 0.6621 (tpp) REVERT: O 11 MET cc_start: 0.2954 (OUTLIER) cc_final: 0.1488 (ttt) REVERT: P 11 MET cc_start: 0.6402 (mmm) cc_final: 0.6034 (mmt) REVERT: P 35 PHE cc_start: 0.8036 (t80) cc_final: 0.7773 (t80) REVERT: P 44 ASP cc_start: 0.8607 (m-30) cc_final: 0.8147 (p0) REVERT: P 76 PHE cc_start: 0.7423 (m-80) cc_final: 0.6880 (m-80) REVERT: Q 37 GLU cc_start: 0.8351 (tm-30) cc_final: 0.8146 (tp30) REVERT: Q 76 PHE cc_start: 0.5389 (m-10) cc_final: 0.4683 (t80) REVERT: R 6 MET cc_start: 0.8368 (mmm) cc_final: 0.7908 (ppp) REVERT: R 7 ASP cc_start: 0.5178 (OUTLIER) cc_final: 0.4670 (p0) REVERT: R 17 MET cc_start: 0.7450 (tpp) cc_final: 0.6955 (tpp) REVERT: S 11 MET cc_start: 0.7087 (tpp) cc_final: 0.6527 (mmt) REVERT: S 73 TYR cc_start: 0.5253 (t80) cc_final: 0.4190 (m-10) REVERT: W 69 ASP cc_start: 0.7457 (m-30) cc_final: 0.7006 (t0) REVERT: W 137 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8040 (tmmm) REVERT: X 1 MET cc_start: 0.1207 (mmp) cc_final: 0.0828 (ttp) REVERT: X 136 ILE cc_start: 0.7092 (OUTLIER) cc_final: 0.6610 (tp) REVERT: X 145 ASN cc_start: 0.7939 (p0) cc_final: 0.7079 (p0) REVERT: Y 30 MET cc_start: 0.6687 (mtm) cc_final: 0.6036 (ppp) REVERT: Y 49 ARG cc_start: 0.7341 (tmm160) cc_final: 0.6383 (mpt180) REVERT: a 118 MET cc_start: 0.7984 (tpp) cc_final: 0.7683 (tpt) REVERT: a 169 LYS cc_start: 0.3229 (tptt) cc_final: 0.2520 (tppt) REVERT: a 257 MET cc_start: 0.9097 (ppp) cc_final: 0.8663 (ppp) REVERT: a 266 MET cc_start: 0.7702 (ttm) cc_final: 0.7472 (ptt) outliers start: 94 outliers final: 67 residues processed: 379 average time/residue: 0.4562 time to fit residues: 293.9061 Evaluate side-chains 375 residues out of total 3805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 303 time to evaluate : 4.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain B residue 15 ARG Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 513 TRP Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 200 ASP Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 285 THR Chi-restraints excluded: chain F residue 372 ASP Chi-restraints excluded: chain F residue 423 THR Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 178 MET Chi-restraints excluded: chain G residue 203 TRP Chi-restraints excluded: chain G residue 276 LEU Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain I residue 75 MET Chi-restraints excluded: chain J residue 63 ILE Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 16 MET Chi-restraints excluded: chain N residue 22 ILE Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 63 ILE Chi-restraints excluded: chain O residue 11 MET Chi-restraints excluded: chain O residue 57 MET Chi-restraints excluded: chain Q residue 53 PHE Chi-restraints excluded: chain R residue 7 ASP Chi-restraints excluded: chain R residue 16 MET Chi-restraints excluded: chain W residue 31 LEU Chi-restraints excluded: chain W residue 137 LYS Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain W residue 150 VAL Chi-restraints excluded: chain W residue 173 VAL Chi-restraints excluded: chain X residue 136 ILE Chi-restraints excluded: chain X residue 140 VAL Chi-restraints excluded: chain Y residue 60 SER Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 60 PHE Chi-restraints excluded: chain a residue 93 MET Chi-restraints excluded: chain a residue 216 TYR Chi-restraints excluded: chain a residue 247 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 438 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 259 optimal weight: 5.9990 chunk 332 optimal weight: 6.9990 chunk 257 optimal weight: 6.9990 chunk 382 optimal weight: 0.6980 chunk 253 optimal weight: 1.9990 chunk 453 optimal weight: 8.9990 chunk 283 optimal weight: 10.0000 chunk 276 optimal weight: 7.9990 chunk 209 optimal weight: 10.0000 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 443 GLN B 27 ASN ** C 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 343 GLN G 131 ASN I 5 ASN Q 3 ASN Y 51 HIS ** a 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 37231 Z= 0.262 Angle : 0.566 11.725 50399 Z= 0.292 Chirality : 0.041 0.227 5875 Planarity : 0.004 0.056 6501 Dihedral : 6.567 115.878 5343 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.58 % Allowed : 14.01 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.47 % 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 (0.12), residues: 4770 helix: 0.99 (0.10), residues: 2588 sheet: 0.52 (0.21), residues: 559 loop : -0.22 (0.16), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP a 235 HIS 0.004 0.001 HIS Y 51 PHE 0.021 0.001 PHE O 53 TYR 0.048 0.001 TYR A 236 ARG 0.007 0.000 ARG X 98 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 3805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 315 time to evaluate : 4.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 409 PHE cc_start: 0.8282 (OUTLIER) cc_final: 0.7895 (p90) REVERT: D 84 LEU cc_start: 0.9495 (OUTLIER) cc_final: 0.9266 (mp) REVERT: E 431 MET cc_start: 0.8022 (ppp) cc_final: 0.7797 (ppp) REVERT: H 24 GLN cc_start: 0.8225 (tp40) cc_final: 0.8009 (mm110) REVERT: I 11 MET cc_start: 0.6733 (mmm) cc_final: 0.6523 (mmm) REVERT: L 28 ILE cc_start: 0.6682 (pt) cc_final: 0.6314 (mm) REVERT: M 11 MET cc_start: 0.7962 (tpt) cc_final: 0.7457 (mtt) REVERT: M 76 PHE cc_start: 0.3690 (m-10) cc_final: 0.2585 (t80) REVERT: N 16 MET cc_start: 0.6916 (mtp) cc_final: 0.6523 (tpp) REVERT: O 11 MET cc_start: 0.2897 (OUTLIER) cc_final: 0.1386 (ttt) REVERT: P 11 MET cc_start: 0.6303 (mmm) cc_final: 0.5895 (mmt) REVERT: P 35 PHE cc_start: 0.8145 (t80) cc_final: 0.7942 (t80) REVERT: P 44 ASP cc_start: 0.8623 (m-30) cc_final: 0.8137 (p0) REVERT: P 76 PHE cc_start: 0.7417 (m-80) cc_final: 0.6904 (m-10) REVERT: Q 76 PHE cc_start: 0.5292 (m-10) cc_final: 0.4590 (t80) REVERT: R 7 ASP cc_start: 0.5072 (OUTLIER) cc_final: 0.4729 (p0) REVERT: R 11 MET cc_start: 0.6676 (tpp) cc_final: 0.5546 (mmt) REVERT: R 17 MET cc_start: 0.7182 (tpp) cc_final: 0.6628 (tpp) REVERT: S 11 MET cc_start: 0.7057 (tpp) cc_final: 0.6588 (mmt) REVERT: S 73 TYR cc_start: 0.5285 (t80) cc_final: 0.4151 (m-10) REVERT: W 137 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.7981 (tmmm) REVERT: X 1 MET cc_start: 0.1140 (mmp) cc_final: 0.0657 (ttt) REVERT: X 136 ILE cc_start: 0.7151 (OUTLIER) cc_final: 0.6678 (tp) REVERT: X 145 ASN cc_start: 0.7868 (p0) cc_final: 0.7078 (p0) REVERT: Y 49 ARG cc_start: 0.7380 (tmm160) cc_final: 0.6417 (mpt180) REVERT: a 118 MET cc_start: 0.8062 (tpp) cc_final: 0.7763 (tpt) REVERT: a 169 LYS cc_start: 0.3257 (tptt) cc_final: 0.2541 (tppt) REVERT: a 257 MET cc_start: 0.9127 (ppp) cc_final: 0.8745 (ppp) REVERT: a 266 MET cc_start: 0.7685 (ttm) cc_final: 0.7314 (ptm) outliers start: 98 outliers final: 69 residues processed: 384 average time/residue: 0.4509 time to fit residues: 294.3891 Evaluate side-chains 378 residues out of total 3805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 303 time to evaluate : 4.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain B residue 15 ARG Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 513 TRP Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 409 PHE Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 200 ASP Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 285 THR Chi-restraints excluded: chain F residue 372 ASP Chi-restraints excluded: chain F residue 423 THR Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 178 MET Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain G residue 203 TRP Chi-restraints excluded: chain G residue 276 LEU Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain J residue 63 ILE Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 16 MET Chi-restraints excluded: chain N residue 22 ILE Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 63 ILE Chi-restraints excluded: chain O residue 11 MET Chi-restraints excluded: chain O residue 57 MET Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain Q residue 53 PHE Chi-restraints excluded: chain R residue 7 ASP Chi-restraints excluded: chain R residue 16 MET Chi-restraints excluded: chain S residue 3 ASN Chi-restraints excluded: chain W residue 31 LEU Chi-restraints excluded: chain W residue 137 LYS Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain W residue 150 VAL Chi-restraints excluded: chain W residue 173 VAL Chi-restraints excluded: chain X residue 136 ILE Chi-restraints excluded: chain X residue 140 VAL Chi-restraints excluded: chain Y residue 44 LEU Chi-restraints excluded: chain Y residue 60 SER Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 60 PHE Chi-restraints excluded: chain a residue 93 MET Chi-restraints excluded: chain a residue 216 TYR Chi-restraints excluded: chain a residue 247 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 280 optimal weight: 0.4980 chunk 180 optimal weight: 2.9990 chunk 270 optimal weight: 0.9990 chunk 136 optimal weight: 3.9990 chunk 89 optimal weight: 9.9990 chunk 87 optimal weight: 1.9990 chunk 288 optimal weight: 0.9990 chunk 308 optimal weight: 20.0000 chunk 223 optimal weight: 0.1980 chunk 42 optimal weight: 4.9990 chunk 356 optimal weight: 7.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 420 GLN C 484 GLN D 43 GLN ** G 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.073 37231 Z= 0.156 Angle : 0.540 9.962 50399 Z= 0.279 Chirality : 0.040 0.299 5875 Planarity : 0.004 0.054 6501 Dihedral : 6.299 115.115 5343 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.87 % Allowed : 15.27 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.47 % 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: 0.80 (0.12), residues: 4770 helix: 1.06 (0.11), residues: 2573 sheet: 0.67 (0.22), residues: 530 loop : -0.20 (0.16), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP a 235 HIS 0.004 0.001 HIS G 54 PHE 0.022 0.001 PHE O 53 TYR 0.040 0.001 TYR M 10 ARG 0.007 0.000 ARG X 98 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 3805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 327 time to evaluate : 4.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 409 PHE cc_start: 0.8287 (OUTLIER) cc_final: 0.7798 (p90) REVERT: D 84 LEU cc_start: 0.9442 (OUTLIER) cc_final: 0.9216 (mp) REVERT: I 11 MET cc_start: 0.6858 (mmm) cc_final: 0.6616 (mmm) REVERT: L 28 ILE cc_start: 0.6580 (pt) cc_final: 0.6236 (mm) REVERT: M 11 MET cc_start: 0.7981 (tpt) cc_final: 0.7405 (mtp) REVERT: M 76 PHE cc_start: 0.3475 (m-10) cc_final: 0.2403 (t80) REVERT: N 16 MET cc_start: 0.6932 (mtp) cc_final: 0.6557 (tpp) REVERT: O 11 MET cc_start: 0.2883 (mmt) cc_final: 0.1402 (ttt) REVERT: P 11 MET cc_start: 0.6364 (mmm) cc_final: 0.5941 (mmt) REVERT: P 35 PHE cc_start: 0.8168 (t80) cc_final: 0.7872 (t80) REVERT: P 44 ASP cc_start: 0.8669 (m-30) cc_final: 0.8003 (p0) REVERT: P 49 LEU cc_start: 0.8716 (mp) cc_final: 0.8401 (mp) REVERT: P 76 PHE cc_start: 0.7506 (m-80) cc_final: 0.7033 (m-10) REVERT: Q 76 PHE cc_start: 0.4907 (m-10) cc_final: 0.4040 (t80) REVERT: R 6 MET cc_start: 0.8307 (mmm) cc_final: 0.7965 (ptt) REVERT: R 11 MET cc_start: 0.6575 (tpp) cc_final: 0.5584 (mmt) REVERT: R 17 MET cc_start: 0.7183 (tpp) cc_final: 0.6677 (tpp) REVERT: S 11 MET cc_start: 0.6941 (tpp) cc_final: 0.6354 (mmt) REVERT: W 137 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8098 (tmmm) REVERT: X 1 MET cc_start: 0.1136 (mmp) cc_final: 0.0880 (ttp) REVERT: X 136 ILE cc_start: 0.6962 (OUTLIER) cc_final: 0.6564 (tt) REVERT: X 145 ASN cc_start: 0.7818 (p0) cc_final: 0.7080 (p0) REVERT: Y 30 MET cc_start: 0.7894 (mtp) cc_final: 0.7080 (ppp) REVERT: Y 49 ARG cc_start: 0.7365 (tmm160) cc_final: 0.6370 (mmt90) REVERT: a 61 ARG cc_start: 0.6339 (tpt170) cc_final: 0.5170 (mmp-170) REVERT: a 93 MET cc_start: 0.8579 (OUTLIER) cc_final: 0.8376 (tpp) REVERT: a 118 MET cc_start: 0.7979 (tpp) cc_final: 0.7715 (tpt) REVERT: a 169 LYS cc_start: 0.3180 (tptt) cc_final: 0.2482 (tppt) REVERT: a 266 MET cc_start: 0.7697 (ttm) cc_final: 0.7415 (ptm) outliers start: 71 outliers final: 54 residues processed: 378 average time/residue: 0.4458 time to fit residues: 284.8072 Evaluate side-chains 361 residues out of total 3805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 302 time to evaluate : 4.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain B residue 15 ARG Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 513 TRP Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 409 PHE Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 312 PHE Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 285 THR Chi-restraints excluded: chain F residue 372 ASP Chi-restraints excluded: chain F residue 423 THR Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 203 TRP Chi-restraints excluded: chain G residue 276 LEU Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain J residue 63 ILE Chi-restraints excluded: chain M residue 16 MET Chi-restraints excluded: chain N residue 22 ILE Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain O residue 57 MET Chi-restraints excluded: chain Q residue 53 PHE Chi-restraints excluded: chain R residue 16 MET Chi-restraints excluded: chain S residue 3 ASN Chi-restraints excluded: chain W residue 137 LYS Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain W residue 150 VAL Chi-restraints excluded: chain W residue 173 VAL Chi-restraints excluded: chain X residue 136 ILE Chi-restraints excluded: chain X residue 140 VAL Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 60 PHE Chi-restraints excluded: chain a residue 93 MET Chi-restraints excluded: chain a residue 247 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 412 optimal weight: 9.9990 chunk 433 optimal weight: 7.9990 chunk 395 optimal weight: 7.9990 chunk 422 optimal weight: 7.9990 chunk 254 optimal weight: 0.7980 chunk 183 optimal weight: 4.9990 chunk 331 optimal weight: 0.0070 chunk 129 optimal weight: 6.9990 chunk 381 optimal weight: 6.9990 chunk 399 optimal weight: 3.9990 chunk 420 optimal weight: 0.5980 overall best weight: 2.0802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 420 GLN ** G 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 51 HIS ** a 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 37231 Z= 0.204 Angle : 0.561 12.084 50399 Z= 0.286 Chirality : 0.041 0.367 5875 Planarity : 0.004 0.055 6501 Dihedral : 6.250 116.633 5342 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.87 % Allowed : 15.64 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.47 % 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: 0.80 (0.12), residues: 4770 helix: 1.07 (0.11), residues: 2580 sheet: 0.67 (0.22), residues: 530 loop : -0.21 (0.16), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP a 235 HIS 0.005 0.001 HIS Y 51 PHE 0.022 0.001 PHE O 53 TYR 0.044 0.001 TYR M 10 ARG 0.007 0.000 ARG X 98 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 3805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 302 time to evaluate : 4.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 409 PHE cc_start: 0.8287 (OUTLIER) cc_final: 0.7708 (p90) REVERT: D 84 LEU cc_start: 0.9451 (OUTLIER) cc_final: 0.9236 (mp) REVERT: H 68 ILE cc_start: 0.8277 (mt) cc_final: 0.7957 (mt) REVERT: H 70 GLU cc_start: 0.8270 (pm20) cc_final: 0.7511 (pm20) REVERT: I 17 MET cc_start: 0.7334 (ptp) cc_final: 0.6377 (ttt) REVERT: L 28 ILE cc_start: 0.6601 (pt) cc_final: 0.6257 (mm) REVERT: M 11 MET cc_start: 0.7992 (tpt) cc_final: 0.7408 (mtm) REVERT: M 76 PHE cc_start: 0.3805 (m-10) cc_final: 0.2688 (t80) REVERT: N 16 MET cc_start: 0.6926 (mtp) cc_final: 0.6339 (tpp) REVERT: O 11 MET cc_start: 0.2941 (mmt) cc_final: 0.1327 (ttt) REVERT: P 11 MET cc_start: 0.6244 (mmm) cc_final: 0.6000 (mmm) REVERT: P 16 MET cc_start: 0.4500 (mmm) cc_final: 0.4291 (mmm) REVERT: P 35 PHE cc_start: 0.8180 (t80) cc_final: 0.7869 (t80) REVERT: P 44 ASP cc_start: 0.8695 (m-30) cc_final: 0.7962 (p0) REVERT: P 49 LEU cc_start: 0.8787 (mp) cc_final: 0.8478 (mp) REVERT: P 76 PHE cc_start: 0.7547 (m-80) cc_final: 0.7071 (m-10) REVERT: Q 76 PHE cc_start: 0.4941 (m-10) cc_final: 0.3945 (t80) REVERT: R 6 MET cc_start: 0.8319 (mmm) cc_final: 0.7950 (ptt) REVERT: R 7 ASP cc_start: 0.4892 (OUTLIER) cc_final: 0.4475 (p0) REVERT: R 11 MET cc_start: 0.6540 (tpp) cc_final: 0.5594 (mmt) REVERT: R 17 MET cc_start: 0.7185 (tpp) cc_final: 0.6657 (tpp) REVERT: S 11 MET cc_start: 0.6815 (tpp) cc_final: 0.6313 (mmt) REVERT: W 137 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8108 (tmmm) REVERT: X 1 MET cc_start: 0.1275 (mmp) cc_final: 0.0866 (ttt) REVERT: X 136 ILE cc_start: 0.6926 (OUTLIER) cc_final: 0.6592 (tt) REVERT: X 145 ASN cc_start: 0.7848 (p0) cc_final: 0.7145 (p0) REVERT: Y 49 ARG cc_start: 0.7372 (tmm160) cc_final: 0.6429 (mpt-90) REVERT: a 93 MET cc_start: 0.8650 (OUTLIER) cc_final: 0.8445 (tpp) REVERT: a 118 MET cc_start: 0.7991 (tpp) cc_final: 0.7724 (tpt) REVERT: a 169 LYS cc_start: 0.3185 (tptt) cc_final: 0.2496 (tppt) REVERT: a 210 ARG cc_start: 0.8673 (ptt180) cc_final: 0.8357 (ptp-170) REVERT: a 257 MET cc_start: 0.8820 (ppp) cc_final: 0.8361 (ppp) REVERT: a 266 MET cc_start: 0.7689 (ttm) cc_final: 0.7402 (ptm) outliers start: 71 outliers final: 54 residues processed: 354 average time/residue: 0.4934 time to fit residues: 298.5029 Evaluate side-chains 359 residues out of total 3805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 299 time to evaluate : 4.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain B residue 15 ARG Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 513 TRP Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 409 PHE Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 200 ASP Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 312 PHE Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 285 THR Chi-restraints excluded: chain F residue 423 THR Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 203 TRP Chi-restraints excluded: chain G residue 276 LEU Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain L residue 75 MET Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 16 MET Chi-restraints excluded: chain N residue 22 ILE Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain O residue 57 MET Chi-restraints excluded: chain R residue 7 ASP Chi-restraints excluded: chain R residue 16 MET Chi-restraints excluded: chain W residue 137 LYS Chi-restraints excluded: chain W residue 150 VAL Chi-restraints excluded: chain W residue 173 VAL Chi-restraints excluded: chain X residue 136 ILE Chi-restraints excluded: chain X residue 140 VAL Chi-restraints excluded: chain Y residue 25 VAL Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 60 PHE Chi-restraints excluded: chain a residue 93 MET Chi-restraints excluded: chain a residue 216 TYR Chi-restraints excluded: chain a residue 247 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 277 optimal weight: 6.9990 chunk 446 optimal weight: 20.0000 chunk 272 optimal weight: 8.9990 chunk 211 optimal weight: 10.0000 chunk 310 optimal weight: 6.9990 chunk 468 optimal weight: 9.9990 chunk 430 optimal weight: 10.0000 chunk 372 optimal weight: 0.8980 chunk 38 optimal weight: 10.0000 chunk 288 optimal weight: 7.9990 chunk 228 optimal weight: 2.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 ASN D 32 GLN F 19 GLN ** G 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 ASN ** G 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 10 GLN ** a 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 95 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.3981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.117 37231 Z= 0.403 Angle : 0.652 11.808 50399 Z= 0.335 Chirality : 0.043 0.321 5875 Planarity : 0.005 0.055 6501 Dihedral : 6.623 119.792 5342 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.84 % Allowed : 15.93 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.47 % 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: 0.61 (0.12), residues: 4770 helix: 0.94 (0.10), residues: 2560 sheet: 0.47 (0.21), residues: 548 loop : -0.32 (0.15), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP a 235 HIS 0.006 0.001 HIS A 479 PHE 0.025 0.002 PHE R 54 TYR 0.054 0.002 TYR A 236 ARG 0.007 0.001 ARG X 98 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 3805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 293 time to evaluate : 4.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 84 LEU cc_start: 0.9521 (OUTLIER) cc_final: 0.9283 (mp) REVERT: H 68 ILE cc_start: 0.8288 (mt) cc_final: 0.7963 (mt) REVERT: H 70 GLU cc_start: 0.8355 (pm20) cc_final: 0.7695 (pm20) REVERT: I 11 MET cc_start: 0.6811 (mmm) cc_final: 0.6174 (mmm) REVERT: L 28 ILE cc_start: 0.6611 (pt) cc_final: 0.6183 (mm) REVERT: M 11 MET cc_start: 0.8021 (tpt) cc_final: 0.7484 (mtt) REVERT: M 76 PHE cc_start: 0.4256 (m-10) cc_final: 0.3321 (t80) REVERT: N 16 MET cc_start: 0.6787 (mtp) cc_final: 0.6204 (tpp) REVERT: O 17 MET cc_start: 0.5626 (ptt) cc_final: 0.5204 (ptt) REVERT: P 11 MET cc_start: 0.6292 (mmm) cc_final: 0.5911 (mmm) REVERT: P 35 PHE cc_start: 0.8212 (t80) cc_final: 0.7806 (t80) REVERT: P 44 ASP cc_start: 0.8846 (m-30) cc_final: 0.8100 (p0) REVERT: P 49 LEU cc_start: 0.8817 (mp) cc_final: 0.8516 (mp) REVERT: P 76 PHE cc_start: 0.7665 (m-80) cc_final: 0.7151 (m-10) REVERT: R 6 MET cc_start: 0.8299 (mmm) cc_final: 0.7886 (ptt) REVERT: R 17 MET cc_start: 0.7026 (tpp) cc_final: 0.6466 (tpp) REVERT: S 11 MET cc_start: 0.7043 (tpp) cc_final: 0.6498 (mmt) REVERT: W 69 ASP cc_start: 0.7418 (m-30) cc_final: 0.7142 (t0) REVERT: W 137 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.7937 (tmmm) REVERT: W 147 MET cc_start: 0.8032 (pmm) cc_final: 0.7602 (pmm) REVERT: X 136 ILE cc_start: 0.7040 (OUTLIER) cc_final: 0.6666 (tt) REVERT: X 145 ASN cc_start: 0.7768 (p0) cc_final: 0.7024 (p0) REVERT: Y 49 ARG cc_start: 0.7381 (tmm160) cc_final: 0.6450 (mpt-90) REVERT: a 118 MET cc_start: 0.7982 (tpp) cc_final: 0.7670 (tpt) REVERT: a 169 LYS cc_start: 0.2965 (tptt) cc_final: 0.2239 (tppt) REVERT: a 210 ARG cc_start: 0.8671 (ptt180) cc_final: 0.8433 (ptp-170) REVERT: a 257 MET cc_start: 0.8895 (ppp) cc_final: 0.8417 (ppp) REVERT: a 266 MET cc_start: 0.7618 (ttm) cc_final: 0.7252 (ptm) outliers start: 70 outliers final: 57 residues processed: 346 average time/residue: 0.4428 time to fit residues: 260.2891 Evaluate side-chains 348 residues out of total 3805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 288 time to evaluate : 4.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain B residue 15 ARG Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 200 ASP Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 285 THR Chi-restraints excluded: chain F residue 423 THR Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 203 TRP Chi-restraints excluded: chain G residue 276 LEU Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 16 MET Chi-restraints excluded: chain N residue 22 ILE Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 63 ILE Chi-restraints excluded: chain O residue 57 MET Chi-restraints excluded: chain R residue 16 MET Chi-restraints excluded: chain W residue 137 LYS Chi-restraints excluded: chain W residue 150 VAL Chi-restraints excluded: chain W residue 173 VAL Chi-restraints excluded: chain X residue 136 ILE Chi-restraints excluded: chain X residue 140 VAL Chi-restraints excluded: chain Y residue 25 VAL Chi-restraints excluded: chain Y residue 26 TRP Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 60 PHE Chi-restraints excluded: chain a residue 247 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 296 optimal weight: 10.0000 chunk 397 optimal weight: 0.9990 chunk 114 optimal weight: 0.9990 chunk 343 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 chunk 103 optimal weight: 8.9990 chunk 373 optimal weight: 0.0470 chunk 156 optimal weight: 2.9990 chunk 383 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 68 optimal weight: 0.9980 overall best weight: 0.7482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 333 GLN F 19 GLN ** G 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 ASN N 5 ASN Q 3 ASN ** a 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.079381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.053168 restraints weight = 143840.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.055272 restraints weight = 70105.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.055283 restraints weight = 33836.292| |-----------------------------------------------------------------------------| r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.072 37231 Z= 0.161 Angle : 0.570 12.217 50399 Z= 0.290 Chirality : 0.041 0.312 5875 Planarity : 0.004 0.054 6501 Dihedral : 6.217 116.865 5340 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.42 % Allowed : 16.61 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.47 % 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: 0.80 (0.12), residues: 4770 helix: 1.09 (0.11), residues: 2565 sheet: 0.64 (0.22), residues: 528 loop : -0.24 (0.15), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP a 235 HIS 0.004 0.001 HIS G 54 PHE 0.034 0.001 PHE R 54 TYR 0.040 0.001 TYR a 94 ARG 0.006 0.000 ARG X 98 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7086.98 seconds wall clock time: 129 minutes 51.96 seconds (7791.96 seconds total)