Starting phenix.real_space_refine on Sun Dec 29 03:09:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gcs_51235/12_2024/9gcs_51235.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gcs_51235/12_2024/9gcs_51235.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9gcs_51235/12_2024/9gcs_51235.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gcs_51235/12_2024/9gcs_51235.map" model { file = "/net/cci-nas-00/data/ceres_data/9gcs_51235/12_2024/9gcs_51235.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gcs_51235/12_2024/9gcs_51235.cif" } resolution = 3.9 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= 0.011 sd= 0.050 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 36 5.49 5 Mg 12 5.21 5 S 254 5.16 5 C 34118 2.51 5 N 9882 2.21 5 O 10438 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 54740 Number of models: 1 Model: "" Number of chains: 34 Chain: "C" Number of atoms: 3298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3298 Classifications: {'peptide': 419} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 400} Chain: "D" Number of atoms: 3298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3298 Classifications: {'peptide': 419} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 400} Chain: "E" Number of atoms: 3298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3298 Classifications: {'peptide': 419} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 400} Chain: "J" Number of atoms: 3298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3298 Classifications: {'peptide': 419} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 400} Chain: "K" Number of atoms: 3298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3298 Classifications: {'peptide': 419} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 400} Chain: "L" Number of atoms: 3298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3298 Classifications: {'peptide': 419} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 400} Chain: "M" Number of atoms: 3298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3298 Classifications: {'peptide': 419} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 400} Chain: "O" Number of atoms: 3298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3298 Classifications: {'peptide': 419} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 400} Chain: "c" Number of atoms: 1478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1478 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 183} Chain: "d" Number of atoms: 1478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1478 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 183} Chain: "e" Number of atoms: 1478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1478 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 183} Chain: "f" Number of atoms: 1478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1478 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 183} Chain: "g" Number of atoms: 1478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1478 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 183} Chain: "h" Number of atoms: 1478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1478 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 183} Chain: "i" Number of atoms: 1478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1478 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 183} Chain: "j" Number of atoms: 1478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1478 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 183} Chain: "k" Number of atoms: 1478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1478 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 183} Chain: "l" Number of atoms: 1478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1478 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 183} Chain: "B" Number of atoms: 3298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3298 Classifications: {'peptide': 419} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 400} Chain: "G" Number of atoms: 3298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3298 Classifications: {'peptide': 419} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 401} Chain: "N" Number of atoms: 3298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3298 Classifications: {'peptide': 419} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 400} Chain: "F" Number of atoms: 3298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3298 Classifications: {'peptide': 419} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 400} 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: 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: "J" 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: "K" 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: "L" 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: "M" 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: "O" 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: "G" 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: "N" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 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} Time building chain proxies: 23.93, per 1000 atoms: 0.44 Number of scatterers: 54740 At special positions: 0 Unit cell: (180.999, 175.266, 243.243, 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 254 16.00 P 36 15.00 Mg 12 11.99 O 10438 8.00 N 9882 7.00 C 34118 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.49 Conformation dependent library (CDL) restraints added in 5.2 seconds 13708 Ramachandran restraints generated. 6854 Oldfield, 0 Emsley, 6854 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12960 Finding SS restraints... Secondary structure from input PDB file: 284 helices and 53 sheets defined 58.2% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.82 Creating SS restraints... Processing helix chain 'C' and resid 3 through 8 Processing helix chain 'C' and resid 10 through 21 removed outlier: 3.519A pdb=" N LEU C 14 " --> pdb=" O PRO C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 44 Processing helix chain 'C' and resid 82 through 90 Processing helix chain 'C' and resid 124 through 128 removed outlier: 3.523A pdb=" N ARG C 128 " --> pdb=" O GLU C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 166 Processing helix chain 'C' and resid 183 through 199 Processing helix chain 'C' and resid 212 through 223 Processing helix chain 'C' and resid 235 through 255 removed outlier: 3.927A pdb=" N HIS C 239 " --> pdb=" O PRO C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 278 Processing helix chain 'C' and resid 290 through 302 Proline residue: C 297 - end of helix removed outlier: 3.649A pdb=" N PHE C 300 " --> pdb=" O ARG C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 335 removed outlier: 3.879A pdb=" N GLU C 329 " --> pdb=" O SER C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 353 Processing helix chain 'C' and resid 367 through 372 Processing helix chain 'C' and resid 374 through 388 Processing helix chain 'C' and resid 391 through 406 removed outlier: 3.768A pdb=" N MET C 405 " --> pdb=" O ASN C 401 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N THR C 406 " --> pdb=" O LYS C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 419 Processing helix chain 'D' and resid 2 through 9 Processing helix chain 'D' and resid 10 through 20 removed outlier: 3.838A pdb=" N ASN D 20 " --> pdb=" O THR D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 46 Processing helix chain 'D' and resid 82 through 90 removed outlier: 3.844A pdb=" N ILE D 86 " --> pdb=" O SER D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 166 removed outlier: 4.265A pdb=" N ALA D 159 " --> pdb=" O GLU D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 199 Processing helix chain 'D' and resid 212 through 223 Processing helix chain 'D' and resid 235 through 256 removed outlier: 3.510A pdb=" N HIS D 256 " --> pdb=" O ARG D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 278 Processing helix chain 'D' and resid 290 through 303 removed outlier: 4.014A pdb=" N ARG D 296 " --> pdb=" O ASN D 292 " (cutoff:3.500A) Proline residue: D 297 - end of helix Processing helix chain 'D' and resid 325 through 335 removed outlier: 3.777A pdb=" N GLU D 329 " --> pdb=" O SER D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 351 Processing helix chain 'D' and resid 368 through 372 removed outlier: 3.689A pdb=" N THR D 372 " --> pdb=" O GLU D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 388 Processing helix chain 'D' and resid 391 through 403 removed outlier: 3.596A pdb=" N ALA D 395 " --> pdb=" O GLY D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 419 Processing helix chain 'E' and resid 3 through 7 Processing helix chain 'E' and resid 11 through 22 removed outlier: 3.802A pdb=" N ILE E 15 " --> pdb=" O VAL E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 45 removed outlier: 3.634A pdb=" N SER E 45 " --> pdb=" O GLN E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 71 Processing helix chain 'E' and resid 82 through 89 Processing helix chain 'E' and resid 132 through 136 Processing helix chain 'E' and resid 156 through 166 Processing helix chain 'E' and resid 183 through 199 Processing helix chain 'E' and resid 212 through 222 Processing helix chain 'E' and resid 235 through 255 removed outlier: 3.707A pdb=" N HIS E 239 " --> pdb=" O PRO E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 278 Processing helix chain 'E' and resid 285 through 289 removed outlier: 4.157A pdb=" N VAL E 289 " --> pdb=" O THR E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 290 through 303 removed outlier: 4.176A pdb=" N ARG E 296 " --> pdb=" O ASN E 292 " (cutoff:3.500A) Proline residue: E 297 - end of helix Processing helix chain 'E' and resid 325 through 334 removed outlier: 3.878A pdb=" N GLU E 329 " --> pdb=" O SER E 325 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU E 334 " --> pdb=" O VAL E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 346 through 352 Processing helix chain 'E' and resid 367 through 371 removed outlier: 3.753A pdb=" N LEU E 370 " --> pdb=" O LYS E 367 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU E 371 " --> pdb=" O GLU E 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 367 through 371' Processing helix chain 'E' and resid 373 through 388 Processing helix chain 'E' and resid 391 through 405 removed outlier: 4.065A pdb=" N MET E 405 " --> pdb=" O ASN E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 419 removed outlier: 3.632A pdb=" N SER E 419 " --> pdb=" O MET E 415 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 9 removed outlier: 4.524A pdb=" N LEU J 6 " --> pdb=" O ASN J 2 " (cutoff:3.500A) Processing helix chain 'J' and resid 10 through 20 removed outlier: 3.609A pdb=" N LEU J 14 " --> pdb=" O PRO J 10 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN J 20 " --> pdb=" O THR J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 46 removed outlier: 3.674A pdb=" N GLY J 46 " --> pdb=" O HIS J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 90 removed outlier: 3.733A pdb=" N ILE J 86 " --> pdb=" O SER J 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 155 through 166 removed outlier: 3.933A pdb=" N ALA J 159 " --> pdb=" O GLU J 155 " (cutoff:3.500A) Processing helix chain 'J' and resid 183 through 199 removed outlier: 3.710A pdb=" N LEU J 187 " --> pdb=" O GLY J 183 " (cutoff:3.500A) Processing helix chain 'J' and resid 212 through 222 Processing helix chain 'J' and resid 235 through 255 Processing helix chain 'J' and resid 266 through 278 Processing helix chain 'J' and resid 290 through 302 Proline residue: J 297 - end of helix Processing helix chain 'J' and resid 346 through 351 Processing helix chain 'J' and resid 373 through 388 removed outlier: 3.535A pdb=" N HIS J 388 " --> pdb=" O ARG J 384 " (cutoff:3.500A) Processing helix chain 'J' and resid 391 through 406 Processing helix chain 'J' and resid 408 through 419 Processing helix chain 'K' and resid 3 through 8 Processing helix chain 'K' and resid 10 through 22 removed outlier: 3.837A pdb=" N LEU K 14 " --> pdb=" O PRO K 10 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLY K 22 " --> pdb=" O GLY K 18 " (cutoff:3.500A) Processing helix chain 'K' and resid 30 through 46 Processing helix chain 'K' and resid 82 through 89 Processing helix chain 'K' and resid 123 through 129 removed outlier: 3.790A pdb=" N ASN K 129 " --> pdb=" O GLU K 125 " (cutoff:3.500A) Processing helix chain 'K' and resid 132 through 136 Processing helix chain 'K' and resid 156 through 166 Processing helix chain 'K' and resid 183 through 199 removed outlier: 3.727A pdb=" N LEU K 187 " --> pdb=" O GLY K 183 " (cutoff:3.500A) Processing helix chain 'K' and resid 214 through 223 Processing helix chain 'K' and resid 235 through 256 removed outlier: 3.674A pdb=" N HIS K 239 " --> pdb=" O PRO K 235 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N HIS K 256 " --> pdb=" O ARG K 252 " (cutoff:3.500A) Processing helix chain 'K' and resid 266 through 278 Processing helix chain 'K' and resid 294 through 302 removed outlier: 3.567A pdb=" N ARG K 299 " --> pdb=" O HIS K 295 " (cutoff:3.500A) Processing helix chain 'K' and resid 325 through 335 removed outlier: 3.745A pdb=" N GLU K 329 " --> pdb=" O SER K 325 " (cutoff:3.500A) Processing helix chain 'K' and resid 346 through 351 Processing helix chain 'K' and resid 367 through 371 removed outlier: 3.626A pdb=" N LEU K 370 " --> pdb=" O LYS K 367 " (cutoff:3.500A) Processing helix chain 'K' and resid 373 through 388 Processing helix chain 'K' and resid 391 through 406 removed outlier: 3.894A pdb=" N MET K 405 " --> pdb=" O ASN K 401 " (cutoff:3.500A) Processing helix chain 'K' and resid 408 through 418 Processing helix chain 'L' and resid 2 through 8 removed outlier: 3.575A pdb=" N ASN L 8 " --> pdb=" O THR L 4 " (cutoff:3.500A) Processing helix chain 'L' and resid 10 through 22 removed outlier: 3.668A pdb=" N LEU L 14 " --> pdb=" O PRO L 10 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 46 Processing helix chain 'L' and resid 82 through 90 removed outlier: 3.635A pdb=" N ILE L 86 " --> pdb=" O SER L 82 " (cutoff:3.500A) Processing helix chain 'L' and resid 123 through 129 removed outlier: 3.555A pdb=" N ARG L 128 " --> pdb=" O PRO L 124 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASN L 129 " --> pdb=" O GLU L 125 " (cutoff:3.500A) Processing helix chain 'L' and resid 132 through 136 Processing helix chain 'L' and resid 156 through 166 removed outlier: 3.734A pdb=" N LEU L 162 " --> pdb=" O THR L 158 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 199 Processing helix chain 'L' and resid 212 through 223 Processing helix chain 'L' and resid 235 through 255 removed outlier: 3.602A pdb=" N HIS L 239 " --> pdb=" O PRO L 235 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU L 255 " --> pdb=" O LYS L 251 " (cutoff:3.500A) Processing helix chain 'L' and resid 266 through 278 Processing helix chain 'L' and resid 294 through 302 removed outlier: 3.813A pdb=" N LYS L 298 " --> pdb=" O LEU L 294 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE L 300 " --> pdb=" O ARG L 296 " (cutoff:3.500A) Processing helix chain 'L' and resid 326 through 335 Processing helix chain 'L' and resid 374 through 388 Processing helix chain 'L' and resid 392 through 404 Processing helix chain 'L' and resid 408 through 414 Processing helix chain 'M' and resid 2 through 9 removed outlier: 4.087A pdb=" N LEU M 6 " --> pdb=" O ASN M 2 " (cutoff:3.500A) Processing helix chain 'M' and resid 10 through 21 removed outlier: 3.854A pdb=" N LEU M 14 " --> pdb=" O PRO M 10 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N MET M 21 " --> pdb=" O LEU M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 30 through 45 removed outlier: 3.636A pdb=" N SER M 45 " --> pdb=" O GLN M 41 " (cutoff:3.500A) Processing helix chain 'M' and resid 67 through 71 Processing helix chain 'M' and resid 82 through 90 Processing helix chain 'M' and resid 123 through 128 removed outlier: 3.536A pdb=" N ARG M 128 " --> pdb=" O PRO M 124 " (cutoff:3.500A) Processing helix chain 'M' and resid 153 through 155 No H-bonds generated for 'chain 'M' and resid 153 through 155' Processing helix chain 'M' and resid 156 through 166 Processing helix chain 'M' and resid 184 through 199 Processing helix chain 'M' and resid 212 through 223 Processing helix chain 'M' and resid 235 through 255 Processing helix chain 'M' and resid 266 through 278 Processing helix chain 'M' and resid 294 through 302 Processing helix chain 'M' and resid 325 through 335 Processing helix chain 'M' and resid 346 through 351 removed outlier: 3.787A pdb=" N ALA M 350 " --> pdb=" O SER M 346 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU M 351 " --> pdb=" O ARG M 347 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 346 through 351' Processing helix chain 'M' and resid 373 through 388 Processing helix chain 'M' and resid 391 through 404 removed outlier: 3.721A pdb=" N LYS M 402 " --> pdb=" O PHE M 398 " (cutoff:3.500A) Processing helix chain 'M' and resid 408 through 419 removed outlier: 3.846A pdb=" N SER M 419 " --> pdb=" O MET M 415 " (cutoff:3.500A) Processing helix chain 'O' and resid 10 through 20 removed outlier: 3.688A pdb=" N ASN O 20 " --> pdb=" O THR O 16 " (cutoff:3.500A) Processing helix chain 'O' and resid 30 through 45 Processing helix chain 'O' and resid 67 through 71 Processing helix chain 'O' and resid 82 through 89 removed outlier: 3.682A pdb=" N PHE O 89 " --> pdb=" O GLN O 85 " (cutoff:3.500A) Processing helix chain 'O' and resid 123 through 129 removed outlier: 3.659A pdb=" N ASN O 129 " --> pdb=" O GLU O 125 " (cutoff:3.500A) Processing helix chain 'O' and resid 153 through 166 Processing helix chain 'O' and resid 183 through 199 removed outlier: 3.915A pdb=" N LEU O 187 " --> pdb=" O GLY O 183 " (cutoff:3.500A) Processing helix chain 'O' and resid 212 through 223 removed outlier: 4.258A pdb=" N ARG O 221 " --> pdb=" O THR O 217 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL O 223 " --> pdb=" O MET O 219 " (cutoff:3.500A) Processing helix chain 'O' and resid 235 through 255 removed outlier: 3.629A pdb=" N HIS O 239 " --> pdb=" O PRO O 235 " (cutoff:3.500A) Processing helix chain 'O' and resid 266 through 278 Processing helix chain 'O' and resid 290 through 302 Proline residue: O 297 - end of helix Processing helix chain 'O' and resid 325 through 335 removed outlier: 3.695A pdb=" N GLU O 329 " --> pdb=" O SER O 325 " (cutoff:3.500A) Processing helix chain 'O' and resid 346 through 351 Processing helix chain 'O' and resid 373 through 388 Processing helix chain 'O' and resid 391 through 404 removed outlier: 3.610A pdb=" N ALA O 404 " --> pdb=" O ILE O 400 " (cutoff:3.500A) Processing helix chain 'O' and resid 408 through 418 removed outlier: 3.895A pdb=" N ARG O 418 " --> pdb=" O GLU O 414 " (cutoff:3.500A) Processing helix chain 'c' and resid 5 through 40 Processing helix chain 'c' and resid 44 through 101 removed outlier: 7.202A pdb=" N THR c 94 " --> pdb=" O GLN c 90 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ALA c 95 " --> pdb=" O GLN c 91 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LEU c 96 " --> pdb=" O HIS c 92 " (cutoff:3.500A) Processing helix chain 'c' and resid 102 through 104 No H-bonds generated for 'chain 'c' and resid 102 through 104' Processing helix chain 'c' and resid 112 through 136 removed outlier: 3.761A pdb=" N ASN c 116 " --> pdb=" O ALA c 112 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA c 129 " --> pdb=" O ALA c 125 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS c 136 " --> pdb=" O SER c 132 " (cutoff:3.500A) Processing helix chain 'c' and resid 143 through 154 removed outlier: 3.954A pdb=" N THR c 152 " --> pdb=" O ASP c 148 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE c 153 " --> pdb=" O ILE c 149 " (cutoff:3.500A) Processing helix chain 'c' and resid 158 through 165 Processing helix chain 'c' and resid 170 through 190 Processing helix chain 'd' and resid 5 through 40 Processing helix chain 'd' and resid 44 through 92 Processing helix chain 'd' and resid 92 through 100 Processing helix chain 'd' and resid 100 through 105 removed outlier: 3.747A pdb=" N MET d 105 " --> pdb=" O ALA d 101 " (cutoff:3.500A) Processing helix chain 'd' and resid 111 through 136 removed outlier: 3.710A pdb=" N LYS d 136 " --> pdb=" O SER d 132 " (cutoff:3.500A) Processing helix chain 'd' and resid 146 through 154 Processing helix chain 'd' and resid 158 through 167 removed outlier: 4.466A pdb=" N GLU d 167 " --> pdb=" O ASP d 163 " (cutoff:3.500A) Processing helix chain 'd' and resid 170 through 190 Processing helix chain 'e' and resid 5 through 40 Processing helix chain 'e' and resid 44 through 92 Processing helix chain 'e' and resid 92 through 100 removed outlier: 3.645A pdb=" N LEU e 100 " --> pdb=" O LEU e 96 " (cutoff:3.500A) Processing helix chain 'e' and resid 101 through 104 Processing helix chain 'e' and resid 111 through 137 removed outlier: 3.528A pdb=" N GLU e 128 " --> pdb=" O ASP e 124 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA e 129 " --> pdb=" O ALA e 125 " (cutoff:3.500A) Processing helix chain 'e' and resid 146 through 154 Processing helix chain 'e' and resid 158 through 165 Processing helix chain 'e' and resid 170 through 190 removed outlier: 4.182A pdb=" N VAL e 190 " --> pdb=" O SER e 186 " (cutoff:3.500A) Processing helix chain 'f' and resid 5 through 40 Processing helix chain 'f' and resid 44 through 100 removed outlier: 6.746A pdb=" N THR f 94 " --> pdb=" O GLN f 90 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ALA f 95 " --> pdb=" O GLN f 91 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU f 96 " --> pdb=" O HIS f 92 " (cutoff:3.500A) Processing helix chain 'f' and resid 101 through 104 Processing helix chain 'f' and resid 111 through 137 removed outlier: 3.838A pdb=" N LYS f 136 " --> pdb=" O SER f 132 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY f 137 " --> pdb=" O TRP f 133 " (cutoff:3.500A) Processing helix chain 'f' and resid 146 through 154 removed outlier: 3.504A pdb=" N LEU f 150 " --> pdb=" O ASP f 146 " (cutoff:3.500A) Processing helix chain 'f' and resid 158 through 166 removed outlier: 4.441A pdb=" N ASP f 163 " --> pdb=" O ALA f 160 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N ASP f 164 " --> pdb=" O SER f 161 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG f 166 " --> pdb=" O ASP f 163 " (cutoff:3.500A) Processing helix chain 'f' and resid 170 through 190 removed outlier: 3.768A pdb=" N VAL f 190 " --> pdb=" O SER f 186 " (cutoff:3.500A) Processing helix chain 'g' and resid 5 through 40 Processing helix chain 'g' and resid 44 through 100 removed outlier: 6.582A pdb=" N THR g 94 " --> pdb=" O GLN g 90 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ALA g 95 " --> pdb=" O GLN g 91 " (cutoff:3.500A) Processing helix chain 'g' and resid 101 through 104 Processing helix chain 'g' and resid 111 through 135 Processing helix chain 'g' and resid 146 through 154 Processing helix chain 'g' and resid 158 through 164 removed outlier: 3.959A pdb=" N ASP g 164 " --> pdb=" O ALA g 160 " (cutoff:3.500A) Processing helix chain 'g' and resid 170 through 190 removed outlier: 4.267A pdb=" N VAL g 190 " --> pdb=" O SER g 186 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 40 Processing helix chain 'h' and resid 44 through 101 removed outlier: 6.861A pdb=" N THR h 94 " --> pdb=" O GLN h 90 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ALA h 95 " --> pdb=" O GLN h 91 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ALA h 99 " --> pdb=" O ALA h 95 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU h 100 " --> pdb=" O LEU h 96 " (cutoff:3.500A) Processing helix chain 'h' and resid 102 through 104 No H-bonds generated for 'chain 'h' and resid 102 through 104' Processing helix chain 'h' and resid 111 through 136 removed outlier: 3.901A pdb=" N ALA h 135 " --> pdb=" O LEU h 131 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS h 136 " --> pdb=" O SER h 132 " (cutoff:3.500A) Processing helix chain 'h' and resid 146 through 154 Processing helix chain 'h' and resid 158 through 166 removed outlier: 3.786A pdb=" N VAL h 162 " --> pdb=" O ASP h 158 " (cutoff:3.500A) Processing helix chain 'h' and resid 170 through 190 Processing helix chain 'i' and resid 5 through 40 Processing helix chain 'i' and resid 44 through 92 removed outlier: 3.561A pdb=" N LEU i 48 " --> pdb=" O ASN i 44 " (cutoff:3.500A) Processing helix chain 'i' and resid 92 through 101 removed outlier: 3.650A pdb=" N LEU i 96 " --> pdb=" O HIS i 92 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ALA i 99 " --> pdb=" O ALA i 95 " (cutoff:3.500A) Processing helix chain 'i' and resid 102 through 104 No H-bonds generated for 'chain 'i' and resid 102 through 104' Processing helix chain 'i' and resid 106 through 110 Processing helix chain 'i' and resid 111 through 135 removed outlier: 3.507A pdb=" N ASN i 116 " --> pdb=" O ALA i 112 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N SER i 132 " --> pdb=" O GLU i 128 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N TRP i 133 " --> pdb=" O ALA i 129 " (cutoff:3.500A) Processing helix chain 'i' and resid 146 through 152 removed outlier: 4.193A pdb=" N THR i 152 " --> pdb=" O ASP i 148 " (cutoff:3.500A) Processing helix chain 'i' and resid 158 through 166 removed outlier: 3.882A pdb=" N VAL i 162 " --> pdb=" O ASP i 158 " (cutoff:3.500A) Processing helix chain 'i' and resid 170 through 190 removed outlier: 3.927A pdb=" N VAL i 190 " --> pdb=" O SER i 186 " (cutoff:3.500A) Processing helix chain 'j' and resid 5 through 39 removed outlier: 3.656A pdb=" N SER j 39 " --> pdb=" O LEU j 35 " (cutoff:3.500A) Processing helix chain 'j' and resid 44 through 100 removed outlier: 6.961A pdb=" N THR j 94 " --> pdb=" O GLN j 90 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ALA j 95 " --> pdb=" O GLN j 91 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU j 96 " --> pdb=" O HIS j 92 " (cutoff:3.500A) Processing helix chain 'j' and resid 100 through 108 removed outlier: 3.791A pdb=" N LEU j 104 " --> pdb=" O LEU j 100 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER j 108 " --> pdb=" O LEU j 104 " (cutoff:3.500A) Processing helix chain 'j' and resid 111 through 137 removed outlier: 4.118A pdb=" N SER j 132 " --> pdb=" O GLU j 128 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N TRP j 133 " --> pdb=" O ALA j 129 " (cutoff:3.500A) Processing helix chain 'j' and resid 143 through 145 No H-bonds generated for 'chain 'j' and resid 143 through 145' Processing helix chain 'j' and resid 146 through 154 removed outlier: 3.602A pdb=" N LEU j 150 " --> pdb=" O ASP j 146 " (cutoff:3.500A) Processing helix chain 'j' and resid 158 through 162 Processing helix chain 'j' and resid 170 through 190 removed outlier: 3.552A pdb=" N VAL j 190 " --> pdb=" O SER j 186 " (cutoff:3.500A) Processing helix chain 'k' and resid 5 through 40 Processing helix chain 'k' and resid 45 through 92 Processing helix chain 'k' and resid 92 through 100 removed outlier: 3.613A pdb=" N LEU k 96 " --> pdb=" O HIS k 92 " (cutoff:3.500A) Processing helix chain 'k' and resid 100 through 109 removed outlier: 3.738A pdb=" N GLU k 109 " --> pdb=" O MET k 105 " (cutoff:3.500A) Processing helix chain 'k' and resid 111 through 134 Processing helix chain 'k' and resid 146 through 154 removed outlier: 4.025A pdb=" N THR k 152 " --> pdb=" O ASP k 148 " (cutoff:3.500A) Processing helix chain 'k' and resid 158 through 165 removed outlier: 3.763A pdb=" N VAL k 162 " --> pdb=" O ASP k 158 " (cutoff:3.500A) Processing helix chain 'k' and resid 170 through 190 removed outlier: 3.629A pdb=" N VAL k 190 " --> pdb=" O SER k 186 " (cutoff:3.500A) Processing helix chain 'l' and resid 5 through 40 removed outlier: 3.619A pdb=" N GLY l 40 " --> pdb=" O ARG l 36 " (cutoff:3.500A) Processing helix chain 'l' and resid 45 through 92 removed outlier: 3.536A pdb=" N ASP l 49 " --> pdb=" O VAL l 45 " (cutoff:3.500A) Processing helix chain 'l' and resid 92 through 100 removed outlier: 3.583A pdb=" N LEU l 96 " --> pdb=" O HIS l 92 " (cutoff:3.500A) Processing helix chain 'l' and resid 100 through 109 removed outlier: 3.904A pdb=" N GLU l 109 " --> pdb=" O MET l 105 " (cutoff:3.500A) Processing helix chain 'l' and resid 111 through 134 Processing helix chain 'l' and resid 135 through 137 No H-bonds generated for 'chain 'l' and resid 135 through 137' Processing helix chain 'l' and resid 146 through 154 Processing helix chain 'l' and resid 158 through 165 removed outlier: 3.535A pdb=" N VAL l 162 " --> pdb=" O ASP l 158 " (cutoff:3.500A) Processing helix chain 'l' and resid 170 through 190 Processing helix chain 'B' and resid 2 through 8 removed outlier: 3.820A pdb=" N LEU B 6 " --> pdb=" O ASN B 2 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASN B 8 " --> pdb=" O THR B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 22 removed outlier: 3.847A pdb=" N LEU B 14 " --> pdb=" O PRO B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 44 removed outlier: 3.588A pdb=" N ILE B 34 " --> pdb=" O ARG B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 89 Processing helix chain 'B' and resid 153 through 166 Processing helix chain 'B' and resid 183 through 199 removed outlier: 3.914A pdb=" N LEU B 187 " --> pdb=" O GLY B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 219 Processing helix chain 'B' and resid 235 through 256 removed outlier: 3.712A pdb=" N HIS B 239 " --> pdb=" O PRO B 235 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N HIS B 256 " --> pdb=" O ARG B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 278 Processing helix chain 'B' and resid 292 through 295 Processing helix chain 'B' and resid 296 through 302 Processing helix chain 'B' and resid 325 through 335 removed outlier: 3.597A pdb=" N GLU B 329 " --> pdb=" O SER B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 353 removed outlier: 4.261A pdb=" N LYS B 352 " --> pdb=" O LYS B 348 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG B 353 " --> pdb=" O ILE B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 372 removed outlier: 4.311A pdb=" N LEU B 371 " --> pdb=" O LYS B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 388 Processing helix chain 'B' and resid 391 through 405 removed outlier: 4.145A pdb=" N MET B 405 " --> pdb=" O ASN B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 418 removed outlier: 3.798A pdb=" N ARG B 418 " --> pdb=" O GLU B 414 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 9 removed outlier: 3.913A pdb=" N THR G 9 " --> pdb=" O GLU G 5 " (cutoff:3.500A) Processing helix chain 'G' and resid 11 through 21 removed outlier: 3.926A pdb=" N ILE G 15 " --> pdb=" O VAL G 11 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR G 16 " --> pdb=" O SER G 12 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N MET G 21 " --> pdb=" O LEU G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 44 Processing helix chain 'G' and resid 67 through 71 Processing helix chain 'G' and resid 82 through 90 Processing helix chain 'G' and resid 125 through 129 Processing helix chain 'G' and resid 155 through 166 Processing helix chain 'G' and resid 183 through 199 Processing helix chain 'G' and resid 214 through 223 removed outlier: 4.712A pdb=" N GLN G 220 " --> pdb=" O VAL G 216 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL G 223 " --> pdb=" O MET G 219 " (cutoff:3.500A) Processing helix chain 'G' and resid 235 through 256 Processing helix chain 'G' and resid 267 through 278 Processing helix chain 'G' and resid 285 through 289 removed outlier: 3.660A pdb=" N GLY G 288 " --> pdb=" O LEU G 285 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL G 289 " --> pdb=" O THR G 286 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 285 through 289' Processing helix chain 'G' and resid 290 through 302 Proline residue: G 297 - end of helix removed outlier: 3.896A pdb=" N PHE G 300 " --> pdb=" O ARG G 296 " (cutoff:3.500A) Processing helix chain 'G' and resid 325 through 336 removed outlier: 3.637A pdb=" N GLU G 329 " --> pdb=" O SER G 325 " (cutoff:3.500A) Processing helix chain 'G' and resid 337 through 339 No H-bonds generated for 'chain 'G' and resid 337 through 339' Processing helix chain 'G' and resid 346 through 352 removed outlier: 3.958A pdb=" N ALA G 350 " --> pdb=" O SER G 346 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU G 351 " --> pdb=" O ARG G 347 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS G 352 " --> pdb=" O LYS G 348 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 346 through 352' Processing helix chain 'G' and resid 367 through 371 Processing helix chain 'G' and resid 374 through 388 Processing helix chain 'G' and resid 391 through 403 removed outlier: 3.579A pdb=" N ALA G 395 " --> pdb=" O GLY G 391 " (cutoff:3.500A) Processing helix chain 'G' and resid 408 through 418 removed outlier: 3.547A pdb=" N PHE G 412 " --> pdb=" O THR G 408 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG G 418 " --> pdb=" O GLU G 414 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 9 Processing helix chain 'N' and resid 10 through 17 removed outlier: 3.881A pdb=" N LEU N 14 " --> pdb=" O PRO N 10 " (cutoff:3.500A) Processing helix chain 'N' and resid 18 through 20 No H-bonds generated for 'chain 'N' and resid 18 through 20' Processing helix chain 'N' and resid 30 through 44 Processing helix chain 'N' and resid 67 through 71 Processing helix chain 'N' and resid 82 through 89 removed outlier: 4.439A pdb=" N PHE N 89 " --> pdb=" O GLN N 85 " (cutoff:3.500A) Processing helix chain 'N' and resid 155 through 166 removed outlier: 3.942A pdb=" N ALA N 159 " --> pdb=" O GLU N 155 " (cutoff:3.500A) Processing helix chain 'N' and resid 184 through 199 Processing helix chain 'N' and resid 212 through 223 Processing helix chain 'N' and resid 235 through 256 removed outlier: 3.682A pdb=" N HIS N 239 " --> pdb=" O PRO N 235 " (cutoff:3.500A) Processing helix chain 'N' and resid 266 through 278 Processing helix chain 'N' and resid 291 through 302 Proline residue: N 297 - end of helix removed outlier: 3.931A pdb=" N PHE N 300 " --> pdb=" O ARG N 296 " (cutoff:3.500A) Processing helix chain 'N' and resid 325 through 335 removed outlier: 3.920A pdb=" N GLU N 329 " --> pdb=" O SER N 325 " (cutoff:3.500A) Processing helix chain 'N' and resid 346 through 352 Processing helix chain 'N' and resid 373 through 388 Processing helix chain 'N' and resid 392 through 405 removed outlier: 4.044A pdb=" N MET N 405 " --> pdb=" O ASN N 401 " (cutoff:3.500A) Processing helix chain 'N' and resid 408 through 418 removed outlier: 3.760A pdb=" N ARG N 418 " --> pdb=" O GLU N 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 8 removed outlier: 3.589A pdb=" N ASN F 8 " --> pdb=" O THR F 4 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 21 Processing helix chain 'F' and resid 31 through 45 removed outlier: 3.858A pdb=" N ILE F 35 " --> pdb=" O LYS F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 90 removed outlier: 3.833A pdb=" N ILE F 86 " --> pdb=" O SER F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 129 removed outlier: 4.077A pdb=" N ASN F 129 " --> pdb=" O GLU F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 136 Processing helix chain 'F' and resid 153 through 166 Processing helix chain 'F' and resid 183 through 199 removed outlier: 3.633A pdb=" N LEU F 187 " --> pdb=" O GLY F 183 " (cutoff:3.500A) Processing helix chain 'F' and resid 212 through 223 removed outlier: 3.566A pdb=" N VAL F 216 " --> pdb=" O ARG F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 235 through 255 Processing helix chain 'F' and resid 266 through 278 Processing helix chain 'F' and resid 291 through 302 removed outlier: 3.731A pdb=" N ARG F 296 " --> pdb=" O ASN F 292 " (cutoff:3.500A) Proline residue: F 297 - end of helix removed outlier: 3.520A pdb=" N GLY F 302 " --> pdb=" O LYS F 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 325 through 333 removed outlier: 4.156A pdb=" N GLU F 329 " --> pdb=" O SER F 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 347 through 353 Processing helix chain 'F' and resid 368 through 372 removed outlier: 3.989A pdb=" N THR F 372 " --> pdb=" O GLU F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 388 Processing helix chain 'F' and resid 392 through 405 removed outlier: 3.735A pdb=" N MET F 405 " --> pdb=" O ASN F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 408 through 419 Processing sheet with id=AA1, first strand: chain 'C' and resid 79 through 81 Processing sheet with id=AA2, first strand: chain 'C' and resid 79 through 81 removed outlier: 3.876A pdb=" N GLU C 118 " --> pdb=" O SER C 98 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 138 through 139 removed outlier: 3.581A pdb=" N ASN C 306 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL C 260 " --> pdb=" O THR C 314 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N ILE C 316 " --> pdb=" O VAL C 260 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE C 262 " --> pdb=" O ILE C 316 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N THR C 318 " --> pdb=" O ILE C 262 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N LEU C 264 " --> pdb=" O THR C 318 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET C 205 " --> pdb=" O ILE C 261 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU C 263 " --> pdb=" O MET C 205 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N VAL C 228 " --> pdb=" O LEU C 204 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL C 206 " --> pdb=" O VAL C 228 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 138 through 139 removed outlier: 3.581A pdb=" N ASN C 306 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N GLY C 174 " --> pdb=" O ALA C 317 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ALA C 319 " --> pdb=" O GLY C 174 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ILE C 176 " --> pdb=" O ALA C 319 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ARG C 173 " --> pdb=" O MET C 341 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N LEU C 343 " --> pdb=" O ARG C 173 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N LEU C 175 " --> pdb=" O LEU C 343 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N LEU C 345 " --> pdb=" O LEU C 175 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL C 177 " --> pdb=" O LEU C 345 " (cutoff:3.500A) removed outlier: 10.453A pdb=" N GLU C 342 " --> pdb=" O ASN C 361 " (cutoff:3.500A) removed outlier: 8.987A pdb=" N ASN C 361 " --> pdb=" O GLU C 342 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N HIS C 344 " --> pdb=" O ASP C 359 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 144 through 145 removed outlier: 4.307A pdb=" N ILE C 168 " --> pdb=" O LEU C 145 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 64 through 66 removed outlier: 3.647A pdb=" N ASP D 95 " --> pdb=" O LEU D 55 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N LYS D 100 " --> pdb=" O VAL D 116 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N VAL D 116 " --> pdb=" O LYS D 100 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 79 through 80 Processing sheet with id=AA8, first strand: chain 'D' and resid 138 through 139 removed outlier: 4.021A pdb=" N ASN D 306 " --> pdb=" O LEU D 139 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 138 through 139 removed outlier: 4.021A pdb=" N ASN D 306 " --> pdb=" O LEU D 139 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU D 342 " --> pdb=" O GLY D 364 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY D 364 " --> pdb=" O GLU D 342 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 144 through 145 removed outlier: 4.316A pdb=" N ILE D 168 " --> pdb=" O LEU D 145 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 209 through 211 removed outlier: 6.690A pdb=" N SER D 230 " --> pdb=" O ILE D 209 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU D 211 " --> pdb=" O SER D 230 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'E' and resid 79 through 81 removed outlier: 6.570A pdb=" N THR E 96 " --> pdb=" O GLU E 118 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLU E 118 " --> pdb=" O THR E 96 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N SER E 98 " --> pdb=" O VAL E 116 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N VAL E 116 " --> pdb=" O SER E 98 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LYS E 100 " --> pdb=" O LEU E 114 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 138 through 139 removed outlier: 3.683A pdb=" N ASN E 306 " --> pdb=" O LEU E 139 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 138 through 139 removed outlier: 3.683A pdb=" N ASN E 306 " --> pdb=" O LEU E 139 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N GLY E 174 " --> pdb=" O ALA E 317 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ALA E 319 " --> pdb=" O GLY E 174 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ILE E 176 " --> pdb=" O ALA E 319 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N ARG E 173 " --> pdb=" O MET E 341 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N LEU E 343 " --> pdb=" O ARG E 173 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LEU E 175 " --> pdb=" O LEU E 343 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 144 through 145 removed outlier: 3.958A pdb=" N ILE E 168 " --> pdb=" O LEU E 145 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 64 through 66 removed outlier: 6.098A pdb=" N THR J 96 " --> pdb=" O GLU J 118 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N GLU J 118 " --> pdb=" O THR J 96 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N SER J 98 " --> pdb=" O VAL J 116 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N VAL J 116 " --> pdb=" O SER J 98 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LYS J 100 " --> pdb=" O LEU J 114 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 228 through 229 removed outlier: 3.858A pdb=" N VAL J 228 " --> pdb=" O VAL J 206 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU J 208 " --> pdb=" O VAL J 228 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE J 261 " --> pdb=" O VAL J 203 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N MET J 205 " --> pdb=" O ILE J 261 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP J 265 " --> pdb=" O LEU J 207 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N VAL J 260 " --> pdb=" O THR J 314 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N ILE J 316 " --> pdb=" O VAL J 260 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE J 262 " --> pdb=" O ILE J 316 " (cutoff:3.500A) removed outlier: 8.640A pdb=" N THR J 318 " --> pdb=" O ILE J 262 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N LEU J 264 " --> pdb=" O THR J 318 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 228 through 229 removed outlier: 3.858A pdb=" N VAL J 228 " --> pdb=" O VAL J 206 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU J 208 " --> pdb=" O VAL J 228 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE J 261 " --> pdb=" O VAL J 203 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N MET J 205 " --> pdb=" O ILE J 261 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP J 265 " --> pdb=" O LEU J 207 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N VAL J 260 " --> pdb=" O THR J 314 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N ILE J 316 " --> pdb=" O VAL J 260 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE J 262 " --> pdb=" O ILE J 316 " (cutoff:3.500A) removed outlier: 8.640A pdb=" N THR J 318 " --> pdb=" O ILE J 262 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N LEU J 264 " --> pdb=" O THR J 318 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLY J 174 " --> pdb=" O ILE J 315 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA J 317 " --> pdb=" O GLY J 174 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 50 through 57 removed outlier: 6.823A pdb=" N LYS K 100 " --> pdb=" O LEU K 114 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N VAL K 116 " --> pdb=" O SER K 98 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N SER K 98 " --> pdb=" O VAL K 116 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N GLU K 118 " --> pdb=" O THR K 96 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N THR K 96 " --> pdb=" O GLU K 118 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 144 through 145 removed outlier: 4.230A pdb=" N ILE K 168 " --> pdb=" O LEU K 145 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 227 through 230 removed outlier: 7.656A pdb=" N VAL K 228 " --> pdb=" O LEU K 204 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N VAL K 206 " --> pdb=" O VAL K 228 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N SER K 230 " --> pdb=" O VAL K 206 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LEU K 208 " --> pdb=" O SER K 230 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE K 261 " --> pdb=" O VAL K 203 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ASP K 265 " --> pdb=" O LEU K 207 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE K 209 " --> pdb=" O ASP K 265 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL K 260 " --> pdb=" O THR K 314 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N ILE K 316 " --> pdb=" O VAL K 260 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE K 262 " --> pdb=" O ILE K 316 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N THR K 318 " --> pdb=" O ILE K 262 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU K 264 " --> pdb=" O THR K 318 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N LEU K 320 " --> pdb=" O LEU K 264 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 227 through 230 removed outlier: 7.656A pdb=" N VAL K 228 " --> pdb=" O LEU K 204 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N VAL K 206 " --> pdb=" O VAL K 228 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N SER K 230 " --> pdb=" O VAL K 206 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LEU K 208 " --> pdb=" O SER K 230 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE K 261 " --> pdb=" O VAL K 203 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ASP K 265 " --> pdb=" O LEU K 207 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE K 209 " --> pdb=" O ASP K 265 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL K 260 " --> pdb=" O THR K 314 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N ILE K 316 " --> pdb=" O VAL K 260 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE K 262 " --> pdb=" O ILE K 316 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N THR K 318 " --> pdb=" O ILE K 262 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU K 264 " --> pdb=" O THR K 318 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N LEU K 320 " --> pdb=" O LEU K 264 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N GLY K 174 " --> pdb=" O ALA K 317 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N ALA K 319 " --> pdb=" O GLY K 174 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ILE K 176 " --> pdb=" O ALA K 319 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 284 through 285 Processing sheet with id=AC6, first strand: chain 'L' and resid 79 through 81 removed outlier: 7.065A pdb=" N THR L 96 " --> pdb=" O GLU L 118 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N GLU L 118 " --> pdb=" O THR L 96 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N SER L 98 " --> pdb=" O VAL L 116 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N VAL L 116 " --> pdb=" O SER L 98 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LYS L 100 " --> pdb=" O LEU L 114 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 138 through 139 removed outlier: 6.716A pdb=" N VAL L 260 " --> pdb=" O THR L 314 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N ILE L 316 " --> pdb=" O VAL L 260 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ILE L 262 " --> pdb=" O ILE L 316 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N THR L 318 " --> pdb=" O ILE L 262 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU L 264 " --> pdb=" O THR L 318 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N LEU L 320 " --> pdb=" O LEU L 264 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASP L 265 " --> pdb=" O LEU L 207 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N VAL L 228 " --> pdb=" O LEU L 204 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N VAL L 206 " --> pdb=" O VAL L 228 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N SER L 230 " --> pdb=" O VAL L 206 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LEU L 208 " --> pdb=" O SER L 230 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 138 through 139 removed outlier: 6.494A pdb=" N GLY L 174 " --> pdb=" O ALA L 317 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ALA L 319 " --> pdb=" O GLY L 174 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ILE L 176 " --> pdb=" O ALA L 319 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU L 342 " --> pdb=" O GLY L 364 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY L 364 " --> pdb=" O GLU L 342 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 144 through 145 removed outlier: 3.951A pdb=" N ILE L 168 " --> pdb=" O LEU L 145 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 284 through 285 removed outlier: 3.532A pdb=" N VAL L 289 " --> pdb=" O LEU L 285 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'M' and resid 79 through 81 removed outlier: 6.369A pdb=" N LYS M 100 " --> pdb=" O VAL M 116 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N VAL M 116 " --> pdb=" O LYS M 100 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ARG M 102 " --> pdb=" O LEU M 114 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N LEU M 114 " --> pdb=" O ARG M 102 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 138 through 139 removed outlier: 3.902A pdb=" N ASN M 306 " --> pdb=" O LEU M 139 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 144 through 145 removed outlier: 4.151A pdb=" N ILE M 168 " --> pdb=" O LEU M 145 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 227 through 231 removed outlier: 7.692A pdb=" N VAL M 228 " --> pdb=" O LEU M 204 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N VAL M 206 " --> pdb=" O VAL M 228 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N SER M 230 " --> pdb=" O VAL M 206 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N LEU M 208 " --> pdb=" O SER M 230 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N GLY M 174 " --> pdb=" O ALA M 317 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ALA M 319 " --> pdb=" O GLY M 174 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N ILE M 176 " --> pdb=" O ALA M 319 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU M 175 " --> pdb=" O LEU M 343 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU M 342 " --> pdb=" O GLY M 364 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLY M 364 " --> pdb=" O GLU M 342 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'M' and resid 284 through 285 removed outlier: 3.652A pdb=" N VAL M 289 " --> pdb=" O LEU M 285 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'O' and resid 64 through 66 removed outlier: 6.340A pdb=" N THR O 96 " --> pdb=" O GLU O 118 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N GLU O 118 " --> pdb=" O THR O 96 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N SER O 98 " --> pdb=" O VAL O 116 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N VAL O 116 " --> pdb=" O SER O 98 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LYS O 100 " --> pdb=" O LEU O 114 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'O' and resid 226 through 231 removed outlier: 6.364A pdb=" N LEU O 204 " --> pdb=" O GLU O 226 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N VAL O 228 " --> pdb=" O LEU O 204 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N VAL O 206 " --> pdb=" O VAL O 228 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N SER O 230 " --> pdb=" O VAL O 206 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N LEU O 208 " --> pdb=" O SER O 230 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASP O 265 " --> pdb=" O LEU O 207 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE O 209 " --> pdb=" O ASP O 265 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'O' and resid 226 through 231 removed outlier: 6.364A pdb=" N LEU O 204 " --> pdb=" O GLU O 226 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N VAL O 228 " --> pdb=" O LEU O 204 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N VAL O 206 " --> pdb=" O VAL O 228 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N SER O 230 " --> pdb=" O VAL O 206 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N LEU O 208 " --> pdb=" O SER O 230 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASP O 265 " --> pdb=" O LEU O 207 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE O 209 " --> pdb=" O ASP O 265 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N GLY O 174 " --> pdb=" O ALA O 317 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ALA O 319 " --> pdb=" O GLY O 174 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ILE O 176 " --> pdb=" O ALA O 319 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 63 through 66 removed outlier: 4.162A pdb=" N ILE B 49 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N THR B 96 " --> pdb=" O VAL B 119 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N VAL B 119 " --> pdb=" O THR B 96 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N SER B 98 " --> pdb=" O ASN B 117 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LYS B 115 " --> pdb=" O LYS B 100 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ARG B 102 " --> pdb=" O LEU B 113 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N LEU B 113 " --> pdb=" O ARG B 102 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 227 through 230 removed outlier: 7.798A pdb=" N VAL B 228 " --> pdb=" O LEU B 204 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N VAL B 206 " --> pdb=" O VAL B 228 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N SER B 230 " --> pdb=" O VAL B 206 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU B 208 " --> pdb=" O SER B 230 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE B 261 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET B 205 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU B 263 " --> pdb=" O MET B 205 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 227 through 230 removed outlier: 7.798A pdb=" N VAL B 228 " --> pdb=" O LEU B 204 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N VAL B 206 " --> pdb=" O VAL B 228 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N SER B 230 " --> pdb=" O VAL B 206 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU B 208 " --> pdb=" O SER B 230 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE B 261 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET B 205 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU B 263 " --> pdb=" O MET B 205 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 284 through 285 removed outlier: 3.800A pdb=" N VAL B 289 " --> pdb=" O LEU B 285 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 79 through 81 removed outlier: 3.878A pdb=" N ASP G 95 " --> pdb=" O LEU G 55 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 79 through 81 removed outlier: 3.878A pdb=" N ASP G 95 " --> pdb=" O LEU G 55 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLU G 118 " --> pdb=" O SER G 98 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 138 through 139 removed outlier: 3.616A pdb=" N ASN G 306 " --> pdb=" O LEU G 139 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL G 260 " --> pdb=" O THR G 314 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N MET G 205 " --> pdb=" O LEU G 263 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 318 through 319 removed outlier: 7.135A pdb=" N ALA G 319 " --> pdb=" O GLY G 174 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ILE G 176 " --> pdb=" O ALA G 319 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'N' and resid 79 through 81 Processing sheet with id=AF1, first strand: chain 'N' and resid 79 through 81 removed outlier: 3.882A pdb=" N GLU N 118 " --> pdb=" O SER N 98 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'N' and resid 138 through 139 removed outlier: 6.295A pdb=" N VAL N 260 " --> pdb=" O THR N 314 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N ILE N 316 " --> pdb=" O VAL N 260 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ILE N 262 " --> pdb=" O ILE N 316 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N THR N 318 " --> pdb=" O ILE N 262 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LEU N 264 " --> pdb=" O THR N 318 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE N 261 " --> pdb=" O VAL N 203 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASP N 265 " --> pdb=" O LEU N 207 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE N 209 " --> pdb=" O ASP N 265 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N VAL N 228 " --> pdb=" O LEU N 204 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N VAL N 206 " --> pdb=" O VAL N 228 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N SER N 230 " --> pdb=" O VAL N 206 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU N 208 " --> pdb=" O SER N 230 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'N' and resid 138 through 139 removed outlier: 5.819A pdb=" N GLY N 174 " --> pdb=" O ALA N 317 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ALA N 319 " --> pdb=" O GLY N 174 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ILE N 176 " --> pdb=" O ALA N 319 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'N' and resid 284 through 285 removed outlier: 3.867A pdb=" N VAL N 289 " --> pdb=" O LEU N 285 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 63 through 66 Processing sheet with id=AF6, first strand: chain 'F' and resid 63 through 66 Processing sheet with id=AF7, first strand: chain 'F' and resid 228 through 231 removed outlier: 7.159A pdb=" N VAL F 228 " --> pdb=" O LEU F 204 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N VAL F 206 " --> pdb=" O VAL F 228 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N SER F 230 " --> pdb=" O VAL F 206 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N LEU F 208 " --> pdb=" O SER F 230 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE F 261 " --> pdb=" O VAL F 203 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N MET F 205 " --> pdb=" O ILE F 261 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE F 209 " --> pdb=" O ASP F 265 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL F 260 " --> pdb=" O THR F 314 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N ILE F 316 " --> pdb=" O VAL F 260 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILE F 262 " --> pdb=" O ILE F 316 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N THR F 318 " --> pdb=" O ILE F 262 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N LEU F 264 " --> pdb=" O THR F 318 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N GLY F 174 " --> pdb=" O ALA F 317 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ALA F 319 " --> pdb=" O GLY F 174 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N ILE F 176 " --> pdb=" O ALA F 319 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 284 through 285 removed outlier: 3.851A pdb=" N VAL F 289 " --> pdb=" O LEU F 285 " (cutoff:3.500A) 3125 hydrogen bonds defined for protein. 9051 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: 24.78 Time building geometry restraints manager: 12.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 18788 1.34 - 1.46: 7939 1.46 - 1.58: 28277 1.58 - 1.69: 60 1.69 - 1.81: 476 Bond restraints: 55540 Sorted by residual: bond pdb=" C HIS G 388 " pdb=" N PRO G 389 " ideal model delta sigma weight residual 1.335 1.365 -0.030 1.30e-02 5.92e+03 5.27e+00 bond pdb=" C ALA e 101 " pdb=" N PRO e 102 " ideal model delta sigma weight residual 1.336 1.360 -0.024 1.08e-02 8.57e+03 5.05e+00 bond pdb=" C HIS D 388 " pdb=" N PRO D 389 " ideal model delta sigma weight residual 1.335 1.357 -0.022 1.36e-02 5.41e+03 2.58e+00 bond pdb=" C HIS N 388 " pdb=" N PRO N 389 " ideal model delta sigma weight residual 1.335 1.355 -0.020 1.30e-02 5.92e+03 2.28e+00 bond pdb=" C HIS M 388 " pdb=" N PRO M 389 " ideal model delta sigma weight residual 1.335 1.353 -0.018 1.30e-02 5.92e+03 1.93e+00 ... (remaining 55535 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 74131 1.83 - 3.65: 676 3.65 - 5.48: 89 5.48 - 7.31: 27 7.31 - 9.13: 5 Bond angle restraints: 74928 Sorted by residual: angle pdb=" N VAL k 45 " pdb=" CA VAL k 45 " pdb=" C VAL k 45 " ideal model delta sigma weight residual 112.96 109.34 3.62 1.00e+00 1.00e+00 1.31e+01 angle pdb=" C VAL M 81 " pdb=" N SER M 82 " pdb=" CA SER M 82 " ideal model delta sigma weight residual 120.97 130.10 -9.13 2.84e+00 1.24e-01 1.03e+01 angle pdb=" C VAL J 354 " pdb=" N PHE J 355 " pdb=" CA PHE J 355 " ideal model delta sigma weight residual 120.26 123.85 -3.59 1.34e+00 5.57e-01 7.16e+00 angle pdb=" N ARG B 296 " pdb=" CA ARG B 296 " pdb=" C ARG B 296 " ideal model delta sigma weight residual 109.81 115.41 -5.60 2.21e+00 2.05e-01 6.42e+00 angle pdb=" C LEU M 3 " pdb=" N THR M 4 " pdb=" CA THR M 4 " ideal model delta sigma weight residual 120.65 123.93 -3.28 1.32e+00 5.74e-01 6.16e+00 ... (remaining 74923 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 32040 17.83 - 35.66: 2015 35.66 - 53.49: 458 53.49 - 71.32: 76 71.32 - 89.15: 19 Dihedral angle restraints: 34608 sinusoidal: 14648 harmonic: 19960 Sorted by residual: dihedral pdb=" CA GLU g 167 " pdb=" C GLU g 167 " pdb=" N LYS g 168 " pdb=" CA LYS g 168 " ideal model delta harmonic sigma weight residual 180.00 158.34 21.66 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA ALA j 101 " pdb=" C ALA j 101 " pdb=" N PRO j 102 " pdb=" CA PRO j 102 " ideal model delta harmonic sigma weight residual -180.00 -161.00 -19.00 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA GLU L 24 " pdb=" C GLU L 24 " pdb=" N ASN L 25 " pdb=" CA ASN L 25 " ideal model delta harmonic sigma weight residual 180.00 163.67 16.33 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 34605 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 5455 0.030 - 0.061: 1997 0.061 - 0.091: 655 0.091 - 0.121: 327 0.121 - 0.151: 20 Chirality restraints: 8454 Sorted by residual: chirality pdb=" CB ILE D 176 " pdb=" CA ILE D 176 " pdb=" CG1 ILE D 176 " pdb=" CG2 ILE D 176 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.73e-01 chirality pdb=" CA ILE F 176 " pdb=" N ILE F 176 " pdb=" C ILE F 176 " pdb=" CB ILE F 176 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.23e-01 chirality pdb=" CB VAL D 227 " pdb=" CA VAL D 227 " pdb=" CG1 VAL D 227 " pdb=" CG2 VAL D 227 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 5.10e-01 ... (remaining 8451 not shown) Planarity restraints: 9770 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR G 9 " 0.028 5.00e-02 4.00e+02 4.24e-02 2.88e+00 pdb=" N PRO G 10 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO G 10 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO G 10 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 278 " -0.027 5.00e-02 4.00e+02 4.08e-02 2.67e+00 pdb=" N PRO G 279 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO G 279 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO G 279 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR M 9 " -0.026 5.00e-02 4.00e+02 3.90e-02 2.44e+00 pdb=" N PRO M 10 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO M 10 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO M 10 " -0.022 5.00e-02 4.00e+02 ... (remaining 9767 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 427 2.48 - 3.08: 40247 3.08 - 3.69: 92651 3.69 - 4.29: 124415 4.29 - 4.90: 200976 Nonbonded interactions: 458716 Sorted by model distance: nonbonded pdb=" O3B ATP C 501 " pdb="MG MG C 502 " model vdw 1.874 2.170 nonbonded pdb=" OG1 THR O 185 " pdb="MG MG O 502 " model vdw 2.057 2.170 nonbonded pdb=" OG1 THR F 185 " pdb="MG MG F 502 " model vdw 2.060 2.170 nonbonded pdb=" OG1 THR G 185 " pdb="MG MG G 502 " model vdw 2.063 2.170 nonbonded pdb=" OG1 THR B 185 " pdb="MG MG B 502 " model vdw 2.065 2.170 ... (remaining 458711 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } ncs_group { reference = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' } 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: 4.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.080 Extract box with map and model: 1.720 Check model and map are aligned: 0.320 Set scattering table: 0.410 Process input model: 99.570 Find NCS groups from input model: 2.110 Set up NCS constraints: 0.510 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 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 : 0.002 0.031 55540 Z= 0.117 Angle : 0.484 9.131 74928 Z= 0.257 Chirality : 0.039 0.151 8454 Planarity : 0.003 0.042 9770 Dihedral : 12.241 89.154 21648 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.98 % Favored : 97.99 % Rotamer: Outliers : 2.21 % Allowed : 9.25 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.27 % Cis-general : 0.17 % 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: 1.04 (0.10), residues: 6854 helix: 1.43 (0.09), residues: 3811 sheet: 0.34 (0.19), residues: 770 loop : -0.34 (0.13), residues: 2273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP l 133 HIS 0.004 0.001 HIS i 73 PHE 0.014 0.001 PHE O 355 TYR 0.007 0.001 TYR l 34 ARG 0.006 0.000 ARG N 299 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13708 Ramachandran restraints generated. 6854 Oldfield, 0 Emsley, 6854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13708 Ramachandran restraints generated. 6854 Oldfield, 0 Emsley, 6854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1138 residues out of total 5838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 1009 time to evaluate : 4.751 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: 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: C 123 LYS cc_start: 0.8945 (ttmt) cc_final: 0.8711 (tmmt) REVERT: C 186 MET cc_start: 0.8363 (ptp) cc_final: 0.8091 (ptp) REVERT: C 265 ASP cc_start: 0.8415 (t0) cc_final: 0.8108 (t0) REVERT: C 329 GLU cc_start: 0.9003 (OUTLIER) cc_final: 0.8667 (pm20) REVERT: C 348 LYS cc_start: 0.9260 (mppt) cc_final: 0.9027 (mppt) REVERT: D 1 MET cc_start: 0.7530 (ptp) cc_final: 0.7276 (ptp) REVERT: D 21 MET cc_start: 0.8684 (ppp) cc_final: 0.8408 (ppp) REVERT: D 62 PHE cc_start: 0.7196 (t80) cc_final: 0.6791 (t80) REVERT: D 147 MET cc_start: 0.8220 (mpp) cc_final: 0.7894 (mpp) REVERT: D 157 LEU cc_start: 0.9144 (pt) cc_final: 0.8573 (tp) REVERT: D 219 MET cc_start: 0.9151 (tpp) cc_final: 0.8895 (tpt) REVERT: D 327 MET cc_start: 0.7487 (ppp) cc_final: 0.7106 (ppp) REVERT: D 329 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7978 (tp30) REVERT: D 332 TYR cc_start: 0.8226 (t80) cc_final: 0.7896 (t80) REVERT: D 415 MET cc_start: 0.9095 (tmm) cc_final: 0.8859 (tmm) REVERT: D 417 LYS cc_start: 0.8700 (pptt) cc_final: 0.8356 (mptt) REVERT: E 1 MET cc_start: 0.7419 (ppp) cc_final: 0.6962 (ppp) REVERT: E 29 MET cc_start: 0.7150 (pmm) cc_final: 0.6883 (pmm) REVERT: E 219 MET cc_start: 0.9266 (mmm) cc_final: 0.8937 (mmm) REVERT: E 240 VAL cc_start: 0.9157 (t) cc_final: 0.8702 (t) REVERT: E 259 ASP cc_start: 0.8131 (m-30) cc_final: 0.7851 (m-30) REVERT: E 329 GLU cc_start: 0.8501 (tm-30) cc_final: 0.8252 (tm-30) REVERT: E 411 ASP cc_start: 0.8581 (m-30) cc_final: 0.8367 (m-30) REVERT: J 21 MET cc_start: 0.5862 (ppp) cc_final: 0.5478 (ppp) REVERT: J 31 LYS cc_start: 0.6495 (mptt) cc_final: 0.6006 (ptpt) REVERT: J 72 TYR cc_start: 0.8185 (m-80) cc_final: 0.7843 (m-10) REVERT: J 157 LEU cc_start: 0.8252 (pp) cc_final: 0.7577 (tt) REVERT: J 205 MET cc_start: 0.6743 (pmm) cc_final: 0.6501 (pmm) REVERT: J 378 GLN cc_start: 0.8717 (OUTLIER) cc_final: 0.8493 (pp30) REVERT: J 380 MET cc_start: 0.7179 (mpp) cc_final: 0.6769 (mmm) REVERT: J 400 ILE cc_start: 0.8560 (mt) cc_final: 0.8341 (tp) REVERT: K 39 LEU cc_start: 0.9575 (mm) cc_final: 0.9328 (tp) REVERT: K 161 VAL cc_start: 0.9463 (p) cc_final: 0.9256 (m) REVERT: K 186 MET cc_start: 0.8177 (pmm) cc_final: 0.7490 (ptp) REVERT: K 189 GLN cc_start: 0.8787 (mm-40) cc_final: 0.8022 (mm-40) REVERT: K 223 VAL cc_start: 0.8295 (OUTLIER) cc_final: 0.8032 (p) REVERT: K 234 GLU cc_start: 0.7767 (pm20) cc_final: 0.7508 (pm20) REVERT: K 241 GLN cc_start: 0.8780 (OUTLIER) cc_final: 0.8463 (pp30) REVERT: K 378 GLN cc_start: 0.9140 (tp-100) cc_final: 0.8595 (tm-30) REVERT: K 390 MET cc_start: 0.7890 (pmm) cc_final: 0.7504 (pmm) REVERT: L 244 GLU cc_start: 0.8342 (mm-30) cc_final: 0.8003 (mm-30) REVERT: L 327 MET cc_start: 0.9012 (mmm) cc_final: 0.8597 (mtp) REVERT: L 400 ILE cc_start: 0.9232 (mm) cc_final: 0.8955 (pt) REVERT: L 413 PHE cc_start: 0.8988 (m-10) cc_final: 0.8496 (m-80) REVERT: M 1 MET cc_start: 0.6438 (ppp) cc_final: 0.6134 (ppp) REVERT: M 4 THR cc_start: 0.8145 (p) cc_final: 0.7941 (p) REVERT: M 244 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7473 (mm-30) REVERT: M 274 TYR cc_start: 0.8681 (m-10) cc_final: 0.8082 (m-10) REVERT: M 327 MET cc_start: 0.8024 (ppp) cc_final: 0.6725 (ppp) REVERT: M 411 ASP cc_start: 0.9233 (t0) cc_final: 0.8972 (t0) REVERT: O 380 MET cc_start: 0.8131 (mmm) cc_final: 0.7691 (mmm) REVERT: O 390 MET cc_start: 0.5775 (OUTLIER) cc_final: 0.4415 (ppp) REVERT: c 64 GLN cc_start: 0.8784 (OUTLIER) cc_final: 0.8571 (mp10) REVERT: d 146 ASP cc_start: 0.7683 (m-30) cc_final: 0.7340 (m-30) REVERT: e 104 LEU cc_start: 0.8944 (mt) cc_final: 0.8690 (mt) REVERT: e 175 MET cc_start: 0.9147 (ptm) cc_final: 0.8796 (ptp) REVERT: f 124 ASP cc_start: 0.9110 (m-30) cc_final: 0.8889 (m-30) REVERT: g 83 ASP cc_start: 0.8629 (m-30) cc_final: 0.8268 (m-30) REVERT: g 130 LEU cc_start: 0.9584 (mm) cc_final: 0.9371 (mm) REVERT: g 168 LYS cc_start: 0.8655 (mmpt) cc_final: 0.8408 (mmmt) REVERT: g 176 ILE cc_start: 0.9662 (pt) cc_final: 0.9103 (pt) REVERT: h 53 ASN cc_start: 0.8947 (t160) cc_final: 0.8655 (t0) REVERT: h 78 HIS cc_start: 0.9155 (t-90) cc_final: 0.8804 (t-90) REVERT: h 116 ASN cc_start: 0.8119 (m-40) cc_final: 0.7798 (m-40) REVERT: i 158 ASP cc_start: 0.8199 (p0) cc_final: 0.7680 (p0) REVERT: j 140 ILE cc_start: 0.8701 (tp) cc_final: 0.8414 (mm) REVERT: j 176 ILE cc_start: 0.9724 (pt) cc_final: 0.9170 (pt) REVERT: j 180 LYS cc_start: 0.9354 (mmtp) cc_final: 0.9095 (mmtp) REVERT: k 11 ASP cc_start: 0.9150 (m-30) cc_final: 0.8858 (m-30) REVERT: l 136 LYS cc_start: 0.6389 (pttm) cc_final: 0.6154 (pttm) REVERT: B 21 MET cc_start: 0.6647 (ppp) cc_final: 0.6418 (ppp) REVERT: B 125 GLU cc_start: 0.8823 (tp30) cc_final: 0.8583 (tp30) REVERT: B 155 GLU cc_start: 0.8171 (tp30) cc_final: 0.7480 (tp30) REVERT: B 209 ILE cc_start: 0.8953 (OUTLIER) cc_final: 0.8671 (tp) REVERT: B 239 HIS cc_start: 0.4706 (m170) cc_final: 0.4319 (m170) REVERT: B 244 GLU cc_start: 0.8865 (pt0) cc_final: 0.8347 (pp20) REVERT: B 381 TRP cc_start: 0.8469 (m100) cc_final: 0.8247 (m100) REVERT: B 390 MET cc_start: 0.8238 (ppp) cc_final: 0.7366 (ppp) REVERT: G 21 MET cc_start: 0.5441 (pmm) cc_final: 0.5232 (pmm) REVERT: G 147 MET cc_start: 0.7483 (mmm) cc_final: 0.6966 (tpp) REVERT: G 418 ARG cc_start: 0.7260 (ptt-90) cc_final: 0.6649 (mmt180) REVERT: N 73 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.7751 (tp) REVERT: N 242 VAL cc_start: 0.8932 (p) cc_final: 0.7924 (p) REVERT: N 358 ILE cc_start: 0.9469 (tp) cc_final: 0.9217 (tp) REVERT: N 397 GLU cc_start: 0.9047 (pt0) cc_final: 0.8815 (pp20) REVERT: N 415 MET cc_start: 0.9124 (ppp) cc_final: 0.8909 (ppp) REVERT: F 186 MET cc_start: 0.6692 (OUTLIER) cc_final: 0.6401 (ptp) REVERT: F 326 LYS cc_start: 0.8865 (tptp) cc_final: 0.8446 (tptp) REVERT: F 327 MET cc_start: 0.8408 (ppp) cc_final: 0.8189 (ppp) REVERT: F 329 GLU cc_start: 0.8907 (mp0) cc_final: 0.8588 (mp0) REVERT: F 415 MET cc_start: 0.8659 (ppp) cc_final: 0.8429 (ppp) REVERT: F 416 MET cc_start: 0.8936 (mmp) cc_final: 0.8579 (mmm) outliers start: 129 outliers final: 26 residues processed: 1105 average time/residue: 0.5159 time to fit residues: 952.6850 Evaluate side-chains 728 residues out of total 5838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 692 time to evaluate : 5.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 329 GLU Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 329 GLU Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 228 VAL Chi-restraints excluded: chain J residue 351 GLU Chi-restraints excluded: chain J residue 378 GLN Chi-restraints excluded: chain J residue 416 MET Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 216 VAL Chi-restraints excluded: chain K residue 223 VAL Chi-restraints excluded: chain K residue 241 GLN Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 227 VAL Chi-restraints excluded: chain L residue 315 ILE Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain M residue 262 ILE Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 390 MET Chi-restraints excluded: chain c residue 64 GLN Chi-restraints excluded: chain i residue 11 ASP Chi-restraints excluded: chain i residue 25 ASN Chi-restraints excluded: chain i residue 151 THR Chi-restraints excluded: chain k residue 15 ASN Chi-restraints excluded: chain k residue 78 HIS Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 378 GLN Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 260 VAL Chi-restraints excluded: chain N residue 354 VAL Chi-restraints excluded: chain F residue 186 MET Chi-restraints excluded: chain F residue 354 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 672 random chunks: chunk 567 optimal weight: 8.9990 chunk 509 optimal weight: 5.9990 chunk 282 optimal weight: 3.9990 chunk 173 optimal weight: 20.0000 chunk 343 optimal weight: 7.9990 chunk 272 optimal weight: 0.6980 chunk 526 optimal weight: 0.8980 chunk 203 optimal weight: 5.9990 chunk 320 optimal weight: 9.9990 chunk 392 optimal weight: 5.9990 chunk 610 optimal weight: 7.9990 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 ASN C 135 ASN C 344 HIS ** D 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 ASN J 85 GLN ** J 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 292 ASN ** J 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 388 HIS M 140 HIS ** M 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 239 HIS M 306 ASN O 292 ASN c 61 GLN c 64 GLN ** d 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 174 ASN ** f 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 174 ASN ** g 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 120 GLN h 53 ASN i 141 ASN ** i 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 116 ASN ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 135 ASN ** G 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 295 HIS ** G 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 193 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 55540 Z= 0.298 Angle : 0.674 13.395 74928 Z= 0.345 Chirality : 0.043 0.266 8454 Planarity : 0.005 0.068 9770 Dihedral : 7.356 81.468 8026 Min Nonbonded Distance : 1.741 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.63 % Favored : 97.34 % Rotamer: Outliers : 2.96 % Allowed : 13.86 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.27 % Cis-general : 0.17 % 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: 0.84 (0.10), residues: 6854 helix: 1.21 (0.08), residues: 3856 sheet: 0.36 (0.21), residues: 653 loop : -0.36 (0.13), residues: 2345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP K 381 HIS 0.019 0.001 HIS J 344 PHE 0.024 0.002 PHE F 133 TYR 0.031 0.002 TYR B 72 ARG 0.013 0.001 ARG N 299 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13708 Ramachandran restraints generated. 6854 Oldfield, 0 Emsley, 6854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13708 Ramachandran restraints generated. 6854 Oldfield, 0 Emsley, 6854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 883 residues out of total 5838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 710 time to evaluate : 4.891 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: 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: C 189 GLN cc_start: 0.8936 (mt0) cc_final: 0.8385 (mp10) REVERT: C 245 MET cc_start: 0.7896 (tmm) cc_final: 0.7549 (tmm) REVERT: C 326 LYS cc_start: 0.8510 (pptt) cc_final: 0.7866 (pttp) REVERT: C 329 GLU cc_start: 0.9018 (OUTLIER) cc_final: 0.8730 (pm20) REVERT: D 1 MET cc_start: 0.7677 (ptp) cc_final: 0.7468 (ptp) REVERT: D 21 MET cc_start: 0.8669 (ppp) cc_final: 0.8369 (ppp) REVERT: D 62 PHE cc_start: 0.7456 (t80) cc_final: 0.6959 (t80) REVERT: D 157 LEU cc_start: 0.9180 (pt) cc_final: 0.8626 (tp) REVERT: D 176 ILE cc_start: 0.9345 (OUTLIER) cc_final: 0.9100 (pt) REVERT: D 327 MET cc_start: 0.7985 (ppp) cc_final: 0.7495 (ppp) REVERT: E 21 MET cc_start: 0.8537 (tmm) cc_final: 0.8181 (tmm) REVERT: E 29 MET cc_start: 0.6943 (pmm) cc_final: 0.6277 (pmm) REVERT: E 147 MET cc_start: 0.8332 (mmm) cc_final: 0.7992 (mmp) REVERT: E 164 LEU cc_start: 0.9598 (OUTLIER) cc_final: 0.9301 (mm) REVERT: E 259 ASP cc_start: 0.8426 (m-30) cc_final: 0.8064 (m-30) REVERT: E 329 GLU cc_start: 0.8591 (tm-30) cc_final: 0.8376 (tm-30) REVERT: E 405 MET cc_start: 0.8959 (ppp) cc_final: 0.8638 (ppp) REVERT: E 414 GLU cc_start: 0.9116 (mm-30) cc_final: 0.8752 (mm-30) REVERT: J 21 MET cc_start: 0.5425 (ppp) cc_final: 0.4516 (tmm) REVERT: J 31 LYS cc_start: 0.6472 (mptt) cc_final: 0.5893 (ptpt) REVERT: J 205 MET cc_start: 0.6661 (pmm) cc_final: 0.6350 (pmm) REVERT: J 228 VAL cc_start: 0.4361 (OUTLIER) cc_final: 0.4131 (m) REVERT: J 374 GLN cc_start: 0.8881 (tp40) cc_final: 0.8619 (tp-100) REVERT: J 380 MET cc_start: 0.7155 (mpp) cc_final: 0.6812 (mpp) REVERT: K 186 MET cc_start: 0.8579 (pmm) cc_final: 0.8108 (ptp) REVERT: K 234 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7666 (pm20) REVERT: K 241 GLN cc_start: 0.8939 (OUTLIER) cc_final: 0.8667 (pp30) REVERT: K 245 MET cc_start: 0.8436 (tpt) cc_final: 0.8186 (tpt) REVERT: K 264 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8791 (tp) REVERT: K 341 MET cc_start: 0.8253 (mmm) cc_final: 0.7113 (mmm) REVERT: K 362 ARG cc_start: 0.9158 (ttm-80) cc_final: 0.8947 (mtm110) REVERT: K 390 MET cc_start: 0.8120 (pmm) cc_final: 0.7864 (pmm) REVERT: L 26 LEU cc_start: 0.9225 (tp) cc_final: 0.9023 (tp) REVERT: L 91 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8942 (pp) REVERT: L 244 GLU cc_start: 0.8502 (mm-30) cc_final: 0.8101 (mm-30) REVERT: L 341 MET cc_start: 0.8786 (tmm) cc_final: 0.8378 (tmm) REVERT: L 413 PHE cc_start: 0.8765 (m-10) cc_final: 0.8511 (m-80) REVERT: M 4 THR cc_start: 0.8775 (p) cc_final: 0.8475 (p) REVERT: M 244 GLU cc_start: 0.8581 (mm-30) cc_final: 0.7993 (mm-30) REVERT: M 274 TYR cc_start: 0.9053 (m-10) cc_final: 0.8626 (m-10) REVERT: M 411 ASP cc_start: 0.9329 (t0) cc_final: 0.9052 (t0) REVERT: O 245 MET cc_start: 0.7358 (mmm) cc_final: 0.7144 (mmm) REVERT: O 341 MET cc_start: 0.6833 (mmm) cc_final: 0.6541 (mmm) REVERT: O 377 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.7035 (mm) REVERT: O 380 MET cc_start: 0.8251 (mmm) cc_final: 0.7733 (mmm) REVERT: O 390 MET cc_start: 0.5760 (OUTLIER) cc_final: 0.4448 (ppp) REVERT: d 146 ASP cc_start: 0.7992 (m-30) cc_final: 0.7737 (m-30) REVERT: e 175 MET cc_start: 0.9242 (ptm) cc_final: 0.8900 (ptp) REVERT: g 83 ASP cc_start: 0.8733 (m-30) cc_final: 0.8351 (m-30) REVERT: g 130 LEU cc_start: 0.9597 (mm) cc_final: 0.9368 (mm) REVERT: g 168 LYS cc_start: 0.8690 (mmpt) cc_final: 0.8476 (mmmt) REVERT: h 53 ASN cc_start: 0.9085 (t0) cc_final: 0.8823 (t0) REVERT: h 74 GLU cc_start: 0.8975 (mt-10) cc_final: 0.8724 (tm-30) REVERT: h 78 HIS cc_start: 0.9198 (t-90) cc_final: 0.8815 (t-90) REVERT: h 116 ASN cc_start: 0.8234 (m-40) cc_final: 0.7918 (m-40) REVERT: h 131 LEU cc_start: 0.9510 (mt) cc_final: 0.9256 (pp) REVERT: h 179 ARG cc_start: 0.9090 (mmm160) cc_final: 0.8530 (mmm160) REVERT: i 158 ASP cc_start: 0.8100 (p0) cc_final: 0.7678 (p0) REVERT: j 124 ASP cc_start: 0.9045 (p0) cc_final: 0.8810 (p0) REVERT: j 140 ILE cc_start: 0.8676 (tp) cc_final: 0.8369 (mm) REVERT: j 176 ILE cc_start: 0.9734 (pt) cc_final: 0.9270 (pt) REVERT: l 85 LEU cc_start: 0.8271 (pp) cc_final: 0.8043 (pp) REVERT: B 80 TYR cc_start: 0.6302 (m-80) cc_final: 0.6048 (m-80) REVERT: B 155 GLU cc_start: 0.8165 (tp30) cc_final: 0.7590 (tp30) REVERT: B 157 LEU cc_start: 0.9345 (tp) cc_final: 0.8735 (mt) REVERT: B 209 ILE cc_start: 0.9084 (OUTLIER) cc_final: 0.8706 (tp) REVERT: B 230 SER cc_start: 0.8441 (p) cc_final: 0.7872 (p) REVERT: B 381 TRP cc_start: 0.8520 (m100) cc_final: 0.8239 (m100) REVERT: B 390 MET cc_start: 0.8282 (ppp) cc_final: 0.7295 (ppp) REVERT: G 21 MET cc_start: 0.5311 (pmm) cc_final: 0.4902 (pmm) REVERT: G 416 MET cc_start: -0.1326 (ttt) cc_final: -0.1957 (ptp) REVERT: G 418 ARG cc_start: 0.7383 (ptt-90) cc_final: 0.6791 (mmt180) REVERT: N 73 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.7619 (tp) REVERT: N 360 TYR cc_start: 0.8755 (t80) cc_final: 0.8222 (t80) REVERT: N 397 GLU cc_start: 0.9183 (pt0) cc_final: 0.8926 (pp20) REVERT: N 415 MET cc_start: 0.9107 (ppp) cc_final: 0.8834 (ppp) REVERT: F 326 LYS cc_start: 0.8805 (tptp) cc_final: 0.8313 (tptp) REVERT: F 327 MET cc_start: 0.8458 (ppp) cc_final: 0.8180 (ppp) REVERT: F 329 GLU cc_start: 0.8852 (mp0) cc_final: 0.8562 (mp0) REVERT: F 416 MET cc_start: 0.8972 (mmp) cc_final: 0.8681 (mmm) outliers start: 173 outliers final: 77 residues processed: 832 average time/residue: 0.4952 time to fit residues: 700.0899 Evaluate side-chains 713 residues out of total 5838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 624 time to evaluate : 4.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 184 LYS Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 295 HIS Chi-restraints excluded: chain C residue 329 GLU Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 295 HIS Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 412 PHE Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 403 LEU Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 228 VAL Chi-restraints excluded: chain J residue 351 GLU Chi-restraints excluded: chain J residue 416 MET Chi-restraints excluded: chain K residue 154 THR Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 216 VAL Chi-restraints excluded: chain K residue 234 GLU Chi-restraints excluded: chain K residue 241 GLN Chi-restraints excluded: chain K residue 264 LEU Chi-restraints excluded: chain K residue 358 ILE Chi-restraints excluded: chain L residue 20 ASN Chi-restraints excluded: chain L residue 91 LEU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 164 LEU Chi-restraints excluded: chain L residue 224 LYS Chi-restraints excluded: chain L residue 227 VAL Chi-restraints excluded: chain L residue 371 LEU Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain M residue 195 ILE Chi-restraints excluded: chain M residue 261 ILE Chi-restraints excluded: chain M residue 262 ILE Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 315 ILE Chi-restraints excluded: chain O residue 377 LEU Chi-restraints excluded: chain O residue 390 MET Chi-restraints excluded: chain c residue 142 TYR Chi-restraints excluded: chain d residue 32 GLN Chi-restraints excluded: chain d residue 124 ASP Chi-restraints excluded: chain f residue 45 VAL Chi-restraints excluded: chain f residue 170 THR Chi-restraints excluded: chain g residue 53 ASN Chi-restraints excluded: chain h residue 142 TYR Chi-restraints excluded: chain h residue 162 VAL Chi-restraints excluded: chain i residue 11 ASP Chi-restraints excluded: chain i residue 25 ASN Chi-restraints excluded: chain i residue 94 THR Chi-restraints excluded: chain i residue 152 THR Chi-restraints excluded: chain j residue 49 ASP Chi-restraints excluded: chain k residue 15 ASN Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 78 HIS Chi-restraints excluded: chain k residue 162 VAL Chi-restraints excluded: chain l residue 158 ASP Chi-restraints excluded: chain l residue 159 VAL Chi-restraints excluded: chain l residue 162 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 275 ASN Chi-restraints excluded: chain B residue 299 ARG Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain B residue 378 GLN Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 219 MET Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain G residue 376 GLU Chi-restraints excluded: chain G residue 411 ASP Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 216 VAL Chi-restraints excluded: chain N residue 260 VAL Chi-restraints excluded: chain N residue 274 TYR Chi-restraints excluded: chain N residue 284 VAL Chi-restraints excluded: chain N residue 348 LYS Chi-restraints excluded: chain N residue 354 VAL Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 205 MET Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 354 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 672 random chunks: chunk 339 optimal weight: 9.9990 chunk 189 optimal weight: 0.9990 chunk 507 optimal weight: 5.9990 chunk 415 optimal weight: 9.9990 chunk 168 optimal weight: 10.0000 chunk 611 optimal weight: 2.9990 chunk 660 optimal weight: 0.4980 chunk 544 optimal weight: 7.9990 chunk 606 optimal weight: 6.9990 chunk 208 optimal weight: 1.9990 chunk 490 optimal weight: 8.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 292 ASN J 378 GLN ** J 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 42 HIS ** K 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 64 GLN ** d 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 141 ASN ** i 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 241 GLN ** G 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 140 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 55540 Z= 0.220 Angle : 0.626 12.481 74928 Z= 0.316 Chirality : 0.042 0.319 8454 Planarity : 0.004 0.056 9770 Dihedral : 7.289 81.289 8006 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.36 % Favored : 97.61 % Rotamer: Outliers : 2.81 % Allowed : 15.28 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.27 % Cis-general : 0.17 % 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: 0.76 (0.10), residues: 6854 helix: 1.17 (0.08), residues: 3842 sheet: 0.21 (0.21), residues: 641 loop : -0.38 (0.13), residues: 2371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP k 133 HIS 0.014 0.001 HIS k 92 PHE 0.017 0.001 PHE C 62 TYR 0.026 0.001 TYR B 72 ARG 0.012 0.000 ARG N 299 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13708 Ramachandran restraints generated. 6854 Oldfield, 0 Emsley, 6854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13708 Ramachandran restraints generated. 6854 Oldfield, 0 Emsley, 6854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 853 residues out of total 5838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 689 time to evaluate : 4.903 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 189 GLN cc_start: 0.8918 (mt0) cc_final: 0.8480 (mp10) REVERT: C 326 LYS cc_start: 0.8525 (pptt) cc_final: 0.7827 (pttp) REVERT: C 329 GLU cc_start: 0.9001 (OUTLIER) cc_final: 0.8699 (pm20) REVERT: C 341 MET cc_start: 0.9215 (ppp) cc_final: 0.8636 (tmm) REVERT: C 414 GLU cc_start: 0.8880 (tp30) cc_final: 0.8115 (tp30) REVERT: C 415 MET cc_start: 0.9017 (tmm) cc_final: 0.8713 (tmm) REVERT: D 1 MET cc_start: 0.7741 (ptp) cc_final: 0.7422 (ptp) REVERT: D 21 MET cc_start: 0.8644 (ppp) cc_final: 0.8306 (ppp) REVERT: D 62 PHE cc_start: 0.7550 (t80) cc_final: 0.7077 (t80) REVERT: D 147 MET cc_start: 0.8104 (mpp) cc_final: 0.7830 (mpp) REVERT: D 157 LEU cc_start: 0.9143 (pt) cc_final: 0.8598 (tp) REVERT: D 219 MET cc_start: 0.9208 (tpt) cc_final: 0.8990 (tpp) REVERT: D 329 GLU cc_start: 0.8117 (tp30) cc_final: 0.7879 (tp30) REVERT: D 417 LYS cc_start: 0.9050 (pptt) cc_final: 0.8477 (mptt) REVERT: E 29 MET cc_start: 0.6999 (pmm) cc_final: 0.6112 (pmm) REVERT: E 147 MET cc_start: 0.8519 (mmm) cc_final: 0.8090 (mmp) REVERT: E 164 LEU cc_start: 0.9594 (OUTLIER) cc_final: 0.9240 (mm) REVERT: E 259 ASP cc_start: 0.8442 (m-30) cc_final: 0.8101 (m-30) REVERT: E 329 GLU cc_start: 0.8598 (tm-30) cc_final: 0.8364 (tm-30) REVERT: E 405 MET cc_start: 0.8991 (ppp) cc_final: 0.8362 (ppp) REVERT: E 414 GLU cc_start: 0.9106 (mm-30) cc_final: 0.8748 (mm-30) REVERT: J 21 MET cc_start: 0.5168 (ppp) cc_final: 0.4278 (tmm) REVERT: J 31 LYS cc_start: 0.6500 (mptt) cc_final: 0.5842 (ptpt) REVERT: J 186 MET cc_start: 0.4021 (pmm) cc_final: 0.2799 (pmm) REVERT: J 380 MET cc_start: 0.7088 (mpp) cc_final: 0.6746 (mpp) REVERT: K 39 LEU cc_start: 0.9602 (mm) cc_final: 0.9354 (tp) REVERT: K 234 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7607 (pm20) REVERT: K 241 GLN cc_start: 0.8956 (OUTLIER) cc_final: 0.8668 (pp30) REVERT: K 245 MET cc_start: 0.8429 (tpt) cc_final: 0.8098 (tpt) REVERT: K 341 MET cc_start: 0.8611 (mmm) cc_final: 0.7955 (mmm) REVERT: K 381 TRP cc_start: 0.8472 (m-10) cc_final: 0.8142 (m-10) REVERT: K 390 MET cc_start: 0.8180 (pmm) cc_final: 0.7951 (pmm) REVERT: L 21 MET cc_start: 0.8620 (OUTLIER) cc_final: 0.8135 (tmm) REVERT: L 26 LEU cc_start: 0.9272 (tp) cc_final: 0.9050 (tp) REVERT: L 58 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8238 (mt) REVERT: L 234 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8548 (mp0) REVERT: L 244 GLU cc_start: 0.8449 (mm-30) cc_final: 0.8041 (mm-30) REVERT: L 259 ASP cc_start: 0.7292 (m-30) cc_final: 0.6830 (m-30) REVERT: L 413 PHE cc_start: 0.8736 (m-10) cc_final: 0.8487 (m-80) REVERT: M 1 MET cc_start: 0.6548 (ppp) cc_final: 0.6101 (ppp) REVERT: M 244 GLU cc_start: 0.8634 (mm-30) cc_final: 0.7929 (mm-30) REVERT: M 274 TYR cc_start: 0.9112 (m-10) cc_final: 0.8608 (m-10) REVERT: M 327 MET cc_start: 0.8023 (OUTLIER) cc_final: 0.7105 (ppp) REVERT: M 333 GLU cc_start: 0.9090 (mt-10) cc_final: 0.8857 (tt0) REVERT: M 411 ASP cc_start: 0.9357 (t0) cc_final: 0.9093 (t0) REVERT: M 417 LYS cc_start: 0.9430 (pttm) cc_final: 0.9198 (pttp) REVERT: O 245 MET cc_start: 0.7454 (mmm) cc_final: 0.7253 (mmm) REVERT: O 380 MET cc_start: 0.8232 (mmm) cc_final: 0.7625 (mmt) REVERT: O 390 MET cc_start: 0.5829 (OUTLIER) cc_final: 0.4515 (ppp) REVERT: c 177 PHE cc_start: 0.9343 (m-10) cc_final: 0.9111 (m-10) REVERT: d 89 MET cc_start: 0.7716 (ttp) cc_final: 0.7411 (tmm) REVERT: d 146 ASP cc_start: 0.8042 (m-30) cc_final: 0.7787 (m-30) REVERT: e 175 MET cc_start: 0.9234 (ptm) cc_final: 0.8847 (ptp) REVERT: f 21 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8903 (pp) REVERT: g 83 ASP cc_start: 0.8721 (m-30) cc_final: 0.8337 (m-30) REVERT: g 130 LEU cc_start: 0.9609 (mm) cc_final: 0.9390 (mm) REVERT: g 168 LYS cc_start: 0.8664 (mmpt) cc_final: 0.8449 (mmmt) REVERT: h 53 ASN cc_start: 0.9075 (t0) cc_final: 0.8748 (t0) REVERT: h 78 HIS cc_start: 0.9175 (t-90) cc_final: 0.8781 (t-90) REVERT: h 131 LEU cc_start: 0.9508 (mt) cc_final: 0.9264 (pp) REVERT: i 158 ASP cc_start: 0.8131 (p0) cc_final: 0.7740 (p0) REVERT: j 140 ILE cc_start: 0.8632 (tp) cc_final: 0.8302 (mm) REVERT: j 180 LYS cc_start: 0.9508 (mmtp) cc_final: 0.9299 (mmmt) REVERT: l 21 LEU cc_start: 0.8747 (mt) cc_final: 0.8510 (pp) REVERT: l 59 LYS cc_start: 0.8893 (pttm) cc_final: 0.8660 (pttm) REVERT: B 72 TYR cc_start: 0.8680 (m-10) cc_final: 0.8447 (m-10) REVERT: B 80 TYR cc_start: 0.6442 (m-80) cc_final: 0.6200 (m-80) REVERT: B 155 GLU cc_start: 0.8152 (tp30) cc_final: 0.7556 (tp30) REVERT: B 300 PHE cc_start: 0.7306 (m-80) cc_final: 0.5837 (m-80) REVERT: B 381 TRP cc_start: 0.8502 (m100) cc_final: 0.8207 (m100) REVERT: B 390 MET cc_start: 0.8239 (ppp) cc_final: 0.7157 (ppp) REVERT: G 416 MET cc_start: -0.1433 (ttt) cc_final: -0.2018 (ptp) REVERT: G 418 ARG cc_start: 0.7431 (ptt-90) cc_final: 0.6820 (mmt180) REVERT: N 73 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.7758 (tp) REVERT: N 164 LEU cc_start: 0.9163 (mm) cc_final: 0.8943 (mm) REVERT: N 215 GLU cc_start: 0.8964 (mp0) cc_final: 0.8654 (mp0) REVERT: N 360 TYR cc_start: 0.8809 (t80) cc_final: 0.8257 (t80) REVERT: N 397 GLU cc_start: 0.9180 (pt0) cc_final: 0.8920 (pp20) REVERT: N 415 MET cc_start: 0.9041 (ppp) cc_final: 0.8762 (ppp) REVERT: F 298 LYS cc_start: 0.8581 (tttp) cc_final: 0.8126 (mtpt) REVERT: F 326 LYS cc_start: 0.8802 (tptp) cc_final: 0.8293 (tptp) REVERT: F 327 MET cc_start: 0.8386 (ppp) cc_final: 0.8086 (ppp) REVERT: F 329 GLU cc_start: 0.8854 (mp0) cc_final: 0.8595 (mp0) outliers start: 164 outliers final: 89 residues processed: 800 average time/residue: 0.5056 time to fit residues: 694.9601 Evaluate side-chains 711 residues out of total 5838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 611 time to evaluate : 4.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 295 HIS Chi-restraints excluded: chain C residue 329 GLU Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain D residue 64 PHE Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 295 HIS Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 262 ILE Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 403 LEU Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 154 THR Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 216 VAL Chi-restraints excluded: chain K residue 234 GLU Chi-restraints excluded: chain K residue 241 GLN Chi-restraints excluded: chain K residue 264 LEU Chi-restraints excluded: chain K residue 358 ILE Chi-restraints excluded: chain L residue 20 ASN Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 91 LEU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 209 ILE Chi-restraints excluded: chain L residue 224 LYS Chi-restraints excluded: chain L residue 227 VAL Chi-restraints excluded: chain L residue 234 GLU Chi-restraints excluded: chain L residue 338 THR Chi-restraints excluded: chain L residue 371 LEU Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain M residue 175 LEU Chi-restraints excluded: chain M residue 261 ILE Chi-restraints excluded: chain M residue 262 ILE Chi-restraints excluded: chain M residue 286 THR Chi-restraints excluded: chain M residue 327 MET Chi-restraints excluded: chain O residue 12 SER Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 164 LEU Chi-restraints excluded: chain O residue 313 LEU Chi-restraints excluded: chain O residue 315 ILE Chi-restraints excluded: chain O residue 369 GLU Chi-restraints excluded: chain O residue 390 MET Chi-restraints excluded: chain c residue 159 VAL Chi-restraints excluded: chain d residue 120 GLN Chi-restraints excluded: chain d residue 124 ASP Chi-restraints excluded: chain e residue 21 LEU Chi-restraints excluded: chain f residue 21 LEU Chi-restraints excluded: chain f residue 45 VAL Chi-restraints excluded: chain f residue 124 ASP Chi-restraints excluded: chain f residue 170 THR Chi-restraints excluded: chain g residue 49 ASP Chi-restraints excluded: chain g residue 53 ASN Chi-restraints excluded: chain h residue 142 TYR Chi-restraints excluded: chain h residue 162 VAL Chi-restraints excluded: chain i residue 11 ASP Chi-restraints excluded: chain i residue 25 ASN Chi-restraints excluded: chain i residue 53 ASN Chi-restraints excluded: chain i residue 146 ASP Chi-restraints excluded: chain i residue 152 THR Chi-restraints excluded: chain j residue 49 ASP Chi-restraints excluded: chain k residue 15 ASN Chi-restraints excluded: chain k residue 78 HIS Chi-restraints excluded: chain k residue 162 VAL Chi-restraints excluded: chain l residue 158 ASP Chi-restraints excluded: chain l residue 162 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 275 ASN Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain G residue 260 VAL Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain G residue 376 GLU Chi-restraints excluded: chain G residue 390 MET Chi-restraints excluded: chain G residue 411 ASP Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 227 VAL Chi-restraints excluded: chain N residue 260 VAL Chi-restraints excluded: chain N residue 274 TYR Chi-restraints excluded: chain N residue 284 VAL Chi-restraints excluded: chain N residue 348 LYS Chi-restraints excluded: chain N residue 354 VAL Chi-restraints excluded: chain N residue 398 PHE Chi-restraints excluded: chain F residue 205 MET Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 354 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 672 random chunks: chunk 604 optimal weight: 8.9990 chunk 459 optimal weight: 1.9990 chunk 317 optimal weight: 9.9990 chunk 67 optimal weight: 0.7980 chunk 291 optimal weight: 5.9990 chunk 410 optimal weight: 9.9990 chunk 613 optimal weight: 20.0000 chunk 649 optimal weight: 9.9990 chunk 320 optimal weight: 10.0000 chunk 581 optimal weight: 2.9990 chunk 175 optimal weight: 6.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 GLN ** E 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 292 ASN J 378 GLN ** J 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 306 ASN ** L 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 239 HIS ** M 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 173 GLN e 44 ASN ** f 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 77 GLN ** f 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 77 GLN i 141 ASN ** j 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 91 GLN ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 HIS ** G 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 340 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 55540 Z= 0.291 Angle : 0.666 13.813 74928 Z= 0.338 Chirality : 0.043 0.243 8454 Planarity : 0.005 0.068 9770 Dihedral : 7.458 86.612 7994 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 18.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.79 % Favored : 97.18 % Rotamer: Outliers : 3.29 % Allowed : 16.70 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.27 % Cis-general : 0.17 % 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: 0.59 (0.10), residues: 6854 helix: 1.01 (0.08), residues: 3851 sheet: 0.05 (0.21), residues: 647 loop : -0.40 (0.13), residues: 2356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP E 381 HIS 0.012 0.001 HIS k 92 PHE 0.029 0.002 PHE B 300 TYR 0.027 0.002 TYR k 69 ARG 0.016 0.001 ARG N 299 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13708 Ramachandran restraints generated. 6854 Oldfield, 0 Emsley, 6854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13708 Ramachandran restraints generated. 6854 Oldfield, 0 Emsley, 6854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 835 residues out of total 5838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 192 poor density : 643 time to evaluate : 4.734 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: symmetry clash revert: symmetry clash REVERT: C 189 GLN cc_start: 0.8957 (mt0) cc_final: 0.8442 (mp10) REVERT: C 326 LYS cc_start: 0.8733 (pptt) cc_final: 0.7985 (pttp) REVERT: C 329 GLU cc_start: 0.9002 (OUTLIER) cc_final: 0.8724 (pm20) REVERT: C 341 MET cc_start: 0.9317 (ppp) cc_final: 0.9083 (ppp) REVERT: C 412 PHE cc_start: 0.9005 (t80) cc_final: 0.8638 (t80) REVERT: C 415 MET cc_start: 0.9070 (tmm) cc_final: 0.8840 (tmm) REVERT: D 21 MET cc_start: 0.8514 (ppp) cc_final: 0.8134 (ppp) REVERT: D 62 PHE cc_start: 0.7681 (t80) cc_final: 0.7207 (t80) REVERT: D 85 GLN cc_start: 0.9171 (OUTLIER) cc_final: 0.8928 (pm20) REVERT: D 157 LEU cc_start: 0.9220 (pt) cc_final: 0.8669 (tp) REVERT: D 245 MET cc_start: 0.8583 (mmt) cc_final: 0.7918 (mpp) REVERT: D 329 GLU cc_start: 0.8380 (tp30) cc_final: 0.8020 (tp30) REVERT: D 390 MET cc_start: 0.8892 (pmm) cc_final: 0.8664 (pmm) REVERT: E 29 MET cc_start: 0.7191 (pmm) cc_final: 0.6577 (pmm) REVERT: E 147 MET cc_start: 0.8593 (mmm) cc_final: 0.8300 (mmm) REVERT: E 219 MET cc_start: 0.9384 (mmm) cc_final: 0.9176 (mmm) REVERT: E 259 ASP cc_start: 0.8501 (m-30) cc_final: 0.8258 (m-30) REVERT: E 368 GLU cc_start: 0.9010 (pm20) cc_final: 0.8784 (pm20) REVERT: E 414 GLU cc_start: 0.9157 (mm-30) cc_final: 0.8819 (mm-30) REVERT: J 21 MET cc_start: 0.4893 (OUTLIER) cc_final: 0.4051 (tmm) REVERT: J 31 LYS cc_start: 0.6551 (mptt) cc_final: 0.5749 (ptpt) REVERT: J 52 ASP cc_start: 0.3540 (p0) cc_final: 0.3161 (p0) REVERT: J 59 GLN cc_start: 0.7737 (mp10) cc_final: 0.7311 (pp30) REVERT: J 91 LEU cc_start: 0.6237 (OUTLIER) cc_final: 0.5819 (pp) REVERT: J 186 MET cc_start: 0.3894 (pmm) cc_final: 0.3076 (pmm) REVERT: J 380 MET cc_start: 0.7021 (mpp) cc_final: 0.6659 (mpp) REVERT: K 39 LEU cc_start: 0.9640 (mm) cc_final: 0.9363 (tp) REVERT: K 186 MET cc_start: 0.8573 (pmm) cc_final: 0.8013 (ptp) REVERT: K 234 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7531 (pm20) REVERT: K 241 GLN cc_start: 0.8971 (OUTLIER) cc_final: 0.8737 (pp30) REVERT: K 245 MET cc_start: 0.8513 (tpt) cc_final: 0.8214 (tpt) REVERT: K 341 MET cc_start: 0.8834 (mmm) cc_final: 0.8606 (mmm) REVERT: K 390 MET cc_start: 0.8274 (pmm) cc_final: 0.7217 (ptt) REVERT: L 26 LEU cc_start: 0.9345 (tp) cc_final: 0.9061 (tp) REVERT: L 58 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8404 (mt) REVERT: L 234 GLU cc_start: 0.8892 (OUTLIER) cc_final: 0.8574 (mp0) REVERT: L 244 GLU cc_start: 0.8561 (mm-30) cc_final: 0.8146 (mm-30) REVERT: L 259 ASP cc_start: 0.7325 (m-30) cc_final: 0.6874 (m-30) REVERT: L 341 MET cc_start: 0.8751 (tmm) cc_final: 0.8363 (tmm) REVERT: L 413 PHE cc_start: 0.8771 (m-10) cc_final: 0.8456 (m-80) REVERT: M 1 MET cc_start: 0.6817 (ppp) cc_final: 0.5599 (mtt) REVERT: M 2 ASN cc_start: 0.7791 (t0) cc_final: 0.7379 (t0) REVERT: M 234 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7510 (pm20) REVERT: M 244 GLU cc_start: 0.8685 (mm-30) cc_final: 0.8037 (mm-30) REVERT: M 327 MET cc_start: 0.8013 (OUTLIER) cc_final: 0.7187 (ppp) REVERT: M 333 GLU cc_start: 0.9122 (mt-10) cc_final: 0.8828 (mt-10) REVERT: M 411 ASP cc_start: 0.9402 (t0) cc_final: 0.9155 (t0) REVERT: O 29 MET cc_start: 0.1302 (tmm) cc_final: 0.1036 (ttp) REVERT: O 80 TYR cc_start: 0.7761 (t80) cc_final: 0.7492 (t80) REVERT: O 164 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.7359 (pp) REVERT: O 245 MET cc_start: 0.7486 (mmm) cc_final: 0.7274 (mmm) REVERT: O 380 MET cc_start: 0.8260 (mmm) cc_final: 0.7698 (mmt) REVERT: O 390 MET cc_start: 0.6027 (OUTLIER) cc_final: 0.4354 (ppp) REVERT: O 394 ASP cc_start: 0.7800 (OUTLIER) cc_final: 0.7344 (p0) REVERT: c 177 PHE cc_start: 0.9249 (m-10) cc_final: 0.8909 (m-10) REVERT: c 180 LYS cc_start: 0.9344 (mmtp) cc_final: 0.9144 (mmtt) REVERT: d 89 MET cc_start: 0.7749 (ttp) cc_final: 0.7389 (tmm) REVERT: d 146 ASP cc_start: 0.8147 (m-30) cc_final: 0.7854 (m-30) REVERT: e 175 MET cc_start: 0.9254 (ptm) cc_final: 0.8878 (ptp) REVERT: f 21 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8986 (pp) REVERT: g 83 ASP cc_start: 0.8848 (m-30) cc_final: 0.8469 (t0) REVERT: g 130 LEU cc_start: 0.9634 (mm) cc_final: 0.9407 (mm) REVERT: g 168 LYS cc_start: 0.8816 (mmpt) cc_final: 0.8562 (mmmt) REVERT: h 53 ASN cc_start: 0.9102 (t0) cc_final: 0.8697 (t0) REVERT: h 78 HIS cc_start: 0.9177 (t-90) cc_final: 0.8810 (t-90) REVERT: i 158 ASP cc_start: 0.8206 (p0) cc_final: 0.7863 (p0) REVERT: i 168 LYS cc_start: 0.8640 (mtmm) cc_final: 0.8387 (mptt) REVERT: l 59 LYS cc_start: 0.8926 (pttm) cc_final: 0.8720 (pttm) REVERT: B 80 TYR cc_start: 0.6670 (m-80) cc_final: 0.6413 (m-80) REVERT: B 155 GLU cc_start: 0.8219 (tp30) cc_final: 0.7612 (tp30) REVERT: B 381 TRP cc_start: 0.8651 (m100) cc_final: 0.8224 (m100) REVERT: B 390 MET cc_start: 0.8287 (OUTLIER) cc_final: 0.7017 (ppp) REVERT: G 416 MET cc_start: -0.1135 (ttt) cc_final: -0.1712 (ptp) REVERT: G 418 ARG cc_start: 0.7516 (ptt-90) cc_final: 0.6858 (mmt180) REVERT: N 164 LEU cc_start: 0.9405 (mm) cc_final: 0.9188 (mm) REVERT: N 234 GLU cc_start: 0.6346 (OUTLIER) cc_final: 0.6068 (pm20) REVERT: N 341 MET cc_start: 0.9068 (tmm) cc_final: 0.8818 (ppp) REVERT: N 415 MET cc_start: 0.9045 (ppp) cc_final: 0.8781 (ppp) REVERT: F 298 LYS cc_start: 0.8672 (tttp) cc_final: 0.8265 (mtpt) outliers start: 192 outliers final: 118 residues processed: 777 average time/residue: 0.4969 time to fit residues: 657.8458 Evaluate side-chains 714 residues out of total 5838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 580 time to evaluate : 4.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 295 HIS Chi-restraints excluded: chain C residue 329 GLU Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain D residue 64 PHE Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 85 GLN Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 295 HIS Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 412 PHE Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 403 LEU Chi-restraints excluded: chain J residue 21 MET Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 161 VAL Chi-restraints excluded: chain J residue 227 VAL Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 133 PHE Chi-restraints excluded: chain K residue 154 THR Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 216 VAL Chi-restraints excluded: chain K residue 227 VAL Chi-restraints excluded: chain K residue 234 GLU Chi-restraints excluded: chain K residue 241 GLN Chi-restraints excluded: chain K residue 264 LEU Chi-restraints excluded: chain K residue 267 ILE Chi-restraints excluded: chain L residue 20 ASN Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 91 LEU Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 227 VAL Chi-restraints excluded: chain L residue 234 GLU Chi-restraints excluded: chain L residue 338 THR Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain M residue 131 ILE Chi-restraints excluded: chain M residue 175 LEU Chi-restraints excluded: chain M residue 234 GLU Chi-restraints excluded: chain M residue 260 VAL Chi-restraints excluded: chain M residue 262 ILE Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 286 THR Chi-restraints excluded: chain M residue 327 MET Chi-restraints excluded: chain M residue 338 THR Chi-restraints excluded: chain O residue 12 SER Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 164 LEU Chi-restraints excluded: chain O residue 313 LEU Chi-restraints excluded: chain O residue 315 ILE Chi-restraints excluded: chain O residue 369 GLU Chi-restraints excluded: chain O residue 390 MET Chi-restraints excluded: chain O residue 394 ASP Chi-restraints excluded: chain c residue 59 LYS Chi-restraints excluded: chain c residue 130 LEU Chi-restraints excluded: chain c residue 142 TYR Chi-restraints excluded: chain d residue 120 GLN Chi-restraints excluded: chain d residue 124 ASP Chi-restraints excluded: chain d residue 173 GLN Chi-restraints excluded: chain e residue 21 LEU Chi-restraints excluded: chain e residue 105 MET Chi-restraints excluded: chain f residue 21 LEU Chi-restraints excluded: chain f residue 45 VAL Chi-restraints excluded: chain f residue 124 ASP Chi-restraints excluded: chain f residue 170 THR Chi-restraints excluded: chain g residue 49 ASP Chi-restraints excluded: chain g residue 53 ASN Chi-restraints excluded: chain h residue 142 TYR Chi-restraints excluded: chain h residue 162 VAL Chi-restraints excluded: chain i residue 11 ASP Chi-restraints excluded: chain i residue 25 ASN Chi-restraints excluded: chain i residue 53 ASN Chi-restraints excluded: chain i residue 94 THR Chi-restraints excluded: chain i residue 152 THR Chi-restraints excluded: chain j residue 49 ASP Chi-restraints excluded: chain j residue 124 ASP Chi-restraints excluded: chain k residue 15 ASN Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 78 HIS Chi-restraints excluded: chain k residue 131 LEU Chi-restraints excluded: chain k residue 162 VAL Chi-restraints excluded: chain l residue 158 ASP Chi-restraints excluded: chain l residue 159 VAL Chi-restraints excluded: chain l residue 162 VAL Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 275 ASN Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain B residue 390 MET Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 126 ASN Chi-restraints excluded: chain G residue 260 VAL Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain G residue 376 GLU Chi-restraints excluded: chain G residue 390 MET Chi-restraints excluded: chain G residue 398 PHE Chi-restraints excluded: chain G residue 401 ASN Chi-restraints excluded: chain G residue 411 ASP Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 203 VAL Chi-restraints excluded: chain N residue 208 LEU Chi-restraints excluded: chain N residue 227 VAL Chi-restraints excluded: chain N residue 234 GLU Chi-restraints excluded: chain N residue 260 VAL Chi-restraints excluded: chain N residue 274 TYR Chi-restraints excluded: chain N residue 284 VAL Chi-restraints excluded: chain N residue 348 LYS Chi-restraints excluded: chain N residue 354 VAL Chi-restraints excluded: chain N residue 370 LEU Chi-restraints excluded: chain N residue 398 PHE Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 354 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 672 random chunks: chunk 540 optimal weight: 7.9990 chunk 368 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 chunk 483 optimal weight: 0.8980 chunk 268 optimal weight: 6.9990 chunk 554 optimal weight: 10.0000 chunk 448 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 331 optimal weight: 20.0000 chunk 583 optimal weight: 8.9990 chunk 163 optimal weight: 1.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 142 ASN ** E 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 140 HIS ** K 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 295 HIS ** M 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 344 HIS ** d 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 173 GLN ** f 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 141 ASN ** j 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 61 GLN ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 HIS ** G 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 55540 Z= 0.259 Angle : 0.656 13.201 74928 Z= 0.330 Chirality : 0.043 0.239 8454 Planarity : 0.004 0.067 9770 Dihedral : 7.531 85.079 7994 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 17.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.70 % Favored : 97.27 % Rotamer: Outliers : 3.41 % Allowed : 17.64 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.27 % Cis-general : 0.17 % 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: 0.58 (0.10), residues: 6854 helix: 1.02 (0.08), residues: 3845 sheet: 0.05 (0.21), residues: 651 loop : -0.44 (0.13), residues: 2358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP E 381 HIS 0.012 0.001 HIS J 388 PHE 0.033 0.001 PHE B 300 TYR 0.023 0.002 TYR B 72 ARG 0.015 0.000 ARG N 299 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13708 Ramachandran restraints generated. 6854 Oldfield, 0 Emsley, 6854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13708 Ramachandran restraints generated. 6854 Oldfield, 0 Emsley, 6854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 809 residues out of total 5838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 199 poor density : 610 time to evaluate : 4.777 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 186 MET cc_start: 0.8448 (ptt) cc_final: 0.8147 (ptt) REVERT: C 189 GLN cc_start: 0.8968 (mt0) cc_final: 0.8473 (mp10) REVERT: C 252 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.8139 (mmp80) REVERT: C 326 LYS cc_start: 0.8858 (pptt) cc_final: 0.8196 (pttp) REVERT: C 329 GLU cc_start: 0.9020 (OUTLIER) cc_final: 0.8757 (pm20) REVERT: C 341 MET cc_start: 0.9337 (ppp) cc_final: 0.9082 (ppp) REVERT: C 412 PHE cc_start: 0.9025 (t80) cc_final: 0.8694 (t80) REVERT: C 415 MET cc_start: 0.9109 (tmm) cc_final: 0.8784 (tmm) REVERT: D 21 MET cc_start: 0.8477 (ppp) cc_final: 0.8093 (ppp) REVERT: D 62 PHE cc_start: 0.7724 (t80) cc_final: 0.7248 (t80) REVERT: D 157 LEU cc_start: 0.9214 (pt) cc_final: 0.8645 (tp) REVERT: D 245 MET cc_start: 0.8573 (mmt) cc_final: 0.7871 (mpp) REVERT: D 327 MET cc_start: 0.7940 (ppp) cc_final: 0.7273 (ppp) REVERT: D 329 GLU cc_start: 0.8376 (tp30) cc_final: 0.8039 (tp30) REVERT: D 381 TRP cc_start: 0.8959 (OUTLIER) cc_final: 0.8619 (m-90) REVERT: D 390 MET cc_start: 0.8830 (pmm) cc_final: 0.8581 (pmm) REVERT: D 417 LYS cc_start: 0.9054 (pptt) cc_final: 0.8584 (mptt) REVERT: E 29 MET cc_start: 0.7244 (pmm) cc_final: 0.6651 (pmm) REVERT: E 164 LEU cc_start: 0.9627 (OUTLIER) cc_final: 0.9282 (mm) REVERT: E 219 MET cc_start: 0.9349 (mmm) cc_final: 0.9101 (mmm) REVERT: E 259 ASP cc_start: 0.8540 (m-30) cc_final: 0.8273 (m-30) REVERT: E 368 GLU cc_start: 0.9006 (pm20) cc_final: 0.8785 (pm20) REVERT: J 21 MET cc_start: 0.4882 (OUTLIER) cc_final: 0.4061 (tmm) REVERT: J 31 LYS cc_start: 0.6577 (mptt) cc_final: 0.5740 (ptpt) REVERT: J 52 ASP cc_start: 0.3537 (p0) cc_final: 0.3192 (p0) REVERT: J 59 GLN cc_start: 0.7771 (mp10) cc_final: 0.7305 (pp30) REVERT: J 91 LEU cc_start: 0.6137 (OUTLIER) cc_final: 0.5782 (pp) REVERT: J 186 MET cc_start: 0.4174 (pmm) cc_final: 0.3492 (pmm) REVERT: J 224 LYS cc_start: 0.4970 (mppt) cc_final: 0.3843 (pttm) REVERT: J 380 MET cc_start: 0.7057 (mpp) cc_final: 0.6634 (mpp) REVERT: K 39 LEU cc_start: 0.9647 (mm) cc_final: 0.9362 (tp) REVERT: K 186 MET cc_start: 0.8586 (pmm) cc_final: 0.7704 (ptm) REVERT: K 234 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7517 (pm20) REVERT: K 245 MET cc_start: 0.8537 (tpt) cc_final: 0.8259 (tpt) REVERT: K 341 MET cc_start: 0.8878 (mmm) cc_final: 0.8569 (mmm) REVERT: K 390 MET cc_start: 0.8298 (OUTLIER) cc_final: 0.7158 (ptt) REVERT: L 21 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.8174 (tmm) REVERT: L 26 LEU cc_start: 0.9300 (tp) cc_final: 0.8969 (tp) REVERT: L 56 GLU cc_start: 0.8271 (tm-30) cc_final: 0.8006 (tm-30) REVERT: L 58 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8475 (mt) REVERT: L 234 GLU cc_start: 0.8872 (OUTLIER) cc_final: 0.8602 (mp0) REVERT: L 244 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8090 (mm-30) REVERT: L 259 ASP cc_start: 0.7365 (m-30) cc_final: 0.6887 (m-30) REVERT: L 341 MET cc_start: 0.8739 (tmm) cc_final: 0.8120 (tmm) REVERT: M 1 MET cc_start: 0.6807 (ppp) cc_final: 0.5936 (mtt) REVERT: M 2 ASN cc_start: 0.7853 (t0) cc_final: 0.7450 (t0) REVERT: M 234 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7624 (pm20) REVERT: M 244 GLU cc_start: 0.8717 (mm-30) cc_final: 0.8053 (mm-30) REVERT: M 333 GLU cc_start: 0.9096 (mt-10) cc_final: 0.8797 (mt-10) REVERT: M 411 ASP cc_start: 0.9410 (t0) cc_final: 0.9194 (t0) REVERT: O 29 MET cc_start: 0.1309 (tmm) cc_final: 0.0968 (ttp) REVERT: O 80 TYR cc_start: 0.7855 (t80) cc_final: 0.7624 (t80) REVERT: O 245 MET cc_start: 0.7460 (mmm) cc_final: 0.7257 (mmm) REVERT: O 380 MET cc_start: 0.8243 (mmm) cc_final: 0.7705 (mmt) REVERT: O 390 MET cc_start: 0.6019 (OUTLIER) cc_final: 0.4396 (ppp) REVERT: O 394 ASP cc_start: 0.7832 (OUTLIER) cc_final: 0.7394 (p0) REVERT: c 177 PHE cc_start: 0.9251 (m-10) cc_final: 0.8945 (m-10) REVERT: d 89 MET cc_start: 0.7775 (ttp) cc_final: 0.7425 (tmm) REVERT: d 146 ASP cc_start: 0.8188 (m-30) cc_final: 0.7883 (m-30) REVERT: d 173 GLN cc_start: 0.8872 (OUTLIER) cc_final: 0.8104 (pp30) REVERT: e 175 MET cc_start: 0.9232 (ptm) cc_final: 0.8845 (ptp) REVERT: f 21 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.9005 (pp) REVERT: g 83 ASP cc_start: 0.8803 (m-30) cc_final: 0.8413 (m-30) REVERT: g 89 MET cc_start: 0.8472 (tpp) cc_final: 0.8255 (tmm) REVERT: g 168 LYS cc_start: 0.8850 (mmpt) cc_final: 0.8595 (mmmt) REVERT: h 53 ASN cc_start: 0.9078 (t0) cc_final: 0.8738 (t0) REVERT: h 131 LEU cc_start: 0.9560 (mt) cc_final: 0.9222 (pp) REVERT: i 158 ASP cc_start: 0.8177 (p0) cc_final: 0.7824 (p0) REVERT: i 168 LYS cc_start: 0.8673 (mtmm) cc_final: 0.8424 (mptt) REVERT: k 78 HIS cc_start: 0.8498 (OUTLIER) cc_final: 0.7882 (t-90) REVERT: l 21 LEU cc_start: 0.8728 (mt) cc_final: 0.8455 (pp) REVERT: B 80 TYR cc_start: 0.6686 (m-80) cc_final: 0.6431 (m-80) REVERT: B 155 GLU cc_start: 0.8214 (tp30) cc_final: 0.7595 (tp30) REVERT: B 327 MET cc_start: 0.8806 (ptp) cc_final: 0.8465 (ppp) REVERT: B 381 TRP cc_start: 0.8626 (m100) cc_final: 0.8287 (m100) REVERT: B 390 MET cc_start: 0.8243 (OUTLIER) cc_final: 0.6972 (ppp) REVERT: B 396 MET cc_start: 0.9319 (mmm) cc_final: 0.8873 (mmt) REVERT: G 147 MET cc_start: 0.8010 (mmp) cc_final: 0.7304 (tpp) REVERT: G 416 MET cc_start: -0.1063 (ttt) cc_final: -0.1613 (ptm) REVERT: G 418 ARG cc_start: 0.7465 (ptt-90) cc_final: 0.6808 (mmt180) REVERT: N 29 MET cc_start: 0.2465 (ptp) cc_final: 0.1934 (ptp) REVERT: N 164 LEU cc_start: 0.9470 (mm) cc_final: 0.9234 (mm) REVERT: N 377 LEU cc_start: 0.9519 (tt) cc_final: 0.9212 (pp) REVERT: N 402 LYS cc_start: 0.8993 (OUTLIER) cc_final: 0.8700 (ptmm) REVERT: N 415 MET cc_start: 0.9048 (ppp) cc_final: 0.8798 (ppp) REVERT: F 298 LYS cc_start: 0.8712 (tttp) cc_final: 0.8344 (mtpt) REVERT: F 415 MET cc_start: 0.8726 (ppp) cc_final: 0.8246 (ppp) REVERT: F 416 MET cc_start: 0.9179 (tpp) cc_final: 0.8712 (mmm) outliers start: 199 outliers final: 120 residues processed: 760 average time/residue: 0.5440 time to fit residues: 716.2154 Evaluate side-chains 710 residues out of total 5838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 571 time to evaluate : 4.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 241 GLN Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 252 ARG Chi-restraints excluded: chain C residue 295 HIS Chi-restraints excluded: chain C residue 329 GLU Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain D residue 64 PHE Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 295 HIS Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 381 TRP Chi-restraints excluded: chain D residue 398 PHE Chi-restraints excluded: chain D residue 412 PHE Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 403 LEU Chi-restraints excluded: chain J residue 21 MET Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 327 MET Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 133 PHE Chi-restraints excluded: chain K residue 154 THR Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 216 VAL Chi-restraints excluded: chain K residue 227 VAL Chi-restraints excluded: chain K residue 228 VAL Chi-restraints excluded: chain K residue 234 GLU Chi-restraints excluded: chain K residue 264 LEU Chi-restraints excluded: chain K residue 267 ILE Chi-restraints excluded: chain K residue 390 MET Chi-restraints excluded: chain L residue 20 ASN Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 91 LEU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 164 LEU Chi-restraints excluded: chain L residue 209 ILE Chi-restraints excluded: chain L residue 227 VAL Chi-restraints excluded: chain L residue 234 GLU Chi-restraints excluded: chain L residue 338 THR Chi-restraints excluded: chain L residue 343 LEU Chi-restraints excluded: chain M residue 45 SER Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain M residue 131 ILE Chi-restraints excluded: chain M residue 175 LEU Chi-restraints excluded: chain M residue 234 GLU Chi-restraints excluded: chain M residue 260 VAL Chi-restraints excluded: chain M residue 261 ILE Chi-restraints excluded: chain M residue 262 ILE Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 286 THR Chi-restraints excluded: chain O residue 12 SER Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 164 LEU Chi-restraints excluded: chain O residue 313 LEU Chi-restraints excluded: chain O residue 369 GLU Chi-restraints excluded: chain O residue 390 MET Chi-restraints excluded: chain O residue 394 ASP Chi-restraints excluded: chain c residue 59 LYS Chi-restraints excluded: chain c residue 100 LEU Chi-restraints excluded: chain c residue 130 LEU Chi-restraints excluded: chain d residue 120 GLN Chi-restraints excluded: chain d residue 124 ASP Chi-restraints excluded: chain d residue 173 GLN Chi-restraints excluded: chain e residue 21 LEU Chi-restraints excluded: chain f residue 21 LEU Chi-restraints excluded: chain f residue 45 VAL Chi-restraints excluded: chain f residue 124 ASP Chi-restraints excluded: chain f residue 170 THR Chi-restraints excluded: chain g residue 49 ASP Chi-restraints excluded: chain g residue 53 ASN Chi-restraints excluded: chain h residue 142 TYR Chi-restraints excluded: chain h residue 162 VAL Chi-restraints excluded: chain i residue 11 ASP Chi-restraints excluded: chain i residue 25 ASN Chi-restraints excluded: chain i residue 53 ASN Chi-restraints excluded: chain i residue 94 THR Chi-restraints excluded: chain i residue 152 THR Chi-restraints excluded: chain j residue 49 ASP Chi-restraints excluded: chain j residue 124 ASP Chi-restraints excluded: chain k residue 15 ASN Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 78 HIS Chi-restraints excluded: chain k residue 131 LEU Chi-restraints excluded: chain k residue 162 VAL Chi-restraints excluded: chain l residue 158 ASP Chi-restraints excluded: chain l residue 159 VAL Chi-restraints excluded: chain l residue 162 VAL Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 275 ASN Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain B residue 390 MET Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 260 VAL Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain G residue 376 GLU Chi-restraints excluded: chain G residue 390 MET Chi-restraints excluded: chain G residue 398 PHE Chi-restraints excluded: chain G residue 401 ASN Chi-restraints excluded: chain G residue 411 ASP Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 203 VAL Chi-restraints excluded: chain N residue 216 VAL Chi-restraints excluded: chain N residue 227 VAL Chi-restraints excluded: chain N residue 253 LEU Chi-restraints excluded: chain N residue 260 VAL Chi-restraints excluded: chain N residue 274 TYR Chi-restraints excluded: chain N residue 284 VAL Chi-restraints excluded: chain N residue 348 LYS Chi-restraints excluded: chain N residue 354 VAL Chi-restraints excluded: chain N residue 398 PHE Chi-restraints excluded: chain N residue 402 LYS Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 354 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 672 random chunks: chunk 218 optimal weight: 2.9990 chunk 584 optimal weight: 0.0050 chunk 128 optimal weight: 8.9990 chunk 381 optimal weight: 5.9990 chunk 160 optimal weight: 5.9990 chunk 650 optimal weight: 5.9990 chunk 539 optimal weight: 8.9990 chunk 301 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 chunk 215 optimal weight: 6.9990 chunk 341 optimal weight: 10.0000 overall best weight: 3.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 173 GLN ** f 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 90 GLN ** g 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 116 ASN ** i 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 141 ASN ** j 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 55540 Z= 0.272 Angle : 0.661 12.984 74928 Z= 0.334 Chirality : 0.043 0.251 8454 Planarity : 0.004 0.073 9770 Dihedral : 7.583 88.551 7991 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 17.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.83 % Favored : 97.14 % Rotamer: Outliers : 3.55 % Allowed : 17.97 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.27 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.10), residues: 6854 helix: 0.99 (0.08), residues: 3863 sheet: -0.07 (0.21), residues: 660 loop : -0.44 (0.13), residues: 2331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 381 HIS 0.011 0.001 HIS J 388 PHE 0.021 0.001 PHE B 300 TYR 0.026 0.002 TYR B 72 ARG 0.014 0.000 ARG N 299 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13708 Ramachandran restraints generated. 6854 Oldfield, 0 Emsley, 6854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13708 Ramachandran restraints generated. 6854 Oldfield, 0 Emsley, 6854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 804 residues out of total 5838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 207 poor density : 597 time to evaluate : 5.020 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: symmetry clash REVERT: C 186 MET cc_start: 0.8558 (ptt) cc_final: 0.8288 (ptt) REVERT: C 189 GLN cc_start: 0.9009 (mt0) cc_final: 0.8508 (mp10) REVERT: C 252 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.8149 (mmp80) REVERT: C 326 LYS cc_start: 0.8914 (pptt) cc_final: 0.8273 (pttp) REVERT: C 329 GLU cc_start: 0.9013 (OUTLIER) cc_final: 0.8758 (pm20) REVERT: C 341 MET cc_start: 0.9351 (ppp) cc_final: 0.9078 (ppp) REVERT: C 412 PHE cc_start: 0.9107 (t80) cc_final: 0.8808 (t80) REVERT: C 415 MET cc_start: 0.9110 (tmm) cc_final: 0.8858 (tmm) REVERT: D 21 MET cc_start: 0.8440 (ppp) cc_final: 0.8051 (ppp) REVERT: D 32 GLN cc_start: 0.8980 (mp10) cc_final: 0.8661 (mm-40) REVERT: D 157 LEU cc_start: 0.9254 (pt) cc_final: 0.8695 (tp) REVERT: D 245 MET cc_start: 0.8624 (mmt) cc_final: 0.7920 (mpp) REVERT: D 309 GLU cc_start: 0.8942 (pp20) cc_final: 0.8691 (pp20) REVERT: D 329 GLU cc_start: 0.8451 (tp30) cc_final: 0.8117 (tp30) REVERT: D 381 TRP cc_start: 0.8974 (OUTLIER) cc_final: 0.8661 (m-90) REVERT: D 390 MET cc_start: 0.8878 (pmm) cc_final: 0.8637 (pmm) REVERT: E 29 MET cc_start: 0.7354 (pmm) cc_final: 0.6763 (pmm) REVERT: E 164 LEU cc_start: 0.9620 (OUTLIER) cc_final: 0.9317 (mm) REVERT: E 219 MET cc_start: 0.9356 (mmm) cc_final: 0.9090 (mmm) REVERT: E 259 ASP cc_start: 0.8556 (m-30) cc_final: 0.8282 (m-30) REVERT: J 21 MET cc_start: 0.4471 (OUTLIER) cc_final: 0.3908 (tmm) REVERT: J 31 LYS cc_start: 0.6631 (mptt) cc_final: 0.5732 (ptpt) REVERT: J 52 ASP cc_start: 0.3710 (p0) cc_final: 0.3412 (p0) REVERT: J 59 GLN cc_start: 0.7862 (mp10) cc_final: 0.7354 (pp30) REVERT: J 91 LEU cc_start: 0.6067 (OUTLIER) cc_final: 0.5663 (pp) REVERT: J 186 MET cc_start: 0.4139 (pmm) cc_final: 0.3472 (pmm) REVERT: J 224 LYS cc_start: 0.5067 (mppt) cc_final: 0.3906 (pttm) REVERT: J 380 MET cc_start: 0.7041 (mpp) cc_final: 0.6645 (mpp) REVERT: K 39 LEU cc_start: 0.9660 (mm) cc_final: 0.9359 (tp) REVERT: K 186 MET cc_start: 0.8662 (pmm) cc_final: 0.7981 (ptm) REVERT: K 234 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7522 (pm20) REVERT: K 245 MET cc_start: 0.8565 (tpt) cc_final: 0.8285 (tpt) REVERT: K 341 MET cc_start: 0.8966 (mmm) cc_final: 0.8599 (mmm) REVERT: K 390 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.7160 (ptt) REVERT: L 21 MET cc_start: 0.8684 (OUTLIER) cc_final: 0.8217 (tmm) REVERT: L 26 LEU cc_start: 0.9299 (tp) cc_final: 0.9036 (tp) REVERT: L 56 GLU cc_start: 0.8251 (tm-30) cc_final: 0.7965 (tm-30) REVERT: L 58 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8576 (mt) REVERT: L 234 GLU cc_start: 0.8885 (OUTLIER) cc_final: 0.8618 (mp0) REVERT: L 244 GLU cc_start: 0.8585 (mm-30) cc_final: 0.8115 (mm-30) REVERT: L 259 ASP cc_start: 0.7364 (m-30) cc_final: 0.6881 (m-30) REVERT: L 341 MET cc_start: 0.8761 (tmm) cc_final: 0.7785 (tmm) REVERT: M 1 MET cc_start: 0.6921 (ppp) cc_final: 0.6371 (mtt) REVERT: M 2 ASN cc_start: 0.8078 (t0) cc_final: 0.7736 (t0) REVERT: M 234 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7632 (pm20) REVERT: M 244 GLU cc_start: 0.8769 (mm-30) cc_final: 0.8240 (mm-30) REVERT: M 333 GLU cc_start: 0.9092 (mt-10) cc_final: 0.8745 (mm-30) REVERT: M 411 ASP cc_start: 0.9412 (t0) cc_final: 0.9192 (t0) REVERT: O 29 MET cc_start: 0.1333 (tmm) cc_final: 0.1039 (ttp) REVERT: O 80 TYR cc_start: 0.7890 (t80) cc_final: 0.7671 (t80) REVERT: O 193 GLN cc_start: 0.7300 (OUTLIER) cc_final: 0.7045 (mp10) REVERT: O 341 MET cc_start: 0.6786 (mmm) cc_final: 0.6487 (mmm) REVERT: O 390 MET cc_start: 0.6185 (OUTLIER) cc_final: 0.4643 (ppp) REVERT: O 394 ASP cc_start: 0.7814 (OUTLIER) cc_final: 0.7381 (p0) REVERT: c 177 PHE cc_start: 0.9275 (m-10) cc_final: 0.8910 (m-10) REVERT: d 89 MET cc_start: 0.7843 (ttp) cc_final: 0.7476 (tmm) REVERT: d 146 ASP cc_start: 0.8133 (m-30) cc_final: 0.7825 (m-30) REVERT: e 175 MET cc_start: 0.9239 (ptm) cc_final: 0.8858 (ptp) REVERT: f 21 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.9009 (pp) REVERT: g 83 ASP cc_start: 0.8837 (m-30) cc_final: 0.8557 (t0) REVERT: g 89 MET cc_start: 0.8550 (tpp) cc_final: 0.8305 (tpp) REVERT: g 168 LYS cc_start: 0.8895 (mmpt) cc_final: 0.8621 (mmmt) REVERT: h 53 ASN cc_start: 0.9133 (t0) cc_final: 0.8723 (t0) REVERT: i 96 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8389 (pp) REVERT: i 158 ASP cc_start: 0.8221 (p0) cc_final: 0.7884 (p0) REVERT: i 168 LYS cc_start: 0.8674 (mtmm) cc_final: 0.8433 (mptt) REVERT: k 78 HIS cc_start: 0.8508 (OUTLIER) cc_final: 0.7863 (t-90) REVERT: l 59 LYS cc_start: 0.8941 (pttm) cc_final: 0.8698 (pttm) REVERT: l 136 LYS cc_start: 0.6844 (pttm) cc_final: 0.6436 (pttm) REVERT: B 80 TYR cc_start: 0.6666 (m-80) cc_final: 0.6405 (m-80) REVERT: B 145 LEU cc_start: 0.6832 (OUTLIER) cc_final: 0.6150 (mm) REVERT: B 155 GLU cc_start: 0.8245 (tp30) cc_final: 0.7617 (tp30) REVERT: B 327 MET cc_start: 0.8812 (ptp) cc_final: 0.8493 (ppp) REVERT: B 381 TRP cc_start: 0.8630 (m100) cc_final: 0.8280 (m100) REVERT: B 390 MET cc_start: 0.8220 (OUTLIER) cc_final: 0.6888 (ppp) REVERT: B 396 MET cc_start: 0.9326 (mmm) cc_final: 0.8846 (mmt) REVERT: B 414 GLU cc_start: 0.9396 (mm-30) cc_final: 0.9180 (mm-30) REVERT: G 147 MET cc_start: 0.8019 (mmp) cc_final: 0.7273 (tpp) REVERT: G 416 MET cc_start: -0.1017 (ttt) cc_final: -0.1550 (ptm) REVERT: G 418 ARG cc_start: 0.7458 (ptt-90) cc_final: 0.6811 (mmt180) REVERT: N 164 LEU cc_start: 0.9503 (mm) cc_final: 0.9246 (mm) REVERT: N 221 ARG cc_start: 0.9401 (ptm-80) cc_final: 0.9085 (ptm-80) REVERT: N 377 LEU cc_start: 0.9529 (tt) cc_final: 0.9229 (pp) REVERT: N 402 LYS cc_start: 0.9032 (OUTLIER) cc_final: 0.8780 (ptmm) REVERT: N 415 MET cc_start: 0.9090 (ppp) cc_final: 0.8868 (ppp) REVERT: F 298 LYS cc_start: 0.8749 (tttp) cc_final: 0.8450 (mtpt) REVERT: F 415 MET cc_start: 0.8765 (ppp) cc_final: 0.8293 (ppp) REVERT: F 416 MET cc_start: 0.9190 (tpp) cc_final: 0.8699 (mmm) outliers start: 207 outliers final: 142 residues processed: 745 average time/residue: 0.4822 time to fit residues: 621.9399 Evaluate side-chains 733 residues out of total 5838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 570 time to evaluate : 4.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 241 GLN Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 252 ARG Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain C residue 295 HIS Chi-restraints excluded: chain C residue 329 GLU Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 394 ASP Chi-restraints excluded: chain D residue 64 PHE Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 295 HIS Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 381 TRP Chi-restraints excluded: chain D residue 398 PHE Chi-restraints excluded: chain D residue 412 PHE Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 403 LEU Chi-restraints excluded: chain J residue 21 MET Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 247 ILE Chi-restraints excluded: chain J residue 327 MET Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 133 PHE Chi-restraints excluded: chain K residue 154 THR Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 162 LEU Chi-restraints excluded: chain K residue 188 LEU Chi-restraints excluded: chain K residue 216 VAL Chi-restraints excluded: chain K residue 227 VAL Chi-restraints excluded: chain K residue 228 VAL Chi-restraints excluded: chain K residue 234 GLU Chi-restraints excluded: chain K residue 264 LEU Chi-restraints excluded: chain K residue 267 ILE Chi-restraints excluded: chain K residue 276 THR Chi-restraints excluded: chain K residue 325 SER Chi-restraints excluded: chain K residue 390 MET Chi-restraints excluded: chain L residue 20 ASN Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 91 LEU Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 164 LEU Chi-restraints excluded: chain L residue 188 LEU Chi-restraints excluded: chain L residue 227 VAL Chi-restraints excluded: chain L residue 234 GLU Chi-restraints excluded: chain L residue 338 THR Chi-restraints excluded: chain L residue 343 LEU Chi-restraints excluded: chain M residue 4 THR Chi-restraints excluded: chain M residue 45 SER Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain M residue 131 ILE Chi-restraints excluded: chain M residue 158 THR Chi-restraints excluded: chain M residue 175 LEU Chi-restraints excluded: chain M residue 234 GLU Chi-restraints excluded: chain M residue 260 VAL Chi-restraints excluded: chain M residue 261 ILE Chi-restraints excluded: chain M residue 262 ILE Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 270 LEU Chi-restraints excluded: chain M residue 286 THR Chi-restraints excluded: chain O residue 12 SER Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 164 LEU Chi-restraints excluded: chain O residue 193 GLN Chi-restraints excluded: chain O residue 274 TYR Chi-restraints excluded: chain O residue 313 LEU Chi-restraints excluded: chain O residue 315 ILE Chi-restraints excluded: chain O residue 369 GLU Chi-restraints excluded: chain O residue 390 MET Chi-restraints excluded: chain O residue 394 ASP Chi-restraints excluded: chain c residue 59 LYS Chi-restraints excluded: chain c residue 100 LEU Chi-restraints excluded: chain c residue 130 LEU Chi-restraints excluded: chain d residue 124 ASP Chi-restraints excluded: chain d residue 173 GLN Chi-restraints excluded: chain e residue 21 LEU Chi-restraints excluded: chain e residue 105 MET Chi-restraints excluded: chain f residue 21 LEU Chi-restraints excluded: chain f residue 45 VAL Chi-restraints excluded: chain f residue 124 ASP Chi-restraints excluded: chain f residue 170 THR Chi-restraints excluded: chain g residue 49 ASP Chi-restraints excluded: chain g residue 53 ASN Chi-restraints excluded: chain h residue 142 TYR Chi-restraints excluded: chain h residue 162 VAL Chi-restraints excluded: chain i residue 11 ASP Chi-restraints excluded: chain i residue 25 ASN Chi-restraints excluded: chain i residue 53 ASN Chi-restraints excluded: chain i residue 94 THR Chi-restraints excluded: chain i residue 96 LEU Chi-restraints excluded: chain i residue 152 THR Chi-restraints excluded: chain j residue 49 ASP Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain j residue 124 ASP Chi-restraints excluded: chain k residue 15 ASN Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 78 HIS Chi-restraints excluded: chain k residue 131 LEU Chi-restraints excluded: chain k residue 162 VAL Chi-restraints excluded: chain l residue 158 ASP Chi-restraints excluded: chain l residue 159 VAL Chi-restraints excluded: chain l residue 162 VAL Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 275 ASN Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain B residue 390 MET Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 260 VAL Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain G residue 376 GLU Chi-restraints excluded: chain G residue 390 MET Chi-restraints excluded: chain G residue 398 PHE Chi-restraints excluded: chain G residue 401 ASN Chi-restraints excluded: chain G residue 411 ASP Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 203 VAL Chi-restraints excluded: chain N residue 208 LEU Chi-restraints excluded: chain N residue 227 VAL Chi-restraints excluded: chain N residue 253 LEU Chi-restraints excluded: chain N residue 260 VAL Chi-restraints excluded: chain N residue 274 TYR Chi-restraints excluded: chain N residue 284 VAL Chi-restraints excluded: chain N residue 348 LYS Chi-restraints excluded: chain N residue 354 VAL Chi-restraints excluded: chain N residue 370 LEU Chi-restraints excluded: chain N residue 398 PHE Chi-restraints excluded: chain N residue 402 LYS Chi-restraints excluded: chain N residue 411 ASP Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 351 GLU Chi-restraints excluded: chain F residue 354 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 672 random chunks: chunk 626 optimal weight: 0.0970 chunk 73 optimal weight: 0.2980 chunk 370 optimal weight: 10.0000 chunk 474 optimal weight: 6.9990 chunk 367 optimal weight: 0.8980 chunk 547 optimal weight: 0.3980 chunk 363 optimal weight: 1.9990 chunk 647 optimal weight: 0.9980 chunk 405 optimal weight: 0.6980 chunk 394 optimal weight: 5.9990 chunk 299 optimal weight: 10.0000 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 ASN C 295 HIS ** J 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 241 GLN ** L 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 256 HIS ** d 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 116 ASN ** f 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 116 ASN i 141 ASN ** j 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 173 GLN k 91 GLN ** l 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN B 32 GLN ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 374 GLN ** F 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 55540 Z= 0.166 Angle : 0.673 14.682 74928 Z= 0.330 Chirality : 0.043 0.229 8454 Planarity : 0.004 0.070 9770 Dihedral : 7.398 88.250 7991 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.54 % Favored : 97.43 % Rotamer: Outliers : 2.57 % Allowed : 19.27 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.27 % Cis-general : 0.17 % 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 (0.10), residues: 6854 helix: 1.05 (0.08), residues: 3854 sheet: -0.06 (0.20), residues: 668 loop : -0.41 (0.13), residues: 2332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 381 HIS 0.012 0.001 HIS J 388 PHE 0.029 0.001 PHE E 62 TYR 0.021 0.001 TYR B 72 ARG 0.011 0.000 ARG N 299 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13708 Ramachandran restraints generated. 6854 Oldfield, 0 Emsley, 6854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13708 Ramachandran restraints generated. 6854 Oldfield, 0 Emsley, 6854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 814 residues out of total 5838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 664 time to evaluate : 4.862 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 189 GLN cc_start: 0.8949 (mt0) cc_final: 0.8447 (mp10) REVERT: C 215 GLU cc_start: 0.9078 (mp0) cc_final: 0.8458 (mp0) REVERT: C 341 MET cc_start: 0.9308 (ppp) cc_final: 0.9056 (ppp) REVERT: C 412 PHE cc_start: 0.9042 (t80) cc_final: 0.8795 (t80) REVERT: C 414 GLU cc_start: 0.8930 (tp30) cc_final: 0.8690 (tp30) REVERT: C 415 MET cc_start: 0.9069 (tmm) cc_final: 0.8738 (tmm) REVERT: D 21 MET cc_start: 0.8436 (ppp) cc_final: 0.8050 (ppp) REVERT: D 32 GLN cc_start: 0.8929 (mp10) cc_final: 0.8679 (mp10) REVERT: D 62 PHE cc_start: 0.7681 (t80) cc_final: 0.7322 (t80) REVERT: D 157 LEU cc_start: 0.9183 (pt) cc_final: 0.8589 (tp) REVERT: D 219 MET cc_start: 0.9232 (tpt) cc_final: 0.9014 (tpp) REVERT: D 245 MET cc_start: 0.8564 (mmt) cc_final: 0.7924 (mpp) REVERT: D 327 MET cc_start: 0.7901 (ppp) cc_final: 0.7673 (ppp) REVERT: D 329 GLU cc_start: 0.8347 (tp30) cc_final: 0.7996 (tp30) REVERT: D 390 MET cc_start: 0.8802 (pmm) cc_final: 0.8569 (pmm) REVERT: D 417 LYS cc_start: 0.9071 (pptt) cc_final: 0.8667 (mptt) REVERT: E 29 MET cc_start: 0.7258 (pmm) cc_final: 0.6718 (pmm) REVERT: E 147 MET cc_start: 0.8423 (mmm) cc_final: 0.8097 (mmp) REVERT: E 157 LEU cc_start: 0.9591 (pt) cc_final: 0.9208 (tt) REVERT: E 164 LEU cc_start: 0.9598 (OUTLIER) cc_final: 0.9347 (mm) REVERT: E 219 MET cc_start: 0.9360 (mmm) cc_final: 0.9101 (mmm) REVERT: E 259 ASP cc_start: 0.8537 (m-30) cc_final: 0.8267 (m-30) REVERT: E 360 TYR cc_start: 0.8438 (t80) cc_final: 0.8153 (t80) REVERT: E 414 GLU cc_start: 0.9180 (mm-30) cc_final: 0.8808 (mm-30) REVERT: E 415 MET cc_start: 0.8725 (tmm) cc_final: 0.8263 (tmm) REVERT: J 21 MET cc_start: 0.4492 (OUTLIER) cc_final: 0.3933 (tmm) REVERT: J 31 LYS cc_start: 0.6693 (mptt) cc_final: 0.5806 (ptpt) REVERT: J 52 ASP cc_start: 0.3609 (p0) cc_final: 0.3296 (p0) REVERT: J 59 GLN cc_start: 0.7797 (mp10) cc_final: 0.7397 (pp30) REVERT: J 91 LEU cc_start: 0.5923 (OUTLIER) cc_final: 0.5633 (pp) REVERT: J 186 MET cc_start: 0.4088 (pmm) cc_final: 0.3407 (pmm) REVERT: J 224 LYS cc_start: 0.5318 (mppt) cc_final: 0.4238 (pttm) REVERT: J 380 MET cc_start: 0.7011 (mpp) cc_final: 0.6778 (mmm) REVERT: K 219 MET cc_start: 0.9434 (tpp) cc_final: 0.9205 (mmm) REVERT: K 234 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7513 (pm20) REVERT: K 241 GLN cc_start: 0.8947 (OUTLIER) cc_final: 0.8740 (pp30) REVERT: K 245 MET cc_start: 0.8542 (tpt) cc_final: 0.8252 (tpt) REVERT: K 341 MET cc_start: 0.8892 (mmm) cc_final: 0.8519 (mmm) REVERT: K 390 MET cc_start: 0.8263 (OUTLIER) cc_final: 0.7144 (ptt) REVERT: L 26 LEU cc_start: 0.9271 (tp) cc_final: 0.8988 (tp) REVERT: L 56 GLU cc_start: 0.8308 (tm-30) cc_final: 0.8011 (tm-30) REVERT: L 58 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8495 (mt) REVERT: L 244 GLU cc_start: 0.8459 (mm-30) cc_final: 0.7982 (mm-30) REVERT: L 259 ASP cc_start: 0.7329 (m-30) cc_final: 0.6845 (m-30) REVERT: L 341 MET cc_start: 0.8770 (tmm) cc_final: 0.8058 (tmm) REVERT: M 1 MET cc_start: 0.7059 (ppp) cc_final: 0.6585 (mtt) REVERT: M 2 ASN cc_start: 0.8089 (t0) cc_final: 0.7753 (t0) REVERT: M 234 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7532 (pm20) REVERT: M 244 GLU cc_start: 0.8665 (mm-30) cc_final: 0.8160 (mm-30) REVERT: M 261 ILE cc_start: 0.9226 (OUTLIER) cc_final: 0.8977 (pt) REVERT: M 265 ASP cc_start: 0.8509 (t0) cc_final: 0.7719 (p0) REVERT: M 333 GLU cc_start: 0.9064 (mt-10) cc_final: 0.8661 (mm-30) REVERT: M 362 ARG cc_start: 0.9250 (ttm-80) cc_final: 0.9004 (ttp-110) REVERT: M 411 ASP cc_start: 0.9374 (t0) cc_final: 0.9135 (t0) REVERT: O 29 MET cc_start: 0.1210 (tmm) cc_final: 0.0918 (ttp) REVERT: O 164 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7610 (pp) REVERT: O 341 MET cc_start: 0.6723 (mmm) cc_final: 0.6413 (mmm) REVERT: O 390 MET cc_start: 0.6026 (OUTLIER) cc_final: 0.4524 (ppp) REVERT: O 394 ASP cc_start: 0.7914 (OUTLIER) cc_final: 0.7446 (p0) REVERT: c 175 MET cc_start: 0.8721 (ppp) cc_final: 0.8497 (pmm) REVERT: d 89 MET cc_start: 0.7744 (ttp) cc_final: 0.7479 (tmm) REVERT: d 146 ASP cc_start: 0.8077 (m-30) cc_final: 0.7791 (m-30) REVERT: e 175 MET cc_start: 0.9192 (ptm) cc_final: 0.8837 (ptp) REVERT: g 83 ASP cc_start: 0.8776 (m-30) cc_final: 0.8513 (t0) REVERT: g 89 MET cc_start: 0.8555 (tpp) cc_final: 0.8280 (tpp) REVERT: g 168 LYS cc_start: 0.8784 (mmpt) cc_final: 0.8521 (mmmt) REVERT: h 131 LEU cc_start: 0.9563 (mt) cc_final: 0.9229 (pp) REVERT: i 158 ASP cc_start: 0.8217 (p0) cc_final: 0.7865 (p0) REVERT: i 168 LYS cc_start: 0.8659 (mtmm) cc_final: 0.8427 (mptt) REVERT: j 51 LEU cc_start: 0.9255 (mt) cc_final: 0.8928 (mp) REVERT: k 78 HIS cc_start: 0.8482 (OUTLIER) cc_final: 0.7879 (t-90) REVERT: k 155 PHE cc_start: 0.5653 (m-80) cc_final: 0.5390 (m-10) REVERT: l 21 LEU cc_start: 0.8692 (mt) cc_final: 0.8431 (pp) REVERT: B 80 TYR cc_start: 0.6706 (m-80) cc_final: 0.6431 (m-80) REVERT: B 155 GLU cc_start: 0.8132 (tp30) cc_final: 0.7488 (tp30) REVERT: B 381 TRP cc_start: 0.8601 (m100) cc_final: 0.8281 (m100) REVERT: B 390 MET cc_start: 0.8114 (OUTLIER) cc_final: 0.6956 (ppp) REVERT: B 414 GLU cc_start: 0.9382 (mm-30) cc_final: 0.9168 (mm-30) REVERT: G 1 MET cc_start: 0.7508 (ppp) cc_final: 0.7231 (ppp) REVERT: G 147 MET cc_start: 0.8052 (mmp) cc_final: 0.7350 (tpp) REVERT: G 222 LEU cc_start: 0.8410 (tt) cc_final: 0.8198 (tt) REVERT: G 416 MET cc_start: -0.0896 (ttt) cc_final: -0.1882 (ptm) REVERT: G 418 ARG cc_start: 0.7476 (ptt-90) cc_final: 0.6865 (mmt180) REVERT: N 29 MET cc_start: 0.2642 (ptp) cc_final: 0.2306 (ptp) REVERT: N 164 LEU cc_start: 0.9505 (mm) cc_final: 0.9226 (mm) REVERT: N 221 ARG cc_start: 0.9369 (ptm-80) cc_final: 0.9055 (ptm-80) REVERT: N 377 LEU cc_start: 0.9535 (OUTLIER) cc_final: 0.9230 (pp) REVERT: N 402 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8821 (ptmm) REVERT: N 403 LEU cc_start: 0.9571 (pp) cc_final: 0.8978 (tt) REVERT: N 415 MET cc_start: 0.9053 (ppp) cc_final: 0.8828 (ppp) REVERT: F 219 MET cc_start: 0.9418 (tpp) cc_final: 0.9206 (tpp) REVERT: F 298 LYS cc_start: 0.8724 (tttp) cc_final: 0.8467 (mtpt) REVERT: F 390 MET cc_start: 0.5848 (ppp) cc_final: 0.5072 (ppp) outliers start: 150 outliers final: 91 residues processed: 771 average time/residue: 0.4914 time to fit residues: 649.3879 Evaluate side-chains 711 residues out of total 5838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 604 time to evaluate : 5.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 241 GLN Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 295 HIS Chi-restraints excluded: chain C residue 405 MET Chi-restraints excluded: chain D residue 64 PHE Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 295 HIS Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain J residue 21 MET Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 247 ILE Chi-restraints excluded: chain J residue 327 MET Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 154 THR Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 188 LEU Chi-restraints excluded: chain K residue 216 VAL Chi-restraints excluded: chain K residue 227 VAL Chi-restraints excluded: chain K residue 234 GLU Chi-restraints excluded: chain K residue 241 GLN Chi-restraints excluded: chain K residue 267 ILE Chi-restraints excluded: chain K residue 390 MET Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 91 LEU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 188 LEU Chi-restraints excluded: chain L residue 209 ILE Chi-restraints excluded: chain L residue 227 VAL Chi-restraints excluded: chain L residue 254 VAL Chi-restraints excluded: chain M residue 45 SER Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain M residue 131 ILE Chi-restraints excluded: chain M residue 175 LEU Chi-restraints excluded: chain M residue 234 GLU Chi-restraints excluded: chain M residue 261 ILE Chi-restraints excluded: chain M residue 262 ILE Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 274 TYR Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 164 LEU Chi-restraints excluded: chain O residue 390 MET Chi-restraints excluded: chain O residue 394 ASP Chi-restraints excluded: chain c residue 100 LEU Chi-restraints excluded: chain c residue 130 LEU Chi-restraints excluded: chain d residue 124 ASP Chi-restraints excluded: chain d residue 173 GLN Chi-restraints excluded: chain f residue 45 VAL Chi-restraints excluded: chain g residue 53 ASN Chi-restraints excluded: chain h residue 142 TYR Chi-restraints excluded: chain h residue 162 VAL Chi-restraints excluded: chain i residue 11 ASP Chi-restraints excluded: chain i residue 25 ASN Chi-restraints excluded: chain i residue 53 ASN Chi-restraints excluded: chain i residue 152 THR Chi-restraints excluded: chain j residue 124 ASP Chi-restraints excluded: chain k residue 15 ASN Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 78 HIS Chi-restraints excluded: chain l residue 158 ASP Chi-restraints excluded: chain l residue 162 VAL Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 275 ASN Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain B residue 390 MET Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 260 VAL Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain G residue 376 GLU Chi-restraints excluded: chain G residue 390 MET Chi-restraints excluded: chain G residue 401 ASN Chi-restraints excluded: chain G residue 411 ASP Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 203 VAL Chi-restraints excluded: chain N residue 208 LEU Chi-restraints excluded: chain N residue 253 LEU Chi-restraints excluded: chain N residue 260 VAL Chi-restraints excluded: chain N residue 284 VAL Chi-restraints excluded: chain N residue 348 LYS Chi-restraints excluded: chain N residue 354 VAL Chi-restraints excluded: chain N residue 377 LEU Chi-restraints excluded: chain N residue 398 PHE Chi-restraints excluded: chain N residue 402 LYS Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 351 GLU Chi-restraints excluded: chain F residue 354 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 672 random chunks: chunk 400 optimal weight: 0.0870 chunk 258 optimal weight: 4.9990 chunk 386 optimal weight: 2.9990 chunk 195 optimal weight: 10.0000 chunk 127 optimal weight: 9.9990 chunk 125 optimal weight: 0.9990 chunk 411 optimal weight: 5.9990 chunk 441 optimal weight: 3.9990 chunk 320 optimal weight: 10.0000 chunk 60 optimal weight: 0.7980 chunk 509 optimal weight: 3.9990 overall best weight: 1.7764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 241 GLN ** L 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 388 HIS ** M 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 173 GLN ** f 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 141 ASN ** j 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 25 ASN ** l 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 378 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 55540 Z= 0.196 Angle : 0.683 17.283 74928 Z= 0.334 Chirality : 0.043 0.371 8454 Planarity : 0.004 0.068 9770 Dihedral : 7.362 86.488 7988 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.73 % Favored : 97.24 % Rotamer: Outliers : 2.47 % Allowed : 20.18 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.27 % Cis-general : 0.17 % 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 (0.10), residues: 6854 helix: 1.04 (0.08), residues: 3855 sheet: -0.05 (0.20), residues: 672 loop : -0.40 (0.13), residues: 2327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 381 HIS 0.012 0.001 HIS J 388 PHE 0.030 0.001 PHE B 300 TYR 0.050 0.002 TYR B 72 ARG 0.011 0.000 ARG N 299 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13708 Ramachandran restraints generated. 6854 Oldfield, 0 Emsley, 6854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13708 Ramachandran restraints generated. 6854 Oldfield, 0 Emsley, 6854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 758 residues out of total 5838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 614 time to evaluate : 4.859 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 186 MET cc_start: 0.8456 (ptt) cc_final: 0.8147 (ptt) REVERT: C 189 GLN cc_start: 0.9001 (mt0) cc_final: 0.8535 (mp10) REVERT: C 215 GLU cc_start: 0.9115 (mp0) cc_final: 0.8491 (mp0) REVERT: C 341 MET cc_start: 0.9312 (ppp) cc_final: 0.9055 (ppp) REVERT: C 390 MET cc_start: 0.9004 (pmm) cc_final: 0.8756 (pmm) REVERT: C 412 PHE cc_start: 0.9069 (t80) cc_final: 0.8787 (t80) REVERT: D 21 MET cc_start: 0.8472 (ppp) cc_final: 0.8076 (ppp) REVERT: D 32 GLN cc_start: 0.8935 (mp10) cc_final: 0.8675 (mp10) REVERT: D 62 PHE cc_start: 0.7690 (t80) cc_final: 0.7296 (t80) REVERT: D 157 LEU cc_start: 0.9193 (pt) cc_final: 0.8606 (tp) REVERT: D 219 MET cc_start: 0.9268 (tpt) cc_final: 0.9042 (tpp) REVERT: D 245 MET cc_start: 0.8625 (mmt) cc_final: 0.7887 (mpp) REVERT: D 329 GLU cc_start: 0.8416 (tp30) cc_final: 0.8055 (tp30) REVERT: D 390 MET cc_start: 0.8869 (pmm) cc_final: 0.8642 (pmm) REVERT: D 417 LYS cc_start: 0.9076 (pptt) cc_final: 0.8732 (mptt) REVERT: E 29 MET cc_start: 0.7247 (pmm) cc_final: 0.6713 (pmm) REVERT: E 147 MET cc_start: 0.8411 (mmm) cc_final: 0.8130 (mmp) REVERT: E 219 MET cc_start: 0.9351 (mmm) cc_final: 0.9098 (mmm) REVERT: E 259 ASP cc_start: 0.8562 (m-30) cc_final: 0.8295 (m-30) REVERT: E 360 TYR cc_start: 0.8455 (t80) cc_final: 0.8146 (t80) REVERT: E 368 GLU cc_start: 0.9021 (pm20) cc_final: 0.8772 (pm20) REVERT: E 414 GLU cc_start: 0.9179 (mm-30) cc_final: 0.8967 (tp30) REVERT: E 415 MET cc_start: 0.8740 (tmm) cc_final: 0.8353 (tmm) REVERT: J 21 MET cc_start: 0.4549 (OUTLIER) cc_final: 0.4016 (tmm) REVERT: J 31 LYS cc_start: 0.6614 (mptt) cc_final: 0.5686 (ptpt) REVERT: J 52 ASP cc_start: 0.3599 (p0) cc_final: 0.3284 (p0) REVERT: J 59 GLN cc_start: 0.7847 (mp10) cc_final: 0.7406 (pp30) REVERT: J 91 LEU cc_start: 0.5973 (OUTLIER) cc_final: 0.5639 (pp) REVERT: J 147 MET cc_start: 0.5227 (mmm) cc_final: 0.4861 (mmt) REVERT: J 186 MET cc_start: 0.4098 (pmm) cc_final: 0.3424 (pmm) REVERT: J 224 LYS cc_start: 0.5346 (mppt) cc_final: 0.4266 (pttm) REVERT: J 295 HIS cc_start: 0.8701 (m-70) cc_final: 0.8410 (m-70) REVERT: J 380 MET cc_start: 0.7027 (mpp) cc_final: 0.6482 (mmm) REVERT: J 416 MET cc_start: 0.3317 (tpt) cc_final: 0.2992 (tpt) REVERT: K 186 MET cc_start: 0.8534 (pmm) cc_final: 0.7423 (ptm) REVERT: K 234 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7498 (pm20) REVERT: K 245 MET cc_start: 0.8493 (tpt) cc_final: 0.8185 (tpt) REVERT: K 341 MET cc_start: 0.8905 (mmm) cc_final: 0.8519 (mmm) REVERT: K 390 MET cc_start: 0.8269 (OUTLIER) cc_final: 0.7113 (ptt) REVERT: L 26 LEU cc_start: 0.9309 (tp) cc_final: 0.8985 (tp) REVERT: L 56 GLU cc_start: 0.8256 (tm-30) cc_final: 0.7981 (tm-30) REVERT: L 58 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8557 (mt) REVERT: L 244 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8011 (mm-30) REVERT: L 259 ASP cc_start: 0.7348 (m-30) cc_final: 0.6861 (m-30) REVERT: L 341 MET cc_start: 0.8812 (tmm) cc_final: 0.7984 (tmm) REVERT: M 1 MET cc_start: 0.7195 (ppp) cc_final: 0.6759 (mtt) REVERT: M 2 ASN cc_start: 0.8073 (t0) cc_final: 0.7683 (t0) REVERT: M 234 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7492 (pm20) REVERT: M 244 GLU cc_start: 0.8714 (mm-30) cc_final: 0.8217 (mm-30) REVERT: M 265 ASP cc_start: 0.8609 (t0) cc_final: 0.7781 (p0) REVERT: M 333 GLU cc_start: 0.9082 (mt-10) cc_final: 0.8698 (mm-30) REVERT: M 411 ASP cc_start: 0.9406 (t0) cc_final: 0.9179 (t0) REVERT: O 29 MET cc_start: 0.1314 (tmm) cc_final: 0.1068 (ttp) REVERT: O 390 MET cc_start: 0.6091 (OUTLIER) cc_final: 0.4492 (ppp) REVERT: O 394 ASP cc_start: 0.7901 (OUTLIER) cc_final: 0.7416 (p0) REVERT: c 89 MET cc_start: 0.7740 (tpt) cc_final: 0.7463 (tpt) REVERT: d 146 ASP cc_start: 0.8104 (m-30) cc_final: 0.7808 (m-30) REVERT: e 175 MET cc_start: 0.9201 (ptm) cc_final: 0.8835 (ptp) REVERT: g 83 ASP cc_start: 0.8803 (m-30) cc_final: 0.8521 (t0) REVERT: g 89 MET cc_start: 0.8607 (tpp) cc_final: 0.8305 (tpp) REVERT: g 168 LYS cc_start: 0.8791 (mmpt) cc_final: 0.8517 (mmmt) REVERT: h 53 ASN cc_start: 0.8933 (m-40) cc_final: 0.8492 (t0) REVERT: h 131 LEU cc_start: 0.9575 (mt) cc_final: 0.9230 (pp) REVERT: i 96 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8391 (pp) REVERT: i 158 ASP cc_start: 0.8260 (p0) cc_final: 0.7932 (p0) REVERT: i 168 LYS cc_start: 0.8674 (mtmm) cc_final: 0.8447 (mptt) REVERT: k 78 HIS cc_start: 0.8472 (OUTLIER) cc_final: 0.7822 (t-90) REVERT: l 21 LEU cc_start: 0.8718 (mt) cc_final: 0.8466 (pp) REVERT: B 155 GLU cc_start: 0.8174 (tp30) cc_final: 0.7555 (tp30) REVERT: B 234 GLU cc_start: 0.5888 (pm20) cc_final: 0.5677 (pm20) REVERT: B 381 TRP cc_start: 0.8585 (m100) cc_final: 0.8278 (m100) REVERT: B 390 MET cc_start: 0.8166 (OUTLIER) cc_final: 0.6932 (ppp) REVERT: B 414 GLU cc_start: 0.9388 (mm-30) cc_final: 0.9178 (mm-30) REVERT: G 147 MET cc_start: 0.8105 (mmp) cc_final: 0.7378 (tpp) REVERT: G 416 MET cc_start: -0.0901 (ttt) cc_final: -0.1879 (ptm) REVERT: G 418 ARG cc_start: 0.7479 (ptt-90) cc_final: 0.6879 (mmt180) REVERT: N 164 LEU cc_start: 0.9525 (mm) cc_final: 0.9028 (mm) REVERT: N 360 TYR cc_start: 0.8931 (t80) cc_final: 0.8636 (t80) REVERT: N 377 LEU cc_start: 0.9542 (OUTLIER) cc_final: 0.9279 (pp) REVERT: N 402 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8855 (ptmm) REVERT: N 415 MET cc_start: 0.9067 (ppp) cc_final: 0.8806 (ppp) REVERT: F 298 LYS cc_start: 0.8720 (tttp) cc_final: 0.8455 (mtpt) REVERT: F 390 MET cc_start: 0.5833 (ppp) cc_final: 0.4935 (ppp) REVERT: F 415 MET cc_start: 0.8691 (ppp) cc_final: 0.8076 (ppp) REVERT: F 416 MET cc_start: 0.9173 (tpp) cc_final: 0.8698 (mmm) outliers start: 144 outliers final: 113 residues processed: 714 average time/residue: 0.4936 time to fit residues: 607.7777 Evaluate side-chains 714 residues out of total 5838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 588 time to evaluate : 4.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 241 GLN Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 295 HIS Chi-restraints excluded: chain C residue 405 MET Chi-restraints excluded: chain D residue 64 PHE Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 295 HIS Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain J residue 21 MET Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 247 ILE Chi-restraints excluded: chain J residue 327 MET Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 154 THR Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 188 LEU Chi-restraints excluded: chain K residue 216 VAL Chi-restraints excluded: chain K residue 227 VAL Chi-restraints excluded: chain K residue 234 GLU Chi-restraints excluded: chain K residue 267 ILE Chi-restraints excluded: chain K residue 390 MET Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 91 LEU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 188 LEU Chi-restraints excluded: chain L residue 209 ILE Chi-restraints excluded: chain L residue 227 VAL Chi-restraints excluded: chain L residue 254 VAL Chi-restraints excluded: chain L residue 338 THR Chi-restraints excluded: chain L residue 343 LEU Chi-restraints excluded: chain M residue 45 SER Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain M residue 131 ILE Chi-restraints excluded: chain M residue 158 THR Chi-restraints excluded: chain M residue 175 LEU Chi-restraints excluded: chain M residue 234 GLU Chi-restraints excluded: chain M residue 242 VAL Chi-restraints excluded: chain M residue 261 ILE Chi-restraints excluded: chain M residue 262 ILE Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 274 TYR Chi-restraints excluded: chain O residue 369 GLU Chi-restraints excluded: chain O residue 390 MET Chi-restraints excluded: chain O residue 394 ASP Chi-restraints excluded: chain c residue 100 LEU Chi-restraints excluded: chain c residue 130 LEU Chi-restraints excluded: chain d residue 120 GLN Chi-restraints excluded: chain d residue 124 ASP Chi-restraints excluded: chain d residue 173 GLN Chi-restraints excluded: chain f residue 45 VAL Chi-restraints excluded: chain f residue 170 THR Chi-restraints excluded: chain g residue 53 ASN Chi-restraints excluded: chain h residue 142 TYR Chi-restraints excluded: chain h residue 162 VAL Chi-restraints excluded: chain i residue 11 ASP Chi-restraints excluded: chain i residue 25 ASN Chi-restraints excluded: chain i residue 53 ASN Chi-restraints excluded: chain i residue 96 LEU Chi-restraints excluded: chain i residue 152 THR Chi-restraints excluded: chain j residue 124 ASP Chi-restraints excluded: chain k residue 15 ASN Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 78 HIS Chi-restraints excluded: chain k residue 131 LEU Chi-restraints excluded: chain l residue 158 ASP Chi-restraints excluded: chain l residue 162 VAL Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 275 ASN Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain B residue 390 MET Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 218 GLU Chi-restraints excluded: chain G residue 260 VAL Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain G residue 376 GLU Chi-restraints excluded: chain G residue 383 LEU Chi-restraints excluded: chain G residue 390 MET Chi-restraints excluded: chain G residue 401 ASN Chi-restraints excluded: chain G residue 411 ASP Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 203 VAL Chi-restraints excluded: chain N residue 208 LEU Chi-restraints excluded: chain N residue 253 LEU Chi-restraints excluded: chain N residue 260 VAL Chi-restraints excluded: chain N residue 284 VAL Chi-restraints excluded: chain N residue 348 LYS Chi-restraints excluded: chain N residue 354 VAL Chi-restraints excluded: chain N residue 377 LEU Chi-restraints excluded: chain N residue 398 PHE Chi-restraints excluded: chain N residue 402 LYS Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 351 GLU Chi-restraints excluded: chain F residue 354 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 672 random chunks: chunk 589 optimal weight: 30.0000 chunk 620 optimal weight: 6.9990 chunk 566 optimal weight: 20.0000 chunk 603 optimal weight: 2.9990 chunk 363 optimal weight: 6.9990 chunk 262 optimal weight: 1.9990 chunk 473 optimal weight: 10.0000 chunk 185 optimal weight: 0.8980 chunk 545 optimal weight: 2.9990 chunk 570 optimal weight: 3.9990 chunk 601 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 295 HIS ** E 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 378 GLN ** J 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 374 GLN ** M 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 173 GLN ** f 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 141 ASN ** j 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 55540 Z= 0.234 Angle : 0.713 17.373 74928 Z= 0.350 Chirality : 0.044 0.351 8454 Planarity : 0.004 0.071 9770 Dihedral : 7.396 84.337 7988 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.87 % Favored : 97.10 % Rotamer: Outliers : 2.76 % Allowed : 20.08 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.27 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.58 (0.10), residues: 6854 helix: 1.02 (0.08), residues: 3855 sheet: -0.05 (0.21), residues: 662 loop : -0.39 (0.13), residues: 2337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 381 HIS 0.012 0.001 HIS J 388 PHE 0.034 0.001 PHE B 300 TYR 0.044 0.002 TYR B 72 ARG 0.013 0.000 ARG N 299 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13708 Ramachandran restraints generated. 6854 Oldfield, 0 Emsley, 6854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13708 Ramachandran restraints generated. 6854 Oldfield, 0 Emsley, 6854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 758 residues out of total 5838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 597 time to evaluate : 4.877 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: C 186 MET cc_start: 0.8491 (ptt) cc_final: 0.8219 (ptt) REVERT: C 189 GLN cc_start: 0.9024 (mt0) cc_final: 0.8546 (mp10) REVERT: C 215 GLU cc_start: 0.9147 (mp0) cc_final: 0.8516 (mp0) REVERT: C 341 MET cc_start: 0.9328 (ppp) cc_final: 0.9044 (ppp) REVERT: C 380 MET cc_start: 0.9077 (mtt) cc_final: 0.8716 (mpp) REVERT: C 390 MET cc_start: 0.9000 (pmm) cc_final: 0.8723 (pmm) REVERT: C 418 ARG cc_start: 0.8758 (mtm110) cc_final: 0.8385 (mtm110) REVERT: D 21 MET cc_start: 0.8418 (ppp) cc_final: 0.8016 (ppp) REVERT: D 32 GLN cc_start: 0.8946 (mp10) cc_final: 0.8441 (mp10) REVERT: D 62 PHE cc_start: 0.7687 (t80) cc_final: 0.7294 (t80) REVERT: D 157 LEU cc_start: 0.9223 (pt) cc_final: 0.8633 (tp) REVERT: D 219 MET cc_start: 0.9289 (tpt) cc_final: 0.9036 (tpp) REVERT: D 245 MET cc_start: 0.8631 (mmt) cc_final: 0.7895 (mpp) REVERT: D 309 GLU cc_start: 0.8944 (pp20) cc_final: 0.8684 (pp20) REVERT: D 329 GLU cc_start: 0.8514 (tp30) cc_final: 0.8166 (tp30) REVERT: D 390 MET cc_start: 0.8928 (pmm) cc_final: 0.8678 (pmm) REVERT: D 417 LYS cc_start: 0.9083 (pptt) cc_final: 0.8812 (mptt) REVERT: E 29 MET cc_start: 0.7249 (pmm) cc_final: 0.6715 (pmm) REVERT: E 144 ARG cc_start: 0.8400 (tpt-90) cc_final: 0.7811 (tpt-90) REVERT: E 147 MET cc_start: 0.8436 (mmm) cc_final: 0.8019 (mmp) REVERT: E 164 LEU cc_start: 0.9633 (mm) cc_final: 0.9373 (mm) REVERT: E 219 MET cc_start: 0.9352 (mmm) cc_final: 0.9084 (mmm) REVERT: E 259 ASP cc_start: 0.8577 (m-30) cc_final: 0.8309 (m-30) REVERT: E 360 TYR cc_start: 0.8490 (t80) cc_final: 0.8170 (t80) REVERT: E 368 GLU cc_start: 0.9048 (pm20) cc_final: 0.8803 (pm20) REVERT: E 415 MET cc_start: 0.8699 (tmm) cc_final: 0.8303 (tmm) REVERT: J 21 MET cc_start: 0.4381 (OUTLIER) cc_final: 0.3634 (ppp) REVERT: J 31 LYS cc_start: 0.6646 (mptt) cc_final: 0.5700 (ptpt) REVERT: J 52 ASP cc_start: 0.3592 (p0) cc_final: 0.3285 (p0) REVERT: J 59 GLN cc_start: 0.7910 (mp10) cc_final: 0.7402 (pp30) REVERT: J 91 LEU cc_start: 0.6037 (OUTLIER) cc_final: 0.5712 (pp) REVERT: J 147 MET cc_start: 0.5458 (mmm) cc_final: 0.5121 (mmt) REVERT: J 186 MET cc_start: 0.4194 (pmm) cc_final: 0.3685 (pmm) REVERT: J 224 LYS cc_start: 0.5482 (mppt) cc_final: 0.4344 (pttm) REVERT: J 295 HIS cc_start: 0.8728 (m-70) cc_final: 0.8443 (m-70) REVERT: J 380 MET cc_start: 0.6984 (mpp) cc_final: 0.6436 (mmm) REVERT: J 416 MET cc_start: 0.3409 (tpt) cc_final: 0.3112 (tpt) REVERT: K 186 MET cc_start: 0.8558 (pmm) cc_final: 0.7564 (ptm) REVERT: K 219 MET cc_start: 0.9452 (tpp) cc_final: 0.9226 (mmm) REVERT: K 234 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7461 (pm20) REVERT: K 245 MET cc_start: 0.8516 (tpt) cc_final: 0.8220 (tpt) REVERT: K 341 MET cc_start: 0.8915 (mmm) cc_final: 0.8540 (mmm) REVERT: K 381 TRP cc_start: 0.8630 (m-10) cc_final: 0.8046 (m-10) REVERT: K 390 MET cc_start: 0.8317 (OUTLIER) cc_final: 0.7162 (ptt) REVERT: L 21 MET cc_start: 0.8677 (OUTLIER) cc_final: 0.8223 (tmm) REVERT: L 26 LEU cc_start: 0.9294 (tp) cc_final: 0.8976 (tp) REVERT: L 56 GLU cc_start: 0.8067 (tm-30) cc_final: 0.7609 (tm-30) REVERT: L 58 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8640 (mt) REVERT: L 244 GLU cc_start: 0.8482 (mm-30) cc_final: 0.8005 (mm-30) REVERT: L 259 ASP cc_start: 0.7394 (m-30) cc_final: 0.6912 (m-30) REVERT: L 341 MET cc_start: 0.8825 (tmm) cc_final: 0.8009 (tmm) REVERT: M 2 ASN cc_start: 0.8100 (t0) cc_final: 0.7692 (t0) REVERT: M 234 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7555 (pm20) REVERT: M 244 GLU cc_start: 0.8718 (mm-30) cc_final: 0.8201 (mm-30) REVERT: M 265 ASP cc_start: 0.8684 (t0) cc_final: 0.7786 (p0) REVERT: M 326 LYS cc_start: 0.8843 (mmmt) cc_final: 0.8395 (ptmm) REVERT: M 333 GLU cc_start: 0.9074 (mt-10) cc_final: 0.8739 (mm-30) REVERT: M 362 ARG cc_start: 0.9271 (ttm-80) cc_final: 0.9017 (ttp-110) REVERT: O 29 MET cc_start: 0.1355 (tmm) cc_final: 0.1121 (ttp) REVERT: O 80 TYR cc_start: 0.7723 (t80) cc_final: 0.7517 (t80) REVERT: O 390 MET cc_start: 0.6216 (OUTLIER) cc_final: 0.4617 (ppp) REVERT: O 394 ASP cc_start: 0.7894 (OUTLIER) cc_final: 0.7442 (p0) REVERT: d 146 ASP cc_start: 0.8138 (m-30) cc_final: 0.7826 (m-30) REVERT: e 175 MET cc_start: 0.9203 (ptm) cc_final: 0.8857 (ptp) REVERT: g 89 MET cc_start: 0.8623 (tpp) cc_final: 0.8299 (tpp) REVERT: g 168 LYS cc_start: 0.8856 (mmpt) cc_final: 0.8577 (mmmt) REVERT: h 131 LEU cc_start: 0.9580 (mt) cc_final: 0.9242 (pp) REVERT: i 96 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8438 (pp) REVERT: i 158 ASP cc_start: 0.8290 (p0) cc_final: 0.7993 (p0) REVERT: i 168 LYS cc_start: 0.8683 (mtmm) cc_final: 0.8453 (mptt) REVERT: k 78 HIS cc_start: 0.8495 (OUTLIER) cc_final: 0.7833 (t-90) REVERT: k 155 PHE cc_start: 0.5772 (m-80) cc_final: 0.5448 (m-10) REVERT: l 21 LEU cc_start: 0.8713 (mt) cc_final: 0.8472 (pp) REVERT: B 145 LEU cc_start: 0.6504 (OUTLIER) cc_final: 0.6286 (mm) REVERT: B 155 GLU cc_start: 0.8191 (tp30) cc_final: 0.7710 (tp30) REVERT: B 381 TRP cc_start: 0.8654 (m100) cc_final: 0.8330 (m100) REVERT: B 390 MET cc_start: 0.8219 (OUTLIER) cc_final: 0.6891 (ppp) REVERT: B 414 GLU cc_start: 0.9412 (mm-30) cc_final: 0.9202 (mm-30) REVERT: G 147 MET cc_start: 0.8127 (mmp) cc_final: 0.7347 (tpp) REVERT: G 416 MET cc_start: -0.0918 (ttt) cc_final: -0.1424 (ptm) REVERT: G 418 ARG cc_start: 0.7471 (ptt-90) cc_final: 0.6840 (mmt180) REVERT: N 29 MET cc_start: 0.2825 (ptp) cc_final: 0.2623 (ptp) REVERT: N 377 LEU cc_start: 0.9554 (OUTLIER) cc_final: 0.9279 (pp) REVERT: N 402 LYS cc_start: 0.9072 (OUTLIER) cc_final: 0.8815 (ptmm) REVERT: N 415 MET cc_start: 0.9091 (ppp) cc_final: 0.8860 (ppp) REVERT: F 298 LYS cc_start: 0.8763 (tttp) cc_final: 0.8503 (mtpt) REVERT: F 415 MET cc_start: 0.8719 (ppp) cc_final: 0.8191 (ppp) REVERT: F 416 MET cc_start: 0.9176 (tpp) cc_final: 0.8702 (mmm) outliers start: 161 outliers final: 122 residues processed: 713 average time/residue: 0.4793 time to fit residues: 591.4313 Evaluate side-chains 712 residues out of total 5838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 575 time to evaluate : 4.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 241 GLN Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 295 HIS Chi-restraints excluded: chain C residue 405 MET Chi-restraints excluded: chain D residue 64 PHE Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 295 HIS Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain J residue 21 MET Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 247 ILE Chi-restraints excluded: chain J residue 327 MET Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 133 PHE Chi-restraints excluded: chain K residue 154 THR Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 188 LEU Chi-restraints excluded: chain K residue 216 VAL Chi-restraints excluded: chain K residue 227 VAL Chi-restraints excluded: chain K residue 234 GLU Chi-restraints excluded: chain K residue 267 ILE Chi-restraints excluded: chain K residue 390 MET Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 91 LEU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 164 LEU Chi-restraints excluded: chain L residue 188 LEU Chi-restraints excluded: chain L residue 209 ILE Chi-restraints excluded: chain L residue 227 VAL Chi-restraints excluded: chain L residue 254 VAL Chi-restraints excluded: chain L residue 338 THR Chi-restraints excluded: chain L residue 343 LEU Chi-restraints excluded: chain M residue 4 THR Chi-restraints excluded: chain M residue 45 SER Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain M residue 131 ILE Chi-restraints excluded: chain M residue 158 THR Chi-restraints excluded: chain M residue 175 LEU Chi-restraints excluded: chain M residue 234 GLU Chi-restraints excluded: chain M residue 242 VAL Chi-restraints excluded: chain M residue 261 ILE Chi-restraints excluded: chain M residue 262 ILE Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 274 TYR Chi-restraints excluded: chain O residue 12 SER Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 313 LEU Chi-restraints excluded: chain O residue 369 GLU Chi-restraints excluded: chain O residue 390 MET Chi-restraints excluded: chain O residue 394 ASP Chi-restraints excluded: chain c residue 100 LEU Chi-restraints excluded: chain c residue 130 LEU Chi-restraints excluded: chain d residue 120 GLN Chi-restraints excluded: chain d residue 124 ASP Chi-restraints excluded: chain e residue 109 GLU Chi-restraints excluded: chain f residue 45 VAL Chi-restraints excluded: chain f residue 170 THR Chi-restraints excluded: chain g residue 49 ASP Chi-restraints excluded: chain g residue 53 ASN Chi-restraints excluded: chain h residue 142 TYR Chi-restraints excluded: chain h residue 162 VAL Chi-restraints excluded: chain i residue 11 ASP Chi-restraints excluded: chain i residue 25 ASN Chi-restraints excluded: chain i residue 53 ASN Chi-restraints excluded: chain i residue 96 LEU Chi-restraints excluded: chain i residue 152 THR Chi-restraints excluded: chain j residue 124 ASP Chi-restraints excluded: chain k residue 15 ASN Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 78 HIS Chi-restraints excluded: chain k residue 131 LEU Chi-restraints excluded: chain l residue 158 ASP Chi-restraints excluded: chain l residue 162 VAL Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 275 ASN Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain B residue 390 MET Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 218 GLU Chi-restraints excluded: chain G residue 260 VAL Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain G residue 376 GLU Chi-restraints excluded: chain G residue 383 LEU Chi-restraints excluded: chain G residue 390 MET Chi-restraints excluded: chain G residue 401 ASN Chi-restraints excluded: chain G residue 411 ASP Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 203 VAL Chi-restraints excluded: chain N residue 208 LEU Chi-restraints excluded: chain N residue 227 VAL Chi-restraints excluded: chain N residue 253 LEU Chi-restraints excluded: chain N residue 260 VAL Chi-restraints excluded: chain N residue 274 TYR Chi-restraints excluded: chain N residue 284 VAL Chi-restraints excluded: chain N residue 348 LYS Chi-restraints excluded: chain N residue 354 VAL Chi-restraints excluded: chain N residue 377 LEU Chi-restraints excluded: chain N residue 398 PHE Chi-restraints excluded: chain N residue 402 LYS Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 351 GLU Chi-restraints excluded: chain F residue 354 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 672 random chunks: chunk 396 optimal weight: 7.9990 chunk 638 optimal weight: 20.0000 chunk 389 optimal weight: 0.9980 chunk 302 optimal weight: 10.0000 chunk 443 optimal weight: 0.9990 chunk 669 optimal weight: 6.9990 chunk 616 optimal weight: 0.0980 chunk 533 optimal weight: 0.5980 chunk 55 optimal weight: 4.9990 chunk 411 optimal weight: 4.9990 chunk 326 optimal weight: 8.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 295 HIS ** E 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 275 ASN ** O 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 53 ASN i 141 ASN ** j 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 ASN ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.3926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 55540 Z= 0.195 Angle : 0.722 16.391 74928 Z= 0.351 Chirality : 0.044 0.352 8454 Planarity : 0.004 0.070 9770 Dihedral : 7.337 84.571 7988 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.90 % Favored : 97.08 % Rotamer: Outliers : 2.40 % Allowed : 20.76 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.27 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.62 (0.10), residues: 6854 helix: 1.06 (0.08), residues: 3797 sheet: -0.04 (0.21), residues: 661 loop : -0.38 (0.13), residues: 2396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 381 HIS 0.012 0.001 HIS J 388 PHE 0.028 0.001 PHE B 300 TYR 0.040 0.002 TYR B 72 ARG 0.012 0.000 ARG N 299 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13708 Ramachandran restraints generated. 6854 Oldfield, 0 Emsley, 6854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13708 Ramachandran restraints generated. 6854 Oldfield, 0 Emsley, 6854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 752 residues out of total 5838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 612 time to evaluate : 4.937 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: C 186 MET cc_start: 0.8397 (ptt) cc_final: 0.8112 (ptt) REVERT: C 189 GLN cc_start: 0.8996 (mt0) cc_final: 0.8502 (mp10) REVERT: C 215 GLU cc_start: 0.9114 (mp0) cc_final: 0.8556 (mp0) REVERT: C 341 MET cc_start: 0.9313 (ppp) cc_final: 0.9051 (ppp) REVERT: C 380 MET cc_start: 0.9103 (mtt) cc_final: 0.8713 (mpp) REVERT: C 390 MET cc_start: 0.8997 (pmm) cc_final: 0.8710 (pmm) REVERT: C 414 GLU cc_start: 0.8931 (tp30) cc_final: 0.8700 (tp30) REVERT: C 418 ARG cc_start: 0.8757 (mtm110) cc_final: 0.8376 (mtm110) REVERT: D 21 MET cc_start: 0.8431 (ppp) cc_final: 0.8022 (ppp) REVERT: D 32 GLN cc_start: 0.8930 (mp10) cc_final: 0.8434 (mp10) REVERT: D 62 PHE cc_start: 0.7646 (t80) cc_final: 0.7243 (t80) REVERT: D 157 LEU cc_start: 0.9220 (pt) cc_final: 0.8613 (tp) REVERT: D 219 MET cc_start: 0.9263 (tpt) cc_final: 0.9011 (tpp) REVERT: D 233 ASP cc_start: 0.8890 (m-30) cc_final: 0.8688 (t0) REVERT: D 245 MET cc_start: 0.8648 (mmt) cc_final: 0.7914 (mpp) REVERT: D 329 GLU cc_start: 0.8513 (tp30) cc_final: 0.8169 (tp30) REVERT: D 390 MET cc_start: 0.8922 (pmm) cc_final: 0.8653 (pmm) REVERT: E 29 MET cc_start: 0.7174 (pmm) cc_final: 0.6666 (pmm) REVERT: E 144 ARG cc_start: 0.8394 (tpt-90) cc_final: 0.7866 (tpt-90) REVERT: E 147 MET cc_start: 0.8414 (mmm) cc_final: 0.7992 (mmp) REVERT: E 219 MET cc_start: 0.9343 (mmm) cc_final: 0.9075 (mmm) REVERT: E 248 GLU cc_start: 0.8577 (tt0) cc_final: 0.8356 (tt0) REVERT: E 259 ASP cc_start: 0.8575 (m-30) cc_final: 0.8301 (m-30) REVERT: E 360 TYR cc_start: 0.8434 (t80) cc_final: 0.8144 (t80) REVERT: E 368 GLU cc_start: 0.9053 (pm20) cc_final: 0.8786 (pm20) REVERT: E 380 MET cc_start: 0.9543 (mtp) cc_final: 0.9305 (mmt) REVERT: E 414 GLU cc_start: 0.9342 (tp30) cc_final: 0.9093 (mm-30) REVERT: E 415 MET cc_start: 0.8733 (tmm) cc_final: 0.8254 (tmm) REVERT: J 21 MET cc_start: 0.4541 (OUTLIER) cc_final: 0.4089 (tmm) REVERT: J 31 LYS cc_start: 0.6679 (mptt) cc_final: 0.5814 (ptpt) REVERT: J 52 ASP cc_start: 0.3569 (p0) cc_final: 0.3276 (p0) REVERT: J 59 GLN cc_start: 0.7902 (mp10) cc_final: 0.7402 (pp30) REVERT: J 91 LEU cc_start: 0.6079 (OUTLIER) cc_final: 0.5774 (pp) REVERT: J 147 MET cc_start: 0.5589 (mmm) cc_final: 0.5343 (mmt) REVERT: J 186 MET cc_start: 0.4069 (pmm) cc_final: 0.3564 (pmm) REVERT: J 224 LYS cc_start: 0.5418 (mppt) cc_final: 0.4303 (pttm) REVERT: J 295 HIS cc_start: 0.8724 (m-70) cc_final: 0.8437 (m-70) REVERT: J 380 MET cc_start: 0.6970 (mpp) cc_final: 0.6446 (mmm) REVERT: J 416 MET cc_start: 0.3335 (tpt) cc_final: 0.3047 (tpt) REVERT: K 186 MET cc_start: 0.8568 (pmm) cc_final: 0.7581 (ptm) REVERT: K 219 MET cc_start: 0.9440 (tpp) cc_final: 0.9211 (mmm) REVERT: K 234 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7538 (pm20) REVERT: K 245 MET cc_start: 0.8473 (tpt) cc_final: 0.8162 (tpt) REVERT: K 248 GLU cc_start: 0.8505 (tt0) cc_final: 0.8247 (tt0) REVERT: K 341 MET cc_start: 0.8899 (mmm) cc_final: 0.8494 (mmm) REVERT: K 390 MET cc_start: 0.8305 (OUTLIER) cc_final: 0.7144 (ptt) REVERT: L 26 LEU cc_start: 0.9279 (tp) cc_final: 0.8954 (tp) REVERT: L 56 GLU cc_start: 0.8136 (tm-30) cc_final: 0.7891 (tm-30) REVERT: L 58 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8572 (mt) REVERT: L 244 GLU cc_start: 0.8495 (mm-30) cc_final: 0.8008 (mm-30) REVERT: L 259 ASP cc_start: 0.7373 (m-30) cc_final: 0.6888 (m-30) REVERT: L 341 MET cc_start: 0.8838 (tmm) cc_final: 0.8124 (tmm) REVERT: M 234 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7487 (pm20) REVERT: M 244 GLU cc_start: 0.8701 (mm-30) cc_final: 0.8187 (mm-30) REVERT: M 265 ASP cc_start: 0.8630 (t0) cc_final: 0.7776 (p0) REVERT: M 326 LYS cc_start: 0.8827 (mmmt) cc_final: 0.8409 (ptmm) REVERT: M 333 GLU cc_start: 0.9079 (mt-10) cc_final: 0.8725 (mm-30) REVERT: M 362 ARG cc_start: 0.9284 (ttm-80) cc_final: 0.9018 (ttp-110) REVERT: O 29 MET cc_start: 0.1326 (tmm) cc_final: 0.1095 (ttp) REVERT: O 390 MET cc_start: 0.6162 (OUTLIER) cc_final: 0.4564 (ppp) REVERT: O 394 ASP cc_start: 0.7880 (OUTLIER) cc_final: 0.7386 (p0) REVERT: d 146 ASP cc_start: 0.8127 (m-30) cc_final: 0.7821 (m-30) REVERT: e 175 MET cc_start: 0.9189 (ptm) cc_final: 0.8863 (ptp) REVERT: g 89 MET cc_start: 0.8655 (tpp) cc_final: 0.8334 (tpp) REVERT: g 168 LYS cc_start: 0.8826 (mmpt) cc_final: 0.8537 (mmmt) REVERT: h 53 ASN cc_start: 0.9097 (OUTLIER) cc_final: 0.8297 (t0) REVERT: h 131 LEU cc_start: 0.9580 (mt) cc_final: 0.9253 (pp) REVERT: i 96 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8453 (pp) REVERT: i 158 ASP cc_start: 0.8287 (p0) cc_final: 0.8022 (p0) REVERT: i 168 LYS cc_start: 0.8680 (mtmm) cc_final: 0.8451 (mptt) REVERT: k 78 HIS cc_start: 0.8473 (OUTLIER) cc_final: 0.7831 (t-90) REVERT: l 21 LEU cc_start: 0.8717 (mt) cc_final: 0.8485 (pp) REVERT: B 80 TYR cc_start: 0.6643 (m-80) cc_final: 0.6226 (m-80) REVERT: B 155 GLU cc_start: 0.8157 (tp30) cc_final: 0.7703 (tp30) REVERT: B 381 TRP cc_start: 0.8643 (m100) cc_final: 0.8331 (m100) REVERT: B 390 MET cc_start: 0.8186 (OUTLIER) cc_final: 0.6920 (ppp) REVERT: B 414 GLU cc_start: 0.9416 (mm-30) cc_final: 0.9205 (mm-30) REVERT: G 147 MET cc_start: 0.8181 (mmp) cc_final: 0.7428 (tpp) REVERT: G 416 MET cc_start: -0.0858 (ttt) cc_final: -0.1561 (ptm) REVERT: G 418 ARG cc_start: 0.7420 (ptt-90) cc_final: 0.6816 (mmt180) REVERT: N 377 LEU cc_start: 0.9546 (OUTLIER) cc_final: 0.9340 (pp) REVERT: N 402 LYS cc_start: 0.9060 (OUTLIER) cc_final: 0.8800 (ptmm) REVERT: N 403 LEU cc_start: 0.9595 (pp) cc_final: 0.8968 (tt) REVERT: N 415 MET cc_start: 0.9098 (ppp) cc_final: 0.8825 (ppp) REVERT: F 298 LYS cc_start: 0.8759 (tttp) cc_final: 0.8505 (mtpt) REVERT: F 415 MET cc_start: 0.8704 (ppp) cc_final: 0.8186 (ppp) REVERT: F 416 MET cc_start: 0.9166 (tpp) cc_final: 0.8704 (mmm) outliers start: 140 outliers final: 114 residues processed: 708 average time/residue: 0.4863 time to fit residues: 597.4013 Evaluate side-chains 713 residues out of total 5838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 585 time to evaluate : 4.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 241 GLN Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain D residue 64 PHE Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 295 HIS Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain J residue 21 MET Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 247 ILE Chi-restraints excluded: chain J residue 327 MET Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 154 THR Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 188 LEU Chi-restraints excluded: chain K residue 216 VAL Chi-restraints excluded: chain K residue 227 VAL Chi-restraints excluded: chain K residue 234 GLU Chi-restraints excluded: chain K residue 267 ILE Chi-restraints excluded: chain K residue 390 MET Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 91 LEU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 164 LEU Chi-restraints excluded: chain L residue 188 LEU Chi-restraints excluded: chain L residue 209 ILE Chi-restraints excluded: chain L residue 227 VAL Chi-restraints excluded: chain L residue 254 VAL Chi-restraints excluded: chain L residue 294 LEU Chi-restraints excluded: chain L residue 338 THR Chi-restraints excluded: chain L residue 343 LEU Chi-restraints excluded: chain L residue 416 MET Chi-restraints excluded: chain M residue 4 THR Chi-restraints excluded: chain M residue 45 SER Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain M residue 131 ILE Chi-restraints excluded: chain M residue 158 THR Chi-restraints excluded: chain M residue 175 LEU Chi-restraints excluded: chain M residue 234 GLU Chi-restraints excluded: chain M residue 242 VAL Chi-restraints excluded: chain M residue 261 ILE Chi-restraints excluded: chain M residue 262 ILE Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 193 GLN Chi-restraints excluded: chain O residue 390 MET Chi-restraints excluded: chain O residue 394 ASP Chi-restraints excluded: chain c residue 100 LEU Chi-restraints excluded: chain c residue 130 LEU Chi-restraints excluded: chain d residue 120 GLN Chi-restraints excluded: chain d residue 124 ASP Chi-restraints excluded: chain f residue 45 VAL Chi-restraints excluded: chain f residue 170 THR Chi-restraints excluded: chain g residue 53 ASN Chi-restraints excluded: chain h residue 53 ASN Chi-restraints excluded: chain h residue 142 TYR Chi-restraints excluded: chain h residue 162 VAL Chi-restraints excluded: chain i residue 11 ASP Chi-restraints excluded: chain i residue 25 ASN Chi-restraints excluded: chain i residue 53 ASN Chi-restraints excluded: chain i residue 96 LEU Chi-restraints excluded: chain i residue 152 THR Chi-restraints excluded: chain j residue 124 ASP Chi-restraints excluded: chain k residue 15 ASN Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 78 HIS Chi-restraints excluded: chain k residue 131 LEU Chi-restraints excluded: chain l residue 158 ASP Chi-restraints excluded: chain l residue 162 VAL Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 275 ASN Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain B residue 390 MET Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 218 GLU Chi-restraints excluded: chain G residue 260 VAL Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain G residue 376 GLU Chi-restraints excluded: chain G residue 383 LEU Chi-restraints excluded: chain G residue 390 MET Chi-restraints excluded: chain G residue 401 ASN Chi-restraints excluded: chain G residue 411 ASP Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 162 LEU Chi-restraints excluded: chain N residue 203 VAL Chi-restraints excluded: chain N residue 208 LEU Chi-restraints excluded: chain N residue 253 LEU Chi-restraints excluded: chain N residue 260 VAL Chi-restraints excluded: chain N residue 284 VAL Chi-restraints excluded: chain N residue 348 LYS Chi-restraints excluded: chain N residue 354 VAL Chi-restraints excluded: chain N residue 377 LEU Chi-restraints excluded: chain N residue 398 PHE Chi-restraints excluded: chain N residue 402 LYS Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 351 GLU Chi-restraints excluded: chain F residue 354 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 672 random chunks: chunk 423 optimal weight: 5.9990 chunk 567 optimal weight: 20.0000 chunk 163 optimal weight: 8.9990 chunk 491 optimal weight: 5.9990 chunk 78 optimal weight: 0.0570 chunk 148 optimal weight: 8.9990 chunk 533 optimal weight: 5.9990 chunk 223 optimal weight: 1.9990 chunk 548 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 98 optimal weight: 0.0040 overall best weight: 1.0116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 53 ASN i 141 ASN ** j 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.062901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.047868 restraints weight = 356672.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.048570 restraints weight = 207534.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.049043 restraints weight = 135640.588| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.3946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 55540 Z= 0.185 Angle : 0.741 16.208 74928 Z= 0.357 Chirality : 0.044 0.349 8454 Planarity : 0.004 0.067 9770 Dihedral : 7.285 84.490 7988 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.89 % Favored : 97.10 % Rotamer: Outliers : 2.38 % Allowed : 21.00 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.27 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.60 (0.10), residues: 6854 helix: 1.04 (0.08), residues: 3797 sheet: -0.01 (0.21), residues: 661 loop : -0.38 (0.13), residues: 2396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP E 381 HIS 0.012 0.001 HIS J 388 PHE 0.026 0.001 PHE B 300 TYR 0.038 0.002 TYR B 72 ARG 0.012 0.000 ARG h 179 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11137.81 seconds wall clock time: 196 minutes 58.44 seconds (11818.44 seconds total)