Starting phenix.real_space_refine on Fri Jan 17 02:58:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gcs_51235/01_2025/9gcs_51235.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gcs_51235/01_2025/9gcs_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_51235/01_2025/9gcs_51235.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gcs_51235/01_2025/9gcs_51235.map" model { file = "/net/cci-nas-00/data/ceres_data/9gcs_51235/01_2025/9gcs_51235.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gcs_51235/01_2025/9gcs_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-5571/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: 23.17, per 1000 atoms: 0.42 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: 10.17 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: 5.89 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: 21.11 Time building geometry restraints manager: 12.01 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: 0.02 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: 4.450 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: 0.060 Extract box with map and model: 1.690 Check model and map are aligned: 0.310 Set scattering table: 0.380 Process input model: 97.410 Find NCS groups from input model: 2.030 Set up NCS constraints: 0.400 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:2.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.110 ------------------------------------------------------------------------------- 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 : 4.770 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: 0.5191 time to fit residues: 959.2613 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 : 4.729 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.065541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.050197 restraints weight = 368634.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.051022 restraints weight = 216872.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.051907 restraints weight = 140505.196| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 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 : 4.742 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: 0.8752 (mt0) cc_final: 0.8220 (mp10) REVERT: C 326 LYS cc_start: 0.8327 (pptt) cc_final: 0.7545 (pttp) REVERT: D 21 MET cc_start: 0.8402 (ppp) cc_final: 0.8146 (ppp) REVERT: D 62 PHE cc_start: 0.7109 (t80) cc_final: 0.6819 (t80) REVERT: D 157 LEU cc_start: 0.9158 (pt) cc_final: 0.8524 (tp) REVERT: D 327 MET cc_start: 0.8098 (ppp) cc_final: 0.7614 (ppp) REVERT: E 21 MET cc_start: 0.8450 (tmm) cc_final: 0.8071 (tmm) REVERT: E 29 MET cc_start: 0.6691 (pmm) cc_final: 0.6052 (pmm) REVERT: E 147 MET cc_start: 0.7972 (mmm) cc_final: 0.7738 (mmp) REVERT: E 164 LEU cc_start: 0.9545 (OUTLIER) cc_final: 0.9314 (mm) REVERT: E 265 ASP cc_start: 0.7823 (t0) cc_final: 0.7609 (t0) REVERT: E 329 GLU cc_start: 0.8239 (tm-30) cc_final: 0.8036 (tm-30) REVERT: E 405 MET cc_start: 0.8687 (ppp) cc_final: 0.8363 (ppp) REVERT: E 414 GLU cc_start: 0.8840 (mm-30) cc_final: 0.8600 (mm-30) REVERT: J 21 MET cc_start: 0.6014 (ppp) cc_final: 0.5373 (tmm) REVERT: J 31 LYS cc_start: 0.7033 (mptt) cc_final: 0.6039 (ptpt) REVERT: J 205 MET cc_start: 0.6375 (pmm) cc_final: 0.6076 (pmm) REVERT: J 228 VAL cc_start: 0.5232 (OUTLIER) cc_final: 0.4614 (m) REVERT: J 380 MET cc_start: 0.7192 (mpp) cc_final: 0.6981 (mpp) REVERT: K 186 MET cc_start: 0.8533 (pmm) cc_final: 0.7922 (ptp) REVERT: K 234 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7718 (pm20) REVERT: K 241 GLN cc_start: 0.8948 (OUTLIER) cc_final: 0.8718 (pp30) REVERT: K 245 MET cc_start: 0.8339 (tpt) cc_final: 0.8090 (tpt) REVERT: K 264 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8816 (tp) REVERT: K 341 MET cc_start: 0.8236 (mmm) cc_final: 0.7110 (mmm) REVERT: L 26 LEU cc_start: 0.9055 (tp) cc_final: 0.8844 (tp) REVERT: L 91 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8771 (pp) REVERT: L 244 GLU cc_start: 0.8336 (mm-30) cc_final: 0.7947 (mm-30) REVERT: L 341 MET cc_start: 0.8706 (tmm) cc_final: 0.8487 (tmm) REVERT: M 4 THR cc_start: 0.8796 (p) cc_final: 0.8496 (p) REVERT: M 244 GLU cc_start: 0.8456 (mm-30) cc_final: 0.7840 (mm-30) REVERT: M 274 TYR cc_start: 0.8962 (m-10) cc_final: 0.8496 (m-10) REVERT: M 411 ASP cc_start: 0.9266 (t0) cc_final: 0.9031 (t0) REVERT: O 245 MET cc_start: 0.8014 (mmm) cc_final: 0.7785 (mmm) REVERT: O 341 MET cc_start: 0.7402 (mmm) cc_final: 0.6545 (mmm) REVERT: O 377 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7889 (mm) REVERT: O 380 MET cc_start: 0.9017 (mmm) cc_final: 0.8390 (mmm) REVERT: O 390 MET cc_start: 0.6743 (OUTLIER) cc_final: 0.6136 (ppp) REVERT: c 64 GLN cc_start: 0.9384 (OUTLIER) cc_final: 0.9020 (mm110) REVERT: d 146 ASP cc_start: 0.8013 (m-30) cc_final: 0.7726 (m-30) REVERT: e 175 MET cc_start: 0.8899 (ptm) cc_final: 0.8625 (ptp) REVERT: g 83 ASP cc_start: 0.8476 (m-30) cc_final: 0.8127 (m-30) REVERT: g 130 LEU cc_start: 0.9449 (mm) cc_final: 0.9227 (mm) REVERT: h 53 ASN cc_start: 0.8884 (t0) cc_final: 0.8616 (t0) REVERT: h 78 HIS cc_start: 0.9108 (t-90) cc_final: 0.8724 (t-90) REVERT: h 116 ASN cc_start: 0.8210 (m-40) cc_final: 0.7895 (m-40) REVERT: h 131 LEU cc_start: 0.9431 (mt) cc_final: 0.9192 (pp) REVERT: h 179 ARG cc_start: 0.8915 (mmm160) cc_final: 0.8382 (mmm160) REVERT: i 158 ASP cc_start: 0.8155 (p0) cc_final: 0.7749 (p0) REVERT: j 51 LEU cc_start: 0.9488 (mt) cc_final: 0.9270 (mt) REVERT: j 124 ASP cc_start: 0.8999 (p0) cc_final: 0.8763 (p0) REVERT: j 140 ILE cc_start: 0.8725 (tp) cc_final: 0.8424 (mm) REVERT: j 176 ILE cc_start: 0.9757 (pt) cc_final: 0.9228 (pt) REVERT: j 180 LYS cc_start: 0.9488 (mmtp) cc_final: 0.9259 (mmtp) REVERT: l 85 LEU cc_start: 0.8566 (pp) cc_final: 0.8271 (pp) REVERT: l 146 ASP cc_start: 0.8909 (t0) cc_final: 0.8571 (t0) REVERT: B 80 TYR cc_start: 0.6289 (m-80) cc_final: 0.6034 (m-80) REVERT: B 155 GLU cc_start: 0.8101 (tp30) cc_final: 0.7527 (tp30) REVERT: B 157 LEU cc_start: 0.9319 (tp) cc_final: 0.8742 (mt) REVERT: B 209 ILE cc_start: 0.9033 (OUTLIER) cc_final: 0.8765 (tp) REVERT: B 230 SER cc_start: 0.8291 (p) cc_final: 0.7854 (p) REVERT: B 381 TRP cc_start: 0.8773 (m100) cc_final: 0.8386 (m100) REVERT: B 390 MET cc_start: 0.8435 (ppp) cc_final: 0.7462 (ppp) REVERT: G 3 LEU cc_start: 0.9641 (tp) cc_final: 0.9291 (mm) REVERT: G 21 MET cc_start: 0.6506 (pmm) cc_final: 0.5795 (pmm) REVERT: G 189 GLN cc_start: 0.9110 (mt0) cc_final: 0.8863 (mt0) REVERT: G 416 MET cc_start: -0.0781 (ttt) cc_final: -0.1467 (ptp) REVERT: G 418 ARG cc_start: 0.7260 (ptt-90) cc_final: 0.6757 (mmt180) REVERT: N 73 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7602 (tp) REVERT: N 360 TYR cc_start: 0.8700 (t80) cc_final: 0.8221 (t80) REVERT: N 397 GLU cc_start: 0.9136 (pt0) cc_final: 0.8897 (pp20) REVERT: N 415 MET cc_start: 0.9185 (ppp) cc_final: 0.8918 (ppp) REVERT: F 326 LYS cc_start: 0.8792 (tptp) cc_final: 0.8297 (tptp) REVERT: F 327 MET cc_start: 0.8462 (ppp) cc_final: 0.8173 (ppp) REVERT: F 329 GLU cc_start: 0.8774 (mp0) cc_final: 0.8527 (mp0) REVERT: F 416 MET cc_start: 0.9060 (mmp) cc_final: 0.8758 (mmm) outliers start: 173 outliers final: 77 residues processed: 832 average time/residue: 0.5119 time to fit residues: 724.6157 Evaluate side-chains 711 residues out of total 5838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 623 time to evaluate : 4.778 ------------------------------------------------------------------------------- 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 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 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 64 GLN 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 618 optimal weight: 0.2980 chunk 511 optimal weight: 3.9990 chunk 128 optimal weight: 6.9990 chunk 284 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 chunk 343 optimal weight: 0.0170 chunk 492 optimal weight: 5.9990 chunk 479 optimal weight: 3.9990 chunk 368 optimal weight: 1.9990 chunk 212 optimal weight: 8.9990 chunk 423 optimal weight: 0.9990 overall best weight: 1.2624 ------------------------------------------------------------------------------- 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 292 ASN ** J 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** d 173 GLN ** 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 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 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 241 GLN 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** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.066109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.050604 restraints weight = 365651.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.051818 restraints weight = 219774.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.052259 restraints weight = 133716.403| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 55540 Z= 0.174 Angle : 0.624 12.992 74928 Z= 0.310 Chirality : 0.042 0.317 8454 Planarity : 0.004 0.054 9770 Dihedral : 7.226 81.968 8006 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.41 % Favored : 97.56 % Rotamer: Outliers : 2.43 % Allowed : 15.47 % Favored : 82.10 % 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: 0.81 (0.10), residues: 6854 helix: 1.19 (0.08), residues: 3855 sheet: 0.29 (0.21), residues: 636 loop : -0.36 (0.13), residues: 2363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 381 HIS 0.014 0.001 HIS k 92 PHE 0.042 0.001 PHE L 413 TYR 0.024 0.001 TYR B 72 ARG 0.010 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 833 residues out of total 5838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 691 time to evaluate : 4.802 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: C 186 MET cc_start: 0.8160 (ptp) cc_final: 0.7942 (ptt) REVERT: C 189 GLN cc_start: 0.8661 (mt0) cc_final: 0.8298 (mp10) REVERT: C 341 MET cc_start: 0.9164 (ppp) cc_final: 0.8779 (tmm) REVERT: D 21 MET cc_start: 0.8381 (ppp) cc_final: 0.8100 (ppp) REVERT: D 62 PHE cc_start: 0.7157 (t80) cc_final: 0.6863 (t80) REVERT: D 157 LEU cc_start: 0.9087 (pt) cc_final: 0.8480 (tp) REVERT: D 327 MET cc_start: 0.8008 (ppp) cc_final: 0.7576 (ppp) REVERT: D 332 TYR cc_start: 0.8217 (t80) cc_final: 0.7970 (t80) REVERT: D 417 LYS cc_start: 0.9036 (pptt) cc_final: 0.8425 (mptt) REVERT: E 29 MET cc_start: 0.6752 (pmm) cc_final: 0.6062 (pmm) REVERT: E 147 MET cc_start: 0.8114 (mmm) cc_final: 0.7855 (mmp) REVERT: E 164 LEU cc_start: 0.9519 (OUTLIER) cc_final: 0.9220 (mm) REVERT: E 219 MET cc_start: 0.9041 (mmm) cc_final: 0.8810 (mmm) REVERT: E 329 GLU cc_start: 0.8230 (tm-30) cc_final: 0.7996 (tm-30) REVERT: E 405 MET cc_start: 0.8659 (ppp) cc_final: 0.8112 (ppp) REVERT: E 414 GLU cc_start: 0.8823 (mm-30) cc_final: 0.8565 (mm-30) REVERT: J 21 MET cc_start: 0.5948 (ppp) cc_final: 0.5197 (tmm) REVERT: J 31 LYS cc_start: 0.7012 (mptt) cc_final: 0.6016 (ptpt) REVERT: J 186 MET cc_start: 0.5656 (pmm) cc_final: 0.5037 (pmm) REVERT: J 228 VAL cc_start: 0.5176 (OUTLIER) cc_final: 0.4808 (m) REVERT: J 415 MET cc_start: 0.4592 (tpp) cc_final: 0.4201 (tpp) REVERT: K 234 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7679 (pm20) REVERT: K 241 GLN cc_start: 0.8928 (OUTLIER) cc_final: 0.8702 (pp30) REVERT: K 245 MET cc_start: 0.8301 (tpt) cc_final: 0.7970 (tpt) REVERT: K 264 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8846 (tp) REVERT: K 341 MET cc_start: 0.8448 (mmm) cc_final: 0.7900 (mmm) REVERT: K 381 TRP cc_start: 0.8554 (m-10) cc_final: 0.8236 (m-10) REVERT: K 415 MET cc_start: 0.8633 (tmm) cc_final: 0.8407 (tmm) REVERT: K 418 ARG cc_start: 0.9158 (ptt90) cc_final: 0.8894 (ptt-90) REVERT: L 244 GLU cc_start: 0.8271 (mm-30) cc_final: 0.7871 (mm-30) REVERT: M 1 MET cc_start: 0.6403 (ppp) cc_final: 0.5912 (ppp) REVERT: M 244 GLU cc_start: 0.8399 (mm-30) cc_final: 0.7743 (mm-30) REVERT: M 261 ILE cc_start: 0.9303 (OUTLIER) cc_final: 0.8891 (pt) REVERT: M 274 TYR cc_start: 0.8928 (m-10) cc_final: 0.8388 (m-10) REVERT: M 327 MET cc_start: 0.7945 (OUTLIER) cc_final: 0.6971 (ppp) REVERT: M 411 ASP cc_start: 0.9276 (t0) cc_final: 0.9051 (t0) REVERT: M 417 LYS cc_start: 0.9470 (pttm) cc_final: 0.9217 (pttp) REVERT: O 245 MET cc_start: 0.8073 (mmm) cc_final: 0.7852 (mmm) REVERT: O 380 MET cc_start: 0.8986 (mmm) cc_final: 0.8246 (mmm) REVERT: O 390 MET cc_start: 0.6753 (OUTLIER) cc_final: 0.6101 (ppp) REVERT: c 64 GLN cc_start: 0.9298 (OUTLIER) cc_final: 0.8881 (mm110) REVERT: d 89 MET cc_start: 0.8004 (ttp) cc_final: 0.7728 (tmm) REVERT: d 146 ASP cc_start: 0.8006 (m-30) cc_final: 0.7734 (m-30) REVERT: e 175 MET cc_start: 0.8793 (ptm) cc_final: 0.8476 (ptp) REVERT: f 21 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8748 (pp) REVERT: g 83 ASP cc_start: 0.8392 (m-30) cc_final: 0.8074 (m-30) REVERT: g 130 LEU cc_start: 0.9448 (mm) cc_final: 0.9220 (mm) REVERT: h 53 ASN cc_start: 0.8873 (t0) cc_final: 0.8470 (t0) REVERT: h 78 HIS cc_start: 0.9121 (t-90) cc_final: 0.8706 (t-90) REVERT: h 116 ASN cc_start: 0.8161 (m-40) cc_final: 0.7841 (m-40) REVERT: h 131 LEU cc_start: 0.9403 (mt) cc_final: 0.9164 (pp) REVERT: i 158 ASP cc_start: 0.8160 (p0) cc_final: 0.7772 (p0) REVERT: j 140 ILE cc_start: 0.8682 (tp) cc_final: 0.8362 (mm) REVERT: j 176 ILE cc_start: 0.9747 (pt) cc_final: 0.9149 (pt) REVERT: j 180 LYS cc_start: 0.9454 (mmtp) cc_final: 0.9229 (mmtp) REVERT: l 21 LEU cc_start: 0.9609 (mt) cc_final: 0.9346 (pp) REVERT: l 146 ASP cc_start: 0.8893 (t0) cc_final: 0.8568 (t0) REVERT: B 72 TYR cc_start: 0.8545 (m-10) cc_final: 0.8276 (m-10) REVERT: B 80 TYR cc_start: 0.6347 (m-80) cc_final: 0.6088 (m-80) REVERT: B 155 GLU cc_start: 0.8042 (tp30) cc_final: 0.7439 (tp30) REVERT: B 300 PHE cc_start: 0.7430 (m-80) cc_final: 0.6002 (m-80) REVERT: B 381 TRP cc_start: 0.8687 (m100) cc_final: 0.8345 (m100) REVERT: B 390 MET cc_start: 0.8384 (ppp) cc_final: 0.7392 (ppp) REVERT: G 3 LEU cc_start: 0.9628 (OUTLIER) cc_final: 0.9270 (mm) REVERT: G 21 MET cc_start: 0.6280 (pmm) cc_final: 0.5870 (pmm) REVERT: G 416 MET cc_start: -0.0802 (ttt) cc_final: -0.1562 (ptp) REVERT: G 418 ARG cc_start: 0.7290 (ptt-90) cc_final: 0.6741 (mmt180) REVERT: N 73 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.7743 (tp) REVERT: N 175 LEU cc_start: 0.9399 (OUTLIER) cc_final: 0.9036 (mp) REVERT: N 360 TYR cc_start: 0.8678 (t80) cc_final: 0.8128 (t80) REVERT: N 397 GLU cc_start: 0.9097 (pt0) cc_final: 0.8832 (pp20) REVERT: F 326 LYS cc_start: 0.8783 (tptp) cc_final: 0.8271 (tptp) REVERT: F 327 MET cc_start: 0.8386 (ppp) cc_final: 0.8086 (ppp) REVERT: F 390 MET cc_start: 0.3956 (ptt) cc_final: 0.3721 (ptt) outliers start: 142 outliers final: 74 residues processed: 788 average time/residue: 0.4962 time to fit residues: 667.9942 Evaluate side-chains 711 residues out of total 5838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 624 time to evaluate : 4.790 ------------------------------------------------------------------------------- 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 295 HIS 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 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 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 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 209 ILE 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 175 LEU Chi-restraints excluded: chain M residue 261 ILE Chi-restraints excluded: chain M residue 262 ILE 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 390 MET Chi-restraints excluded: chain c residue 64 GLN 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 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 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 49 ASP Chi-restraints excluded: chain k residue 15 ASN 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 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 3 LEU Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 219 MET 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 175 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 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 354 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 672 random chunks: chunk 209 optimal weight: 4.9990 chunk 123 optimal weight: 20.0000 chunk 669 optimal weight: 0.9990 chunk 547 optimal weight: 0.9980 chunk 602 optimal weight: 10.0000 chunk 412 optimal weight: 0.9980 chunk 137 optimal weight: 30.0000 chunk 454 optimal weight: 1.9990 chunk 131 optimal weight: 30.0000 chunk 379 optimal weight: 8.9990 chunk 435 optimal weight: 0.9980 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 292 ASN J 378 GLN ** 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 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 173 GLN f 77 GLN ** 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** ** 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 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.066306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.050777 restraints weight = 361737.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.051944 restraints weight = 219785.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.052607 restraints weight = 138175.830| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 55540 Z= 0.168 Angle : 0.622 13.574 74928 Z= 0.308 Chirality : 0.042 0.267 8454 Planarity : 0.004 0.053 9770 Dihedral : 7.117 78.099 7998 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.54 % Favored : 97.43 % Rotamer: Outliers : 2.59 % Allowed : 16.55 % Favored : 80.87 % 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: 0.79 (0.10), residues: 6854 helix: 1.18 (0.08), residues: 3856 sheet: 0.12 (0.21), residues: 645 loop : -0.32 (0.13), residues: 2353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP l 133 HIS 0.011 0.001 HIS B 239 PHE 0.029 0.001 PHE L 413 TYR 0.019 0.001 TYR M 332 ARG 0.010 0.000 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 834 residues out of total 5838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 683 time to evaluate : 4.807 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: C 184 LYS cc_start: 0.8872 (OUTLIER) cc_final: 0.8528 (pttm) REVERT: C 189 GLN cc_start: 0.8781 (mt0) cc_final: 0.8218 (mp10) REVERT: C 360 TYR cc_start: 0.8473 (t80) cc_final: 0.8176 (t80) REVERT: D 21 MET cc_start: 0.8407 (ppp) cc_final: 0.8107 (ppp) REVERT: D 62 PHE cc_start: 0.7232 (t80) cc_final: 0.6902 (t80) REVERT: D 157 LEU cc_start: 0.9093 (pt) cc_final: 0.8510 (tp) REVERT: D 329 GLU cc_start: 0.7723 (tp30) cc_final: 0.7494 (tp30) REVERT: E 29 MET cc_start: 0.6798 (pmm) cc_final: 0.6119 (pmm) REVERT: E 219 MET cc_start: 0.9177 (mmm) cc_final: 0.8926 (mmm) REVERT: E 329 GLU cc_start: 0.8292 (tm-30) cc_final: 0.8062 (tm-30) REVERT: E 414 GLU cc_start: 0.8814 (mm-30) cc_final: 0.8590 (mm-30) REVERT: J 21 MET cc_start: 0.5929 (ppp) cc_final: 0.5158 (tmm) REVERT: J 31 LYS cc_start: 0.7000 (mptt) cc_final: 0.5982 (ptpt) REVERT: J 91 LEU cc_start: 0.6669 (OUTLIER) cc_final: 0.6399 (pp) REVERT: J 186 MET cc_start: 0.5724 (pmm) cc_final: 0.5145 (pmm) REVERT: J 228 VAL cc_start: 0.5310 (OUTLIER) cc_final: 0.5032 (m) REVERT: K 161 VAL cc_start: 0.9513 (t) cc_final: 0.9309 (m) REVERT: K 186 MET cc_start: 0.8273 (pmm) cc_final: 0.7234 (ptp) REVERT: K 234 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7636 (pm20) REVERT: K 241 GLN cc_start: 0.8933 (OUTLIER) cc_final: 0.8695 (pp30) REVERT: K 245 MET cc_start: 0.8344 (tpt) cc_final: 0.7988 (tpt) REVERT: K 264 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8828 (tp) REVERT: K 341 MET cc_start: 0.8536 (mmm) cc_final: 0.7908 (mmm) REVERT: K 406 THR cc_start: 0.8862 (OUTLIER) cc_final: 0.8362 (p) REVERT: L 244 GLU cc_start: 0.8378 (mm-30) cc_final: 0.7999 (mm-30) REVERT: L 341 MET cc_start: 0.8697 (tmm) cc_final: 0.8330 (tmm) REVERT: M 1 MET cc_start: 0.6277 (ppp) cc_final: 0.5768 (ppp) REVERT: M 244 GLU cc_start: 0.8434 (mm-30) cc_final: 0.7759 (mm-30) REVERT: M 274 TYR cc_start: 0.8983 (m-10) cc_final: 0.8351 (m-10) REVERT: M 327 MET cc_start: 0.7928 (OUTLIER) cc_final: 0.7011 (ppp) REVERT: M 333 GLU cc_start: 0.8703 (tt0) cc_final: 0.8395 (mm-30) REVERT: M 411 ASP cc_start: 0.9314 (t0) cc_final: 0.9072 (t0) REVERT: M 417 LYS cc_start: 0.9444 (pttm) cc_final: 0.9236 (pttp) REVERT: O 29 MET cc_start: 0.1622 (tmm) cc_final: 0.1420 (ttp) REVERT: O 245 MET cc_start: 0.8089 (mmm) cc_final: 0.7862 (mmm) REVERT: O 341 MET cc_start: 0.7222 (mmm) cc_final: 0.6457 (mmm) REVERT: O 380 MET cc_start: 0.9017 (mmm) cc_final: 0.8351 (mmt) REVERT: O 390 MET cc_start: 0.6763 (OUTLIER) cc_final: 0.5868 (ppp) REVERT: O 394 ASP cc_start: 0.8664 (OUTLIER) cc_final: 0.8157 (p0) REVERT: c 64 GLN cc_start: 0.9302 (OUTLIER) cc_final: 0.8893 (mm110) REVERT: d 89 MET cc_start: 0.7993 (ttp) cc_final: 0.7716 (tmm) REVERT: d 146 ASP cc_start: 0.8008 (m-30) cc_final: 0.7721 (m-30) REVERT: d 173 GLN cc_start: 0.8960 (OUTLIER) cc_final: 0.8084 (pp30) REVERT: e 175 MET cc_start: 0.8913 (ptm) cc_final: 0.8578 (ptp) REVERT: f 21 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8841 (pp) REVERT: g 78 HIS cc_start: 0.8335 (OUTLIER) cc_final: 0.8135 (p-80) REVERT: g 83 ASP cc_start: 0.8465 (m-30) cc_final: 0.8126 (m-30) REVERT: g 105 MET cc_start: 0.7626 (mtm) cc_final: 0.7261 (ptp) REVERT: g 130 LEU cc_start: 0.9474 (mm) cc_final: 0.9230 (mm) REVERT: h 53 ASN cc_start: 0.8946 (t0) cc_final: 0.8617 (t0) REVERT: h 78 HIS cc_start: 0.9105 (t-90) cc_final: 0.8685 (t-90) REVERT: h 116 ASN cc_start: 0.8202 (m-40) cc_final: 0.7933 (m-40) REVERT: h 131 LEU cc_start: 0.9400 (mt) cc_final: 0.9187 (pp) REVERT: h 179 ARG cc_start: 0.8924 (mmm160) cc_final: 0.8519 (mmm160) REVERT: i 158 ASP cc_start: 0.8145 (p0) cc_final: 0.7771 (p0) REVERT: i 168 LYS cc_start: 0.8666 (mtmm) cc_final: 0.8402 (mptt) REVERT: j 140 ILE cc_start: 0.8672 (tp) cc_final: 0.8373 (mm) REVERT: l 146 ASP cc_start: 0.8898 (t0) cc_final: 0.8578 (t0) REVERT: B 72 TYR cc_start: 0.8587 (m-10) cc_final: 0.8334 (m-10) REVERT: B 80 TYR cc_start: 0.6474 (m-80) cc_final: 0.6213 (m-80) REVERT: B 155 GLU cc_start: 0.8063 (tp30) cc_final: 0.7443 (tp30) REVERT: B 292 ASN cc_start: 0.9066 (t0) cc_final: 0.8717 (p0) REVERT: B 299 ARG cc_start: 0.8448 (ttp80) cc_final: 0.8215 (ttp80) REVERT: B 381 TRP cc_start: 0.8759 (m100) cc_final: 0.8349 (m100) REVERT: B 390 MET cc_start: 0.8413 (OUTLIER) cc_final: 0.7362 (ppp) REVERT: G 3 LEU cc_start: 0.9633 (OUTLIER) cc_final: 0.9287 (mm) REVERT: G 21 MET cc_start: 0.6325 (pmm) cc_final: 0.5939 (pmm) REVERT: G 341 MET cc_start: 0.6447 (tmm) cc_final: 0.6079 (tmm) REVERT: G 416 MET cc_start: -0.0733 (ttt) cc_final: -0.1129 (ptp) REVERT: G 418 ARG cc_start: 0.7347 (ptt-90) cc_final: 0.6815 (mmt180) REVERT: N 73 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.7736 (tp) REVERT: N 397 GLU cc_start: 0.9088 (pt0) cc_final: 0.8836 (pp20) REVERT: N 405 MET cc_start: 0.8312 (ppp) cc_final: 0.8077 (ppp) REVERT: F 175 LEU cc_start: 0.9302 (pt) cc_final: 0.9046 (mm) REVERT: F 326 LYS cc_start: 0.8816 (tptp) cc_final: 0.8607 (tptp) REVERT: F 414 GLU cc_start: 0.9237 (mm-30) cc_final: 0.9014 (pp20) outliers start: 151 outliers final: 85 residues processed: 789 average time/residue: 0.4953 time to fit residues: 669.4697 Evaluate side-chains 724 residues out of total 5838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 622 time to evaluate : 4.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 184 LYS Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 295 HIS 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 191 ILE Chi-restraints excluded: chain D residue 295 HIS Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 403 LEU Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 228 VAL 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 406 THR 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 209 ILE Chi-restraints excluded: chain L residue 227 VAL 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 262 ILE Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 327 MET Chi-restraints excluded: chain M residue 381 TRP 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 390 MET Chi-restraints excluded: chain O residue 394 ASP Chi-restraints excluded: chain c residue 64 GLN 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 g residue 53 ASN Chi-restraints excluded: chain g residue 78 HIS 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 49 ASP Chi-restraints excluded: chain j residue 124 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 B residue 390 MET Chi-restraints excluded: chain G residue 3 LEU Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain G residue 219 MET 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 4 THR Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 208 LEU Chi-restraints excluded: chain N residue 234 GLU 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 398 PHE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 672 random chunks: chunk 342 optimal weight: 7.9990 chunk 100 optimal weight: 0.7980 chunk 458 optimal weight: 4.9990 chunk 155 optimal weight: 6.9990 chunk 494 optimal weight: 10.0000 chunk 584 optimal weight: 10.0000 chunk 556 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 364 optimal weight: 2.9990 chunk 394 optimal weight: 10.0000 overall best weight: 3.5588 ------------------------------------------------------------------------------- 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** ** E 241 GLN ** 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 ** K 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 239 HIS ** M 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 295 HIS ** 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 174 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 193 GLN ** 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 140 HIS F 340 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.063447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.047862 restraints weight = 363441.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.048881 restraints weight = 217000.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.050066 restraints weight = 136258.156| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2817 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= 0.285 Angle : 0.668 13.188 74928 Z= 0.338 Chirality : 0.043 0.211 8454 Planarity : 0.004 0.057 9770 Dihedral : 7.324 81.955 7995 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.57 % Favored : 97.40 % Rotamer: Outliers : 2.98 % Allowed : 17.21 % Favored : 79.80 % 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: 0.73 (0.10), residues: 6854 helix: 1.13 (0.08), residues: 3849 sheet: 0.09 (0.21), residues: 654 loop : -0.35 (0.13), residues: 2351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP E 381 HIS 0.012 0.001 HIS J 388 PHE 0.028 0.002 PHE B 300 TYR 0.021 0.002 TYR M 360 ARG 0.013 0.001 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 810 residues out of total 5838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 636 time to evaluate : 4.826 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: 0.8801 (mt0) cc_final: 0.8342 (mp10) REVERT: D 21 MET cc_start: 0.8258 (ppp) cc_final: 0.7946 (ppp) REVERT: D 85 GLN cc_start: 0.8901 (OUTLIER) cc_final: 0.8684 (pm20) REVERT: D 157 LEU cc_start: 0.9166 (pt) cc_final: 0.8534 (tp) REVERT: D 245 MET cc_start: 0.8359 (mmt) cc_final: 0.7790 (mpp) REVERT: D 390 MET cc_start: 0.8493 (pmm) cc_final: 0.8267 (pmm) REVERT: D 417 LYS cc_start: 0.9055 (pptt) cc_final: 0.8525 (mptt) REVERT: E 29 MET cc_start: 0.6901 (pmm) cc_final: 0.6350 (pmm) REVERT: E 164 LEU cc_start: 0.9586 (mm) cc_final: 0.9277 (mm) REVERT: E 219 MET cc_start: 0.9163 (mmm) cc_final: 0.8818 (mmm) REVERT: E 265 ASP cc_start: 0.7983 (t0) cc_final: 0.7743 (t0) REVERT: J 21 MET cc_start: 0.5661 (OUTLIER) cc_final: 0.4918 (tmm) REVERT: J 31 LYS cc_start: 0.6904 (mptt) cc_final: 0.5840 (ptpt) REVERT: J 52 ASP cc_start: 0.4995 (p0) cc_final: 0.4755 (p0) REVERT: J 59 GLN cc_start: 0.8692 (mp10) cc_final: 0.7816 (pp30) REVERT: J 186 MET cc_start: 0.6097 (pmm) cc_final: 0.5638 (pmm) REVERT: J 228 VAL cc_start: 0.5420 (OUTLIER) cc_final: 0.5036 (m) REVERT: K 161 VAL cc_start: 0.9520 (t) cc_final: 0.9315 (m) REVERT: K 186 MET cc_start: 0.8388 (pmm) cc_final: 0.7354 (ptp) REVERT: K 234 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7644 (pm20) REVERT: K 241 GLN cc_start: 0.8955 (OUTLIER) cc_final: 0.8748 (pp30) REVERT: K 245 MET cc_start: 0.8372 (tpt) cc_final: 0.8055 (tpt) REVERT: L 21 MET cc_start: 0.8409 (OUTLIER) cc_final: 0.7947 (tmm) REVERT: L 26 LEU cc_start: 0.9100 (tp) cc_final: 0.8841 (tp) REVERT: L 244 GLU cc_start: 0.8400 (mm-30) cc_final: 0.7985 (mm-30) REVERT: L 341 MET cc_start: 0.8713 (tmm) cc_final: 0.8313 (tmm) REVERT: M 1 MET cc_start: 0.6446 (ppp) cc_final: 0.5377 (mtt) REVERT: M 2 ASN cc_start: 0.7556 (t0) cc_final: 0.7270 (t0) REVERT: M 244 GLU cc_start: 0.8532 (mm-30) cc_final: 0.7859 (mm-30) REVERT: M 327 MET cc_start: 0.8038 (OUTLIER) cc_final: 0.7181 (ppp) REVERT: M 333 GLU cc_start: 0.8685 (tt0) cc_final: 0.8379 (mm-30) REVERT: O 29 MET cc_start: 0.1484 (tmm) cc_final: 0.1232 (ttp) REVERT: O 66 ARG cc_start: 0.4974 (OUTLIER) cc_final: 0.4589 (mmm-85) REVERT: O 164 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7670 (pp) REVERT: O 193 GLN cc_start: 0.7941 (OUTLIER) cc_final: 0.7698 (mp10) REVERT: O 245 MET cc_start: 0.8119 (mmm) cc_final: 0.7889 (mmm) REVERT: O 341 MET cc_start: 0.7544 (mmm) cc_final: 0.6794 (mmm) REVERT: O 380 MET cc_start: 0.9043 (mmm) cc_final: 0.8357 (mmt) REVERT: O 390 MET cc_start: 0.6826 (OUTLIER) cc_final: 0.5875 (ppp) REVERT: O 394 ASP cc_start: 0.8631 (OUTLIER) cc_final: 0.8169 (p0) REVERT: c 64 GLN cc_start: 0.9294 (OUTLIER) cc_final: 0.8961 (mm110) REVERT: c 180 LYS cc_start: 0.9303 (mmtp) cc_final: 0.9035 (mmtt) REVERT: d 89 MET cc_start: 0.8018 (ttp) cc_final: 0.7690 (tmm) REVERT: d 146 ASP cc_start: 0.8087 (m-30) cc_final: 0.7782 (m-30) REVERT: d 173 GLN cc_start: 0.9032 (OUTLIER) cc_final: 0.8383 (pp30) REVERT: e 175 MET cc_start: 0.8916 (ptm) cc_final: 0.8628 (ptp) REVERT: f 21 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8889 (pp) REVERT: g 83 ASP cc_start: 0.8469 (m-30) cc_final: 0.8098 (m-30) REVERT: g 105 MET cc_start: 0.7619 (mtm) cc_final: 0.7411 (ptp) REVERT: g 130 LEU cc_start: 0.9462 (mm) cc_final: 0.9250 (mm) REVERT: h 53 ASN cc_start: 0.8962 (t0) cc_final: 0.8516 (t0) REVERT: i 158 ASP cc_start: 0.8166 (p0) cc_final: 0.7813 (p0) REVERT: l 21 LEU cc_start: 0.9627 (mt) cc_final: 0.9368 (pp) REVERT: l 146 ASP cc_start: 0.8922 (t0) cc_final: 0.8578 (t0) REVERT: B 80 TYR cc_start: 0.6586 (m-80) cc_final: 0.6357 (m-80) REVERT: B 147 MET cc_start: 0.7961 (mpp) cc_final: 0.7755 (mmm) REVERT: B 155 GLU cc_start: 0.8152 (tp30) cc_final: 0.7542 (tp30) REVERT: B 299 ARG cc_start: 0.8656 (ttp80) cc_final: 0.8361 (ttp80) REVERT: B 300 PHE cc_start: 0.6862 (m-80) cc_final: 0.6301 (m-80) REVERT: B 381 TRP cc_start: 0.8793 (m100) cc_final: 0.8389 (m100) REVERT: B 390 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.7186 (ppp) REVERT: G 3 LEU cc_start: 0.9621 (OUTLIER) cc_final: 0.9226 (mm) REVERT: G 341 MET cc_start: 0.6543 (tmm) cc_final: 0.6225 (tmm) REVERT: G 416 MET cc_start: -0.0635 (ttt) cc_final: -0.1206 (ptp) REVERT: G 418 ARG cc_start: 0.7373 (ptt-90) cc_final: 0.6813 (mmt180) REVERT: N 73 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.7718 (tp) REVERT: N 221 ARG cc_start: 0.9298 (ptm-80) cc_final: 0.8969 (ptm-80) REVERT: N 341 MET cc_start: 0.9075 (tmm) cc_final: 0.8766 (ppp) REVERT: N 360 TYR cc_start: 0.8791 (t80) cc_final: 0.8383 (t80) REVERT: N 415 MET cc_start: 0.8802 (ppp) cc_final: 0.8589 (ppp) REVERT: F 186 MET cc_start: 0.5964 (pmm) cc_final: 0.5361 (ptp) REVERT: F 298 LYS cc_start: 0.8762 (tttp) cc_final: 0.8186 (mtpt) REVERT: F 326 LYS cc_start: 0.8794 (tptp) cc_final: 0.8435 (tptp) REVERT: F 415 MET cc_start: 0.8802 (ppp) cc_final: 0.8439 (ppp) REVERT: F 416 MET cc_start: 0.9341 (tpp) cc_final: 0.8777 (mmm) outliers start: 174 outliers final: 109 residues processed: 755 average time/residue: 0.5073 time to fit residues: 659.1414 Evaluate side-chains 712 residues out of total 5838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 585 time to evaluate : 4.779 ------------------------------------------------------------------------------- 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 292 ASN Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 295 HIS 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 191 ILE 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 412 PHE Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 157 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 137 THR Chi-restraints excluded: chain J residue 162 LEU Chi-restraints excluded: chain J residue 228 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 21 MET Chi-restraints excluded: chain L residue 91 LEU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 227 VAL 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 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 M residue 327 MET Chi-restraints excluded: chain M residue 338 THR Chi-restraints excluded: chain M residue 381 TRP Chi-restraints excluded: chain O residue 12 SER Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 66 ARG 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 313 LEU 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 64 GLN 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 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 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 3 LEU Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 126 ASN Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain G residue 219 MET 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 216 VAL 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 398 PHE Chi-restraints excluded: chain N residue 411 ASP 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 672 random chunks: chunk 502 optimal weight: 10.0000 chunk 457 optimal weight: 2.9990 chunk 203 optimal weight: 0.9990 chunk 610 optimal weight: 6.9990 chunk 214 optimal weight: 8.9990 chunk 651 optimal weight: 7.9990 chunk 552 optimal weight: 7.9990 chunk 84 optimal weight: 9.9990 chunk 649 optimal weight: 9.9990 chunk 436 optimal weight: 4.9990 chunk 189 optimal weight: 0.8980 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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 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 292 ASN ** 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 306 ASN ** K 344 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 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 116 ASN d 173 GLN ** f 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 77 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 91 GLN ** l 53 ASN ** 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** ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.062616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.047308 restraints weight = 360486.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.048138 restraints weight = 219316.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.049857 restraints weight = 133956.617| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 55540 Z= 0.267 Angle : 0.666 14.544 74928 Z= 0.336 Chirality : 0.043 0.259 8454 Planarity : 0.004 0.062 9770 Dihedral : 7.500 88.119 7995 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.83 % Favored : 97.14 % Rotamer: Outliers : 3.00 % Allowed : 18.19 % Favored : 78.81 % 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: 0.63 (0.10), residues: 6854 helix: 1.05 (0.08), residues: 3853 sheet: 0.05 (0.21), residues: 659 loop : -0.39 (0.13), residues: 2342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP E 381 HIS 0.011 0.001 HIS J 388 PHE 0.044 0.002 PHE M 232 TYR 0.021 0.002 TYR M 332 ARG 0.015 0.001 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 791 residues out of total 5838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 616 time to evaluate : 4.925 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: 0.7894 (ptt) cc_final: 0.7645 (ptt) REVERT: C 189 GLN cc_start: 0.8873 (mt0) cc_final: 0.8399 (mp10) REVERT: D 21 MET cc_start: 0.8255 (ppp) cc_final: 0.7913 (ppp) REVERT: D 157 LEU cc_start: 0.9150 (pt) cc_final: 0.8485 (tp) REVERT: D 245 MET cc_start: 0.8419 (mmt) cc_final: 0.7826 (mpp) REVERT: D 327 MET cc_start: 0.8017 (ppp) cc_final: 0.7275 (ppp) REVERT: D 390 MET cc_start: 0.8417 (pmm) cc_final: 0.8157 (pmm) REVERT: E 29 MET cc_start: 0.6961 (pmm) cc_final: 0.6427 (pmm) REVERT: E 164 LEU cc_start: 0.9605 (mm) cc_final: 0.9260 (mm) REVERT: E 414 GLU cc_start: 0.8664 (mm-30) cc_final: 0.8421 (tp30) REVERT: J 21 MET cc_start: 0.5488 (OUTLIER) cc_final: 0.4721 (tmm) REVERT: J 31 LYS cc_start: 0.6925 (mptt) cc_final: 0.5847 (ptpt) REVERT: J 59 GLN cc_start: 0.8734 (mp10) cc_final: 0.7797 (pp30) REVERT: J 186 MET cc_start: 0.6230 (pmm) cc_final: 0.5956 (pmm) REVERT: J 224 LYS cc_start: 0.6947 (mppt) cc_final: 0.5302 (pttm) REVERT: J 228 VAL cc_start: 0.5166 (OUTLIER) cc_final: 0.4965 (m) REVERT: K 186 MET cc_start: 0.8421 (pmm) cc_final: 0.7366 (ptm) REVERT: K 234 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7565 (pm20) REVERT: K 241 GLN cc_start: 0.8988 (OUTLIER) cc_final: 0.8783 (pp30) REVERT: K 245 MET cc_start: 0.8451 (tpt) cc_final: 0.8145 (tpt) REVERT: K 341 MET cc_start: 0.8680 (mmm) cc_final: 0.8456 (mmm) REVERT: L 26 LEU cc_start: 0.9161 (tp) cc_final: 0.8895 (tp) REVERT: L 56 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7699 (tm-30) REVERT: L 244 GLU cc_start: 0.8422 (mm-30) cc_final: 0.7992 (mm-30) REVERT: L 341 MET cc_start: 0.8726 (tmm) cc_final: 0.8018 (tmm) REVERT: M 1 MET cc_start: 0.6515 (ppp) cc_final: 0.5686 (mtt) REVERT: M 2 ASN cc_start: 0.7545 (t0) cc_final: 0.7281 (t0) REVERT: M 234 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7705 (pm20) REVERT: M 244 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8110 (mm-30) REVERT: M 333 GLU cc_start: 0.8781 (tt0) cc_final: 0.8453 (mm-30) REVERT: O 29 MET cc_start: 0.1464 (tmm) cc_final: 0.1220 (ttp) REVERT: O 193 GLN cc_start: 0.7782 (OUTLIER) cc_final: 0.7524 (mp10) REVERT: O 245 MET cc_start: 0.8130 (mmm) cc_final: 0.7914 (mmm) REVERT: O 341 MET cc_start: 0.7696 (mmm) cc_final: 0.7028 (mmm) REVERT: O 380 MET cc_start: 0.9036 (mmm) cc_final: 0.8345 (mmt) REVERT: O 390 MET cc_start: 0.6977 (OUTLIER) cc_final: 0.6079 (ppp) REVERT: O 394 ASP cc_start: 0.8563 (OUTLIER) cc_final: 0.8080 (p0) REVERT: c 64 GLN cc_start: 0.9322 (OUTLIER) cc_final: 0.8925 (mm110) REVERT: c 180 LYS cc_start: 0.9262 (mmtp) cc_final: 0.9011 (mmtt) REVERT: d 89 MET cc_start: 0.8063 (ttp) cc_final: 0.7739 (tmm) REVERT: d 146 ASP cc_start: 0.8141 (m-30) cc_final: 0.7825 (m-30) REVERT: e 175 MET cc_start: 0.8950 (ptm) cc_final: 0.8623 (ptp) REVERT: g 130 LEU cc_start: 0.9487 (mm) cc_final: 0.9283 (mm) REVERT: h 53 ASN cc_start: 0.9008 (t0) cc_final: 0.8623 (t0) REVERT: h 131 LEU cc_start: 0.9442 (mt) cc_final: 0.9119 (pp) REVERT: i 158 ASP cc_start: 0.8230 (p0) cc_final: 0.7886 (p0) REVERT: i 168 LYS cc_start: 0.8673 (mtmm) cc_final: 0.8457 (mptt) REVERT: k 78 HIS cc_start: 0.8420 (OUTLIER) cc_final: 0.7979 (t-90) REVERT: l 146 ASP cc_start: 0.8909 (t0) cc_final: 0.8570 (t0) REVERT: B 80 TYR cc_start: 0.6610 (m-80) cc_final: 0.6382 (m-80) REVERT: B 155 GLU cc_start: 0.8150 (tp30) cc_final: 0.7531 (tp30) REVERT: B 299 ARG cc_start: 0.8578 (ttp80) cc_final: 0.8201 (ttp80) REVERT: B 381 TRP cc_start: 0.8836 (m100) cc_final: 0.8406 (m100) REVERT: B 390 MET cc_start: 0.8367 (OUTLIER) cc_final: 0.7131 (ppp) REVERT: G 3 LEU cc_start: 0.9612 (OUTLIER) cc_final: 0.9224 (mm) REVERT: G 21 MET cc_start: 0.5378 (pmm) cc_final: 0.5136 (pmm) REVERT: G 341 MET cc_start: 0.6611 (tmm) cc_final: 0.6324 (tmm) REVERT: G 416 MET cc_start: -0.0591 (ttt) cc_final: -0.1216 (ptm) REVERT: G 418 ARG cc_start: 0.7387 (ptt-90) cc_final: 0.6804 (mmt180) REVERT: N 221 ARG cc_start: 0.9274 (ptm-80) cc_final: 0.8985 (ptm-80) REVERT: F 298 LYS cc_start: 0.8837 (tttp) cc_final: 0.8378 (mtpt) REVERT: F 326 LYS cc_start: 0.8832 (tptp) cc_final: 0.8631 (tptp) outliers start: 175 outliers final: 118 residues processed: 745 average time/residue: 0.4928 time to fit residues: 631.1529 Evaluate side-chains 714 residues out of total 5838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 584 time to evaluate : 4.810 ------------------------------------------------------------------------------- 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 244 GLU Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain C residue 295 HIS 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 295 HIS Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 412 PHE Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 157 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 J residue 21 MET Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 228 VAL 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 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 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 91 LEU Chi-restraints excluded: chain L residue 101 ILE 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 338 THR 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 101 ILE 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 193 GLN Chi-restraints excluded: chain O residue 313 LEU 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 64 GLN Chi-restraints excluded: chain c residue 100 LEU Chi-restraints excluded: chain c residue 130 LEU Chi-restraints excluded: chain c residue 142 TYR Chi-restraints excluded: chain d residue 124 ASP Chi-restraints excluded: chain d residue 173 GLN Chi-restraints excluded: chain e residue 105 MET 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 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 162 VAL Chi-restraints excluded: chain l residue 158 ASP Chi-restraints excluded: chain l residue 162 VAL 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 315 ILE Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain B residue 390 MET Chi-restraints excluded: chain G residue 3 LEU Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 219 MET 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 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 411 ASP 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 103 optimal weight: 0.6980 chunk 422 optimal weight: 2.9990 chunk 559 optimal weight: 20.0000 chunk 642 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 164 optimal weight: 10.0000 chunk 367 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 249 optimal weight: 4.9990 chunk 570 optimal weight: 10.0000 chunk 339 optimal weight: 1.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- 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 ** 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 344 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 173 GLN ** 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 77 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** ** j 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 53 ASN ** 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** ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.062541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.047448 restraints weight = 355922.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.047953 restraints weight = 193992.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.048969 restraints weight = 132885.771| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 55540 Z= 0.249 Angle : 0.680 13.427 74928 Z= 0.339 Chirality : 0.043 0.345 8454 Planarity : 0.004 0.070 9770 Dihedral : 7.518 89.232 7995 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.93 % Favored : 97.04 % Rotamer: Outliers : 2.71 % Allowed : 19.22 % Favored : 78.07 % 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: 0.60 (0.10), residues: 6854 helix: 1.06 (0.08), residues: 3840 sheet: -0.07 (0.20), residues: 677 loop : -0.42 (0.13), residues: 2337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP E 381 HIS 0.012 0.001 HIS J 388 PHE 0.048 0.002 PHE L 413 TYR 0.049 0.002 TYR B 72 ARG 0.014 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 767 residues out of total 5838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 609 time to evaluate : 4.864 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: C 186 MET cc_start: 0.7894 (ptt) cc_final: 0.7548 (ptt) REVERT: C 189 GLN cc_start: 0.8817 (mt0) cc_final: 0.8349 (mp10) REVERT: C 241 GLN cc_start: 0.8972 (OUTLIER) cc_final: 0.8581 (pp30) REVERT: C 341 MET cc_start: 0.9275 (ppp) cc_final: 0.8952 (tmm) REVERT: C 414 GLU cc_start: 0.8962 (tp30) cc_final: 0.8758 (tp30) REVERT: C 415 MET cc_start: 0.9051 (tmm) cc_final: 0.8747 (tmm) REVERT: D 21 MET cc_start: 0.8239 (ppp) cc_final: 0.7866 (ppp) REVERT: D 157 LEU cc_start: 0.9173 (pt) cc_final: 0.8504 (tp) REVERT: D 245 MET cc_start: 0.8395 (mmt) cc_final: 0.7832 (mpp) REVERT: D 390 MET cc_start: 0.8467 (pmm) cc_final: 0.8199 (pmm) REVERT: D 417 LYS cc_start: 0.9086 (pptt) cc_final: 0.8610 (mptt) REVERT: E 29 MET cc_start: 0.7145 (pmm) cc_final: 0.6602 (pmm) REVERT: E 164 LEU cc_start: 0.9573 (mm) cc_final: 0.9252 (mm) REVERT: E 414 GLU cc_start: 0.8832 (mm-30) cc_final: 0.8596 (tp30) REVERT: J 21 MET cc_start: 0.5320 (OUTLIER) cc_final: 0.4638 (tmm) REVERT: J 31 LYS cc_start: 0.6921 (mptt) cc_final: 0.5868 (ptpt) REVERT: J 59 GLN cc_start: 0.8697 (mp10) cc_final: 0.7763 (pp30) REVERT: J 186 MET cc_start: 0.6363 (pmm) cc_final: 0.5944 (pmm) REVERT: J 224 LYS cc_start: 0.6996 (mppt) cc_final: 0.5404 (pttm) REVERT: J 228 VAL cc_start: 0.5363 (OUTLIER) cc_final: 0.5138 (m) REVERT: K 186 MET cc_start: 0.8686 (pmm) cc_final: 0.7877 (ptm) REVERT: K 234 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7607 (pm20) REVERT: K 245 MET cc_start: 0.8454 (tpt) cc_final: 0.8147 (tpt) REVERT: K 341 MET cc_start: 0.8726 (mmm) cc_final: 0.8473 (mmm) REVERT: L 26 LEU cc_start: 0.9156 (tp) cc_final: 0.8876 (tp) REVERT: L 56 GLU cc_start: 0.8051 (tm-30) cc_final: 0.7667 (tm-30) REVERT: L 244 GLU cc_start: 0.8367 (mm-30) cc_final: 0.7900 (mm-30) REVERT: L 341 MET cc_start: 0.8668 (tmm) cc_final: 0.7968 (tmm) REVERT: L 410 ASP cc_start: 0.9157 (m-30) cc_final: 0.8666 (m-30) REVERT: M 1 MET cc_start: 0.6907 (ppp) cc_final: 0.6393 (mtt) REVERT: M 2 ASN cc_start: 0.7778 (t0) cc_final: 0.7475 (t0) REVERT: M 234 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7770 (pm20) REVERT: M 244 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8263 (mm-30) REVERT: M 333 GLU cc_start: 0.8806 (tt0) cc_final: 0.8458 (mm-30) REVERT: O 29 MET cc_start: 0.1450 (tmm) cc_final: 0.1219 (ttp) REVERT: O 193 GLN cc_start: 0.7819 (OUTLIER) cc_final: 0.7574 (mp10) REVERT: O 245 MET cc_start: 0.8079 (mmm) cc_final: 0.7861 (mmm) REVERT: O 341 MET cc_start: 0.7726 (mmm) cc_final: 0.7098 (mmm) REVERT: O 390 MET cc_start: 0.6998 (OUTLIER) cc_final: 0.6162 (ppp) REVERT: O 394 ASP cc_start: 0.8607 (OUTLIER) cc_final: 0.8137 (p0) REVERT: c 64 GLN cc_start: 0.9286 (OUTLIER) cc_final: 0.8892 (mm110) REVERT: d 89 MET cc_start: 0.8143 (ttp) cc_final: 0.7804 (tmm) REVERT: d 146 ASP cc_start: 0.8219 (m-30) cc_final: 0.7893 (m-30) REVERT: e 175 MET cc_start: 0.8943 (ptm) cc_final: 0.8630 (ptp) REVERT: h 53 ASN cc_start: 0.8994 (t0) cc_final: 0.8543 (t0) REVERT: h 131 LEU cc_start: 0.9462 (mt) cc_final: 0.9104 (pp) REVERT: i 158 ASP cc_start: 0.8234 (p0) cc_final: 0.7895 (p0) REVERT: i 168 LYS cc_start: 0.8725 (mtmm) cc_final: 0.8487 (mptt) REVERT: k 78 HIS cc_start: 0.8454 (OUTLIER) cc_final: 0.7994 (t-90) REVERT: l 21 LEU cc_start: 0.9642 (mt) cc_final: 0.9388 (pp) REVERT: l 146 ASP cc_start: 0.8960 (t0) cc_final: 0.8623 (t0) REVERT: B 80 TYR cc_start: 0.6713 (m-80) cc_final: 0.6460 (m-80) REVERT: B 155 GLU cc_start: 0.8156 (tp30) cc_final: 0.7533 (tp30) REVERT: B 245 MET cc_start: 0.8916 (ppp) cc_final: 0.8695 (ppp) REVERT: B 299 ARG cc_start: 0.8547 (ttp80) cc_final: 0.8272 (ttp80) REVERT: B 381 TRP cc_start: 0.8834 (m100) cc_final: 0.8414 (m100) REVERT: B 390 MET cc_start: 0.8354 (OUTLIER) cc_final: 0.7105 (ppp) REVERT: B 396 MET cc_start: 0.9448 (mmm) cc_final: 0.8968 (mmt) REVERT: G 21 MET cc_start: 0.5671 (pmm) cc_final: 0.5434 (pmm) REVERT: G 341 MET cc_start: 0.6624 (tmm) cc_final: 0.6338 (tmm) REVERT: G 416 MET cc_start: -0.0365 (ttt) cc_final: -0.0986 (ptm) REVERT: G 418 ARG cc_start: 0.7374 (ptt-90) cc_final: 0.6808 (mmt180) REVERT: N 221 ARG cc_start: 0.9225 (ptm-80) cc_final: 0.8949 (ptm-80) REVERT: F 298 LYS cc_start: 0.8836 (tttp) cc_final: 0.8381 (mtpt) REVERT: F 326 LYS cc_start: 0.8878 (tptp) cc_final: 0.8675 (tptp) REVERT: F 390 MET cc_start: 0.6138 (ppp) cc_final: 0.5293 (ppp) REVERT: F 415 MET cc_start: 0.8818 (ppp) cc_final: 0.8379 (ppp) REVERT: F 416 MET cc_start: 0.9340 (tpp) cc_final: 0.8762 (mmm) outliers start: 158 outliers final: 114 residues processed: 719 average time/residue: 0.4861 time to fit residues: 604.5925 Evaluate side-chains 702 residues out of total 5838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 577 time to evaluate : 4.722 ------------------------------------------------------------------------------- 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 292 ASN Chi-restraints excluded: chain C residue 295 HIS 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 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 412 PHE Chi-restraints excluded: chain E residue 64 PHE 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 J residue 21 MET Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 228 VAL 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 325 SER 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 209 ILE Chi-restraints excluded: chain L residue 224 LYS Chi-restraints excluded: chain L residue 227 VAL Chi-restraints excluded: chain L residue 338 THR 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 370 LEU 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 390 MET Chi-restraints excluded: chain O residue 394 ASP Chi-restraints excluded: chain c residue 59 LYS Chi-restraints excluded: chain c residue 64 GLN 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 e residue 105 MET 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 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 209 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 219 MET 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 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 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 652 optimal weight: 6.9990 chunk 483 optimal weight: 0.9990 chunk 249 optimal weight: 2.9990 chunk 409 optimal weight: 20.0000 chunk 42 optimal weight: 4.9990 chunk 92 optimal weight: 8.9990 chunk 615 optimal weight: 2.9990 chunk 236 optimal weight: 0.8980 chunk 164 optimal weight: 10.0000 chunk 122 optimal weight: 6.9990 chunk 505 optimal weight: 4.9990 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 295 HIS ** E 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 241 GLN ** 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 ** K 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 344 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** ** d 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** j 173 GLN ** k 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 91 GLN ** 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 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.062281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.046936 restraints weight = 360599.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.047899 restraints weight = 203207.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.048736 restraints weight = 130934.273| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 55540 Z= 0.232 Angle : 0.691 14.204 74928 Z= 0.342 Chirality : 0.043 0.328 8454 Planarity : 0.004 0.071 9770 Dihedral : 7.515 86.873 7992 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.87 % Favored : 97.10 % Rotamer: Outliers : 2.71 % Allowed : 19.56 % Favored : 77.73 % 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: 1.06 (0.08), residues: 3834 sheet: -0.02 (0.20), residues: 662 loop : -0.40 (0.13), residues: 2358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP E 381 HIS 0.012 0.001 HIS J 388 PHE 0.046 0.002 PHE d 177 TYR 0.037 0.002 TYR B 72 ARG 0.014 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 767 residues out of total 5838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 609 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: C 186 MET cc_start: 0.7901 (ptt) cc_final: 0.7412 (ptt) REVERT: C 189 GLN cc_start: 0.8839 (mt0) cc_final: 0.8369 (mp10) REVERT: C 215 GLU cc_start: 0.8888 (mp0) cc_final: 0.8535 (mp0) REVERT: C 241 GLN cc_start: 0.8854 (OUTLIER) cc_final: 0.8459 (pp30) REVERT: C 252 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.8256 (mmp80) REVERT: C 341 MET cc_start: 0.9282 (ppp) cc_final: 0.8938 (tmm) REVERT: C 414 GLU cc_start: 0.8897 (tp30) cc_final: 0.8337 (tp30) REVERT: C 415 MET cc_start: 0.9103 (tmm) cc_final: 0.8848 (tmm) REVERT: C 418 ARG cc_start: 0.8899 (mtm110) cc_final: 0.8417 (ptt-90) REVERT: D 21 MET cc_start: 0.8194 (ppp) cc_final: 0.7808 (ppp) REVERT: D 157 LEU cc_start: 0.9164 (pt) cc_final: 0.8502 (tp) REVERT: D 245 MET cc_start: 0.8409 (mmt) cc_final: 0.7810 (mpp) REVERT: D 327 MET cc_start: 0.8107 (ppp) cc_final: 0.7378 (ppp) REVERT: D 381 TRP cc_start: 0.8585 (OUTLIER) cc_final: 0.8279 (m-90) REVERT: D 390 MET cc_start: 0.8535 (pmm) cc_final: 0.8265 (pmm) REVERT: E 29 MET cc_start: 0.7115 (pmm) cc_final: 0.6604 (pmm) REVERT: E 164 LEU cc_start: 0.9580 (mm) cc_final: 0.9262 (mm) REVERT: E 414 GLU cc_start: 0.8831 (mm-30) cc_final: 0.8613 (tp30) REVERT: J 21 MET cc_start: 0.5258 (OUTLIER) cc_final: 0.4462 (ppp) REVERT: J 31 LYS cc_start: 0.6898 (mptt) cc_final: 0.5779 (ptpt) REVERT: J 147 MET cc_start: 0.4764 (mmm) cc_final: 0.4548 (mmt) REVERT: J 186 MET cc_start: 0.6225 (pmm) cc_final: 0.5750 (pmm) REVERT: J 224 LYS cc_start: 0.7043 (mppt) cc_final: 0.5441 (pttm) REVERT: K 186 MET cc_start: 0.8577 (pmm) cc_final: 0.7842 (ptm) REVERT: K 219 MET cc_start: 0.9297 (tpp) cc_final: 0.9078 (mmm) REVERT: K 234 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7591 (pm20) REVERT: K 245 MET cc_start: 0.8468 (tpt) cc_final: 0.8167 (tpt) REVERT: K 341 MET cc_start: 0.8808 (mmm) cc_final: 0.8547 (mmm) REVERT: L 26 LEU cc_start: 0.9128 (tp) cc_final: 0.8838 (tp) REVERT: L 56 GLU cc_start: 0.8006 (tm-30) cc_final: 0.7647 (tm-30) REVERT: L 244 GLU cc_start: 0.8367 (mm-30) cc_final: 0.7923 (mm-30) REVERT: L 341 MET cc_start: 0.8679 (tmm) cc_final: 0.7937 (tmm) REVERT: M 1 MET cc_start: 0.6959 (ppp) cc_final: 0.6580 (mtt) REVERT: M 2 ASN cc_start: 0.7737 (t0) cc_final: 0.7455 (t0) REVERT: M 234 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7814 (pm20) REVERT: M 244 GLU cc_start: 0.8591 (mm-30) cc_final: 0.8086 (mm-30) REVERT: M 265 ASP cc_start: 0.8326 (t0) cc_final: 0.7664 (p0) REVERT: M 333 GLU cc_start: 0.8738 (tt0) cc_final: 0.8391 (mm-30) REVERT: O 29 MET cc_start: 0.1528 (tmm) cc_final: 0.1304 (ttp) REVERT: O 164 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.7869 (pp) REVERT: O 193 GLN cc_start: 0.7887 (OUTLIER) cc_final: 0.7650 (mp10) REVERT: O 245 MET cc_start: 0.8128 (mmm) cc_final: 0.7918 (mmm) REVERT: O 341 MET cc_start: 0.7751 (mmm) cc_final: 0.7169 (mmm) REVERT: O 380 MET cc_start: 0.9087 (mmt) cc_final: 0.8547 (mmt) REVERT: O 390 MET cc_start: 0.6969 (OUTLIER) cc_final: 0.6067 (ppp) REVERT: O 394 ASP cc_start: 0.8598 (OUTLIER) cc_final: 0.8107 (p0) REVERT: c 64 GLN cc_start: 0.9253 (OUTLIER) cc_final: 0.8856 (mm110) REVERT: c 89 MET cc_start: 0.7998 (tpt) cc_final: 0.7740 (tpt) REVERT: c 177 PHE cc_start: 0.9424 (m-10) cc_final: 0.9220 (m-10) REVERT: d 89 MET cc_start: 0.8137 (ttp) cc_final: 0.7792 (tmm) REVERT: d 146 ASP cc_start: 0.8130 (m-30) cc_final: 0.7805 (m-30) REVERT: e 175 MET cc_start: 0.8849 (ptm) cc_final: 0.8544 (ptp) REVERT: h 131 LEU cc_start: 0.9464 (mt) cc_final: 0.9129 (pp) REVERT: i 158 ASP cc_start: 0.8306 (p0) cc_final: 0.8000 (p0) REVERT: i 168 LYS cc_start: 0.8716 (mtmm) cc_final: 0.8482 (mptt) REVERT: k 78 HIS cc_start: 0.8425 (OUTLIER) cc_final: 0.7982 (t-90) REVERT: k 103 GLU cc_start: 0.6010 (mp0) cc_final: 0.5389 (pm20) REVERT: l 21 LEU cc_start: 0.9661 (mt) cc_final: 0.9420 (pp) REVERT: l 146 ASP cc_start: 0.9039 (t0) cc_final: 0.8722 (t0) REVERT: B 80 TYR cc_start: 0.6739 (m-80) cc_final: 0.6485 (m-80) REVERT: B 155 GLU cc_start: 0.8151 (tp30) cc_final: 0.7525 (tp30) REVERT: B 299 ARG cc_start: 0.8577 (ttp80) cc_final: 0.8290 (ttp80) REVERT: B 381 TRP cc_start: 0.8831 (m100) cc_final: 0.8451 (m100) REVERT: B 390 MET cc_start: 0.8333 (OUTLIER) cc_final: 0.7037 (ppp) REVERT: B 396 MET cc_start: 0.9430 (mmm) cc_final: 0.8921 (mmt) REVERT: B 414 GLU cc_start: 0.9400 (mm-30) cc_final: 0.9162 (mm-30) REVERT: G 21 MET cc_start: 0.5729 (pmm) cc_final: 0.5494 (pmm) REVERT: G 147 MET cc_start: 0.7895 (mmm) cc_final: 0.7191 (mmp) REVERT: G 341 MET cc_start: 0.6671 (tmm) cc_final: 0.6384 (tmm) REVERT: G 416 MET cc_start: -0.0459 (ttt) cc_final: -0.1038 (ptm) REVERT: G 418 ARG cc_start: 0.7403 (ptt-90) cc_final: 0.6844 (mmt180) REVERT: N 245 MET cc_start: 0.8467 (ppp) cc_final: 0.8263 (ppp) REVERT: N 265 ASP cc_start: 0.8557 (t0) cc_final: 0.8307 (t70) REVERT: F 298 LYS cc_start: 0.8818 (tttp) cc_final: 0.8467 (mtpt) REVERT: F 326 LYS cc_start: 0.8902 (tptp) cc_final: 0.8701 (tptp) REVERT: F 390 MET cc_start: 0.6013 (ppp) cc_final: 0.5044 (ppp) REVERT: F 415 MET cc_start: 0.8817 (ppp) cc_final: 0.8427 (ppp) REVERT: F 416 MET cc_start: 0.9330 (tpp) cc_final: 0.8793 (mmm) outliers start: 158 outliers final: 116 residues processed: 721 average time/residue: 0.4845 time to fit residues: 601.2217 Evaluate side-chains 700 residues out of total 5838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 571 time to evaluate : 4.801 ------------------------------------------------------------------------------- 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 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 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 403 LEU Chi-restraints excluded: chain D residue 412 PHE Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 162 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 416 MET Chi-restraints excluded: chain J residue 21 MET 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 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 264 LEU Chi-restraints excluded: chain K residue 267 ILE Chi-restraints excluded: chain K residue 325 SER 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 224 LYS Chi-restraints excluded: chain L residue 227 VAL Chi-restraints excluded: chain L residue 338 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 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 390 MET Chi-restraints excluded: chain O residue 394 ASP Chi-restraints excluded: chain c residue 64 GLN 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 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 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 94 THR 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 209 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 219 MET 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 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 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 550 optimal weight: 5.9990 chunk 165 optimal weight: 5.9990 chunk 455 optimal weight: 4.9990 chunk 119 optimal weight: 0.9990 chunk 523 optimal weight: 8.9990 chunk 351 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 14 optimal weight: 10.0000 chunk 81 optimal weight: 0.9980 chunk 285 optimal weight: 5.9990 chunk 669 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 295 HIS ** E 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 241 GLN ** 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 ** K 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 344 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** ** d 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 53 ASN ** 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** ** B 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.062507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.047419 restraints weight = 356291.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.048000 restraints weight = 193483.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.048980 restraints weight = 133066.663| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 55540 Z= 0.212 Angle : 0.705 18.064 74928 Z= 0.345 Chirality : 0.043 0.322 8454 Planarity : 0.004 0.072 9770 Dihedral : 7.458 83.958 7991 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.96 % Favored : 97.01 % Rotamer: Outliers : 2.67 % Allowed : 19.78 % Favored : 77.54 % 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: 0.62 (0.10), residues: 6854 helix: 1.06 (0.08), residues: 3828 sheet: -0.03 (0.20), residues: 662 loop : -0.39 (0.13), residues: 2364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP E 381 HIS 0.012 0.001 HIS J 388 PHE 0.045 0.001 PHE d 177 TYR 0.033 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 765 residues out of total 5838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 609 time to evaluate : 4.837 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 186 MET cc_start: 0.7973 (ptt) cc_final: 0.7536 (ptt) REVERT: C 189 GLN cc_start: 0.8810 (mt0) cc_final: 0.8363 (mp10) REVERT: C 215 GLU cc_start: 0.8808 (mp0) cc_final: 0.8560 (mp0) REVERT: C 252 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.8258 (mmp80) REVERT: C 295 HIS cc_start: 0.9030 (OUTLIER) cc_final: 0.8479 (p-80) REVERT: C 341 MET cc_start: 0.9277 (ppp) cc_final: 0.8938 (tmm) REVERT: C 418 ARG cc_start: 0.8787 (mtm110) cc_final: 0.8528 (ptp-170) REVERT: D 21 MET cc_start: 0.8209 (ppp) cc_final: 0.7815 (ppp) REVERT: D 157 LEU cc_start: 0.9144 (pt) cc_final: 0.8465 (tp) REVERT: D 245 MET cc_start: 0.8446 (mmt) cc_final: 0.7876 (mpp) REVERT: D 381 TRP cc_start: 0.8620 (OUTLIER) cc_final: 0.8315 (m-90) REVERT: D 390 MET cc_start: 0.8529 (pmm) cc_final: 0.8262 (pmm) REVERT: D 417 LYS cc_start: 0.9100 (pptt) cc_final: 0.8720 (mptt) REVERT: E 29 MET cc_start: 0.7156 (pmm) cc_final: 0.6645 (pmm) REVERT: E 164 LEU cc_start: 0.9582 (mm) cc_final: 0.9281 (mm) REVERT: E 360 TYR cc_start: 0.8586 (t80) cc_final: 0.8373 (t80) REVERT: E 414 GLU cc_start: 0.8829 (mm-30) cc_final: 0.8625 (tp30) REVERT: J 21 MET cc_start: 0.5194 (OUTLIER) cc_final: 0.4441 (ppp) REVERT: J 31 LYS cc_start: 0.6917 (mptt) cc_final: 0.5843 (ptpt) REVERT: J 186 MET cc_start: 0.6151 (pmm) cc_final: 0.5722 (pmm) REVERT: J 224 LYS cc_start: 0.7141 (mppt) cc_final: 0.5540 (pttm) REVERT: J 344 HIS cc_start: 0.7438 (m-70) cc_final: 0.7178 (m-70) REVERT: K 186 MET cc_start: 0.8653 (pmm) cc_final: 0.7961 (ptm) REVERT: K 234 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7562 (pm20) REVERT: K 245 MET cc_start: 0.8529 (tpt) cc_final: 0.8234 (tpt) REVERT: K 341 MET cc_start: 0.8783 (mmm) cc_final: 0.8508 (mmm) REVERT: L 244 GLU cc_start: 0.8315 (mm-30) cc_final: 0.7859 (mm-30) REVERT: L 341 MET cc_start: 0.8661 (tmm) cc_final: 0.7977 (tmm) REVERT: M 1 MET cc_start: 0.7150 (ppp) cc_final: 0.6885 (mtt) REVERT: M 2 ASN cc_start: 0.7751 (t0) cc_final: 0.7438 (t0) REVERT: M 234 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7809 (pm20) REVERT: M 244 GLU cc_start: 0.8581 (mm-30) cc_final: 0.8079 (mm-30) REVERT: M 265 ASP cc_start: 0.8126 (t0) cc_final: 0.7508 (p0) REVERT: M 333 GLU cc_start: 0.8777 (tt0) cc_final: 0.8444 (mm-30) REVERT: O 29 MET cc_start: 0.1431 (tmm) cc_final: 0.1223 (ttp) REVERT: O 164 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7850 (pp) REVERT: O 193 GLN cc_start: 0.7877 (OUTLIER) cc_final: 0.7635 (mp10) REVERT: O 341 MET cc_start: 0.7729 (mmm) cc_final: 0.7195 (mmm) REVERT: O 380 MET cc_start: 0.9110 (mmt) cc_final: 0.8585 (mmt) REVERT: O 390 MET cc_start: 0.7078 (OUTLIER) cc_final: 0.6241 (ppp) REVERT: O 394 ASP cc_start: 0.8604 (OUTLIER) cc_final: 0.8108 (p0) REVERT: c 64 GLN cc_start: 0.9279 (OUTLIER) cc_final: 0.8997 (mm110) REVERT: c 177 PHE cc_start: 0.9432 (m-10) cc_final: 0.9149 (m-10) REVERT: d 89 MET cc_start: 0.8210 (ttp) cc_final: 0.7848 (tmm) REVERT: d 146 ASP cc_start: 0.8148 (m-30) cc_final: 0.7823 (m-30) REVERT: e 175 MET cc_start: 0.8901 (ptm) cc_final: 0.8610 (ptp) REVERT: h 53 ASN cc_start: 0.8842 (m-40) cc_final: 0.8315 (t0) REVERT: h 131 LEU cc_start: 0.9483 (mt) cc_final: 0.9143 (pp) REVERT: i 96 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8432 (pp) REVERT: i 158 ASP cc_start: 0.8300 (p0) cc_final: 0.8011 (p0) REVERT: i 168 LYS cc_start: 0.8739 (mtmm) cc_final: 0.8498 (mptt) REVERT: k 78 HIS cc_start: 0.8409 (OUTLIER) cc_final: 0.7950 (t-90) REVERT: k 103 GLU cc_start: 0.5970 (mp0) cc_final: 0.5314 (pm20) REVERT: l 21 LEU cc_start: 0.9664 (mt) cc_final: 0.9436 (pp) REVERT: l 146 ASP cc_start: 0.9050 (t0) cc_final: 0.8727 (t0) REVERT: B 80 TYR cc_start: 0.6799 (m-80) cc_final: 0.6519 (m-80) REVERT: B 155 GLU cc_start: 0.8127 (tp30) cc_final: 0.7487 (tp30) REVERT: B 299 ARG cc_start: 0.8551 (ttp80) cc_final: 0.8299 (ttp80) REVERT: B 381 TRP cc_start: 0.8870 (m100) cc_final: 0.8463 (m100) REVERT: B 390 MET cc_start: 0.8351 (OUTLIER) cc_final: 0.7091 (ppp) REVERT: B 396 MET cc_start: 0.9461 (mmm) cc_final: 0.8946 (mmt) REVERT: B 414 GLU cc_start: 0.9418 (mm-30) cc_final: 0.9179 (mm-30) REVERT: G 21 MET cc_start: 0.5677 (pmm) cc_final: 0.5446 (pmm) REVERT: G 147 MET cc_start: 0.7881 (mmm) cc_final: 0.7172 (mmp) REVERT: G 341 MET cc_start: 0.6672 (tmm) cc_final: 0.6380 (tmm) REVERT: G 416 MET cc_start: -0.0416 (ttt) cc_final: -0.1465 (ptm) REVERT: G 418 ARG cc_start: 0.7369 (ptt-90) cc_final: 0.6832 (mmt180) REVERT: N 205 MET cc_start: 0.8033 (mmm) cc_final: 0.7729 (mmm) REVERT: N 265 ASP cc_start: 0.8570 (t0) cc_final: 0.8325 (t70) REVERT: N 360 TYR cc_start: 0.8845 (t80) cc_final: 0.8631 (t80) REVERT: F 298 LYS cc_start: 0.8829 (tttp) cc_final: 0.8419 (mtpt) REVERT: F 326 LYS cc_start: 0.8924 (tptp) cc_final: 0.8720 (tptp) REVERT: F 415 MET cc_start: 0.8774 (ppp) cc_final: 0.8412 (ppp) REVERT: F 416 MET cc_start: 0.9347 (tpp) cc_final: 0.8801 (mmm) outliers start: 156 outliers final: 122 residues processed: 717 average time/residue: 0.4820 time to fit residues: 597.3624 Evaluate side-chains 716 residues out of total 5838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 580 time to evaluate : 4.788 ------------------------------------------------------------------------------- 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 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 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 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 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 403 LEU Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 162 LEU 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 137 THR Chi-restraints excluded: chain J residue 209 ILE 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 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 325 SER 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 209 ILE Chi-restraints excluded: chain L residue 224 LYS Chi-restraints excluded: chain L residue 227 VAL Chi-restraints excluded: chain L residue 231 THR Chi-restraints excluded: chain L residue 338 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 326 LYS 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 390 MET Chi-restraints excluded: chain O residue 394 ASP Chi-restraints excluded: chain c residue 59 LYS Chi-restraints excluded: chain c residue 64 GLN 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 21 LEU Chi-restraints excluded: chain e residue 105 MET 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 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 94 THR 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 209 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 219 MET 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 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 411 ASP Chi-restraints excluded: chain F residue 26 LEU 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 256 optimal weight: 0.9990 chunk 525 optimal weight: 0.9990 chunk 455 optimal weight: 1.9990 chunk 429 optimal weight: 8.9990 chunk 556 optimal weight: 2.9990 chunk 206 optimal weight: 0.0170 chunk 318 optimal weight: 30.0000 chunk 573 optimal weight: 10.0000 chunk 382 optimal weight: 5.9990 chunk 129 optimal weight: 0.9990 chunk 621 optimal weight: 3.9990 overall best weight: 1.0026 ------------------------------------------------------------------------------- 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 E 142 ASN J 142 ASN ** J 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 292 ASN ** K 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 344 HIS ** 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** ** d 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** 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 ** 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 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.063093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.048172 restraints weight = 358847.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.048886 restraints weight = 192905.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.049653 restraints weight = 131210.108| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 55540 Z= 0.183 Angle : 0.721 15.761 74928 Z= 0.350 Chirality : 0.043 0.327 8454 Planarity : 0.004 0.068 9770 Dihedral : 7.355 81.499 7991 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.79 % Favored : 97.20 % Rotamer: Outliers : 2.31 % Allowed : 20.30 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.27 % Cis-general : 0.17 % Twisted Proline : 0.43 % 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: 0.70 (0.10), residues: 6854 helix: 1.15 (0.08), residues: 3774 sheet: -0.02 (0.20), residues: 672 loop : -0.36 (0.13), residues: 2408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP E 381 HIS 0.013 0.001 HIS J 388 PHE 0.041 0.001 PHE d 177 TYR 0.034 0.002 TYR K 360 ARG 0.012 0.000 ARG h 179 ********************** 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 762 residues out of total 5838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 627 time to evaluate : 4.806 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 186 MET cc_start: 0.7955 (ptt) cc_final: 0.7400 (ptt) REVERT: C 189 GLN cc_start: 0.8799 (mt0) cc_final: 0.8330 (mp10) REVERT: C 252 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.8238 (mmp80) REVERT: C 295 HIS cc_start: 0.8911 (OUTLIER) cc_final: 0.8025 (p-80) REVERT: C 341 MET cc_start: 0.9228 (ppp) cc_final: 0.8882 (tmm) REVERT: C 418 ARG cc_start: 0.8760 (mtm110) cc_final: 0.8490 (ptp-170) REVERT: D 21 MET cc_start: 0.8199 (ppp) cc_final: 0.7794 (ppp) REVERT: D 157 LEU cc_start: 0.9118 (pt) cc_final: 0.8411 (tp) REVERT: D 245 MET cc_start: 0.8414 (mmt) cc_final: 0.7724 (mpp) REVERT: D 390 MET cc_start: 0.8489 (pmm) cc_final: 0.8224 (pmm) REVERT: E 29 MET cc_start: 0.7218 (pmm) cc_final: 0.6791 (pmm) REVERT: E 164 LEU cc_start: 0.9553 (mm) cc_final: 0.9324 (mm) REVERT: E 315 ILE cc_start: 0.9495 (tt) cc_final: 0.9228 (pt) REVERT: E 360 TYR cc_start: 0.8527 (t80) cc_final: 0.8290 (t80) REVERT: J 21 MET cc_start: 0.5154 (OUTLIER) cc_final: 0.4581 (tmm) REVERT: J 31 LYS cc_start: 0.6914 (mptt) cc_final: 0.5925 (ptpt) REVERT: J 186 MET cc_start: 0.6023 (pmm) cc_final: 0.5581 (pmm) REVERT: J 224 LYS cc_start: 0.7168 (mppt) cc_final: 0.5631 (pttm) REVERT: J 344 HIS cc_start: 0.7374 (m-70) cc_final: 0.7119 (m-70) REVERT: K 186 MET cc_start: 0.8549 (pmm) cc_final: 0.7791 (ptm) REVERT: K 234 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7640 (pm20) REVERT: K 245 MET cc_start: 0.8499 (tpt) cc_final: 0.8196 (tpt) REVERT: K 341 MET cc_start: 0.8787 (mmm) cc_final: 0.8507 (mmm) REVERT: L 26 LEU cc_start: 0.9131 (tp) cc_final: 0.8827 (tp) REVERT: L 244 GLU cc_start: 0.8260 (mm-30) cc_final: 0.7815 (mm-30) REVERT: L 341 MET cc_start: 0.8640 (tmm) cc_final: 0.8072 (tmm) REVERT: M 2 ASN cc_start: 0.7723 (t0) cc_final: 0.7421 (t0) REVERT: M 234 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7656 (pm20) REVERT: M 244 GLU cc_start: 0.8529 (mm-30) cc_final: 0.8039 (mm-30) REVERT: M 265 ASP cc_start: 0.8124 (t0) cc_final: 0.7472 (p0) REVERT: M 333 GLU cc_start: 0.8814 (tt0) cc_final: 0.8463 (mm-30) REVERT: O 164 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7866 (pp) REVERT: O 193 GLN cc_start: 0.7869 (OUTLIER) cc_final: 0.7641 (mp10) REVERT: O 341 MET cc_start: 0.7692 (mmm) cc_final: 0.7155 (mmm) REVERT: O 380 MET cc_start: 0.9072 (mmt) cc_final: 0.8530 (mmt) REVERT: O 390 MET cc_start: 0.7039 (OUTLIER) cc_final: 0.6161 (ppp) REVERT: O 394 ASP cc_start: 0.8588 (OUTLIER) cc_final: 0.8058 (p0) REVERT: c 64 GLN cc_start: 0.9276 (OUTLIER) cc_final: 0.8976 (mm110) REVERT: c 177 PHE cc_start: 0.9383 (m-10) cc_final: 0.9105 (m-10) REVERT: d 89 MET cc_start: 0.8232 (ttp) cc_final: 0.7884 (ppp) REVERT: d 146 ASP cc_start: 0.8113 (m-30) cc_final: 0.7801 (m-30) REVERT: e 175 MET cc_start: 0.8864 (ptm) cc_final: 0.8576 (ptp) REVERT: g 89 MET cc_start: 0.8545 (tpp) cc_final: 0.8238 (tpp) REVERT: h 53 ASN cc_start: 0.8829 (m-40) cc_final: 0.8310 (t0) REVERT: h 131 LEU cc_start: 0.9481 (mt) cc_final: 0.9135 (pp) REVERT: i 96 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8419 (pp) REVERT: i 158 ASP cc_start: 0.8290 (p0) cc_final: 0.8020 (p0) REVERT: i 168 LYS cc_start: 0.8715 (mtmm) cc_final: 0.8459 (mptt) REVERT: j 180 LYS cc_start: 0.9616 (mmtp) cc_final: 0.9350 (mmmt) REVERT: k 78 HIS cc_start: 0.8409 (OUTLIER) cc_final: 0.7970 (t-90) REVERT: k 103 GLU cc_start: 0.5956 (mp0) cc_final: 0.5321 (pm20) REVERT: k 155 PHE cc_start: 0.6370 (m-80) cc_final: 0.5594 (m-10) REVERT: l 21 LEU cc_start: 0.9674 (mt) cc_final: 0.9451 (pp) REVERT: l 146 ASP cc_start: 0.9061 (t0) cc_final: 0.8761 (t0) REVERT: B 72 TYR cc_start: 0.8627 (m-10) cc_final: 0.8384 (m-10) REVERT: B 80 TYR cc_start: 0.6755 (m-80) cc_final: 0.6462 (m-80) REVERT: B 155 GLU cc_start: 0.8088 (tp30) cc_final: 0.7622 (tp30) REVERT: B 299 ARG cc_start: 0.8590 (ttp80) cc_final: 0.8276 (ttp80) REVERT: B 381 TRP cc_start: 0.8886 (m100) cc_final: 0.8495 (m100) REVERT: B 390 MET cc_start: 0.8331 (OUTLIER) cc_final: 0.7132 (ppp) REVERT: B 414 GLU cc_start: 0.9429 (mm-30) cc_final: 0.9188 (mm-30) REVERT: G 21 MET cc_start: 0.5721 (pmm) cc_final: 0.5479 (pmm) REVERT: G 147 MET cc_start: 0.7861 (mmm) cc_final: 0.7191 (mmp) REVERT: G 341 MET cc_start: 0.6652 (tmm) cc_final: 0.6363 (tmm) REVERT: G 416 MET cc_start: -0.0398 (OUTLIER) cc_final: -0.1123 (ptm) REVERT: G 418 ARG cc_start: 0.7296 (ptt-90) cc_final: 0.6805 (mmt180) REVERT: N 205 MET cc_start: 0.7998 (mmm) cc_final: 0.7744 (mmm) REVERT: N 245 MET cc_start: 0.8529 (ppp) cc_final: 0.8321 (ppp) REVERT: N 265 ASP cc_start: 0.8601 (t0) cc_final: 0.8365 (t70) REVERT: F 175 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.9151 (mm) REVERT: F 253 LEU cc_start: 0.9038 (pp) cc_final: 0.8820 (pp) REVERT: F 264 LEU cc_start: 0.8138 (pt) cc_final: 0.7798 (pp) REVERT: F 298 LYS cc_start: 0.8808 (tttp) cc_final: 0.8427 (mtpt) REVERT: F 326 LYS cc_start: 0.8918 (tptp) cc_final: 0.8710 (tptp) REVERT: F 415 MET cc_start: 0.8713 (ppp) cc_final: 0.8363 (ppp) REVERT: F 416 MET cc_start: 0.9338 (tpp) cc_final: 0.8820 (mmm) outliers start: 135 outliers final: 105 residues processed: 721 average time/residue: 0.4899 time to fit residues: 608.5576 Evaluate side-chains 714 residues out of total 5838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 594 time to evaluate : 4.845 ------------------------------------------------------------------------------- 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 252 ARG Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain C residue 295 HIS Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain D residue 64 PHE Chi-restraints excluded: chain D residue 116 VAL 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 D residue 403 LEU Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 162 LEU 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 E residue 416 MET Chi-restraints excluded: chain J residue 21 MET 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 267 ILE 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 209 ILE Chi-restraints excluded: chain L residue 224 LYS Chi-restraints excluded: chain L residue 227 VAL Chi-restraints excluded: chain L residue 231 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 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 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 390 MET Chi-restraints excluded: chain O residue 394 ASP Chi-restraints excluded: chain c residue 64 GLN 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 21 LEU Chi-restraints excluded: chain e residue 105 MET 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 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 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 162 VAL Chi-restraints excluded: chain B residue 116 VAL 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 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 219 MET 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 G residue 416 MET 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 F residue 175 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 470 optimal weight: 1.9990 chunk 224 optimal weight: 3.9990 chunk 151 optimal weight: 30.0000 chunk 315 optimal weight: 10.0000 chunk 338 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 238 optimal weight: 0.9980 chunk 515 optimal weight: 3.9990 chunk 556 optimal weight: 30.0000 chunk 236 optimal weight: 8.9990 chunk 406 optimal weight: 10.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 292 ASN ** 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 L 388 HIS ** M 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 86 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 GLN ** 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 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.062669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.047533 restraints weight = 366648.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.048191 restraints weight = 197796.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.049361 restraints weight = 135985.493| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 55540 Z= 0.221 Angle : 0.728 15.791 74928 Z= 0.355 Chirality : 0.044 0.322 8454 Planarity : 0.004 0.070 9770 Dihedral : 7.367 81.138 7991 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.90 % Favored : 97.08 % Rotamer: Outliers : 2.31 % Allowed : 20.66 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.27 % Cis-general : 0.17 % Twisted Proline : 0.43 % 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: 0.64 (0.10), residues: 6854 helix: 1.07 (0.08), residues: 3831 sheet: -0.03 (0.21), residues: 657 loop : -0.37 (0.13), residues: 2366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 381 HIS 0.013 0.001 HIS J 388 PHE 0.044 0.001 PHE M 232 TYR 0.032 0.002 TYR B 72 ARG 0.012 0.000 ARG N 299 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16398.97 seconds wall clock time: 285 minutes 57.27 seconds (17157.27 seconds total)