Starting phenix.real_space_refine on Tue Apr 7 12:39:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cmm_45750/04_2026/9cmm_45750.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cmm_45750/04_2026/9cmm_45750.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cmm_45750/04_2026/9cmm_45750.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cmm_45750/04_2026/9cmm_45750.map" model { file = "/net/cci-nas-00/data/ceres_data/9cmm_45750/04_2026/9cmm_45750.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cmm_45750/04_2026/9cmm_45750.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 24 5.49 5 Mg 8 5.21 5 S 185 5.16 5 C 17113 2.51 5 N 4639 2.21 5 O 5280 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27249 Number of models: 1 Model: "" Number of chains: 16 Chain: "B" Number of atoms: 3348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3348 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 3345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3345 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 3357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3357 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "Q" Number of atoms: 3357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3357 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 3401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3401 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 416} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "I" Number of atoms: 3391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3391 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 416} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 3401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3401 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 416} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 3385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3385 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 416} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.92, per 1000 atoms: 0.22 Number of scatterers: 27249 At special positions: 0 Unit cell: (115.54, 111.3, 204.58, 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 185 16.00 P 24 15.00 Mg 8 11.99 O 5280 8.00 N 4639 7.00 C 17113 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: 2.19 Conformation dependent library (CDL) restraints added in 1.0 seconds 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6392 Finding SS restraints... Secondary structure from input PDB file: 170 helices and 21 sheets defined 55.9% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'B' and resid 10 through 29 Processing helix chain 'B' and resid 40 through 46 removed outlier: 4.010A pdb=" N LEU B 44 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ARG B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 55 through 57 No H-bonds generated for 'chain 'B' and resid 55 through 57' Processing helix chain 'B' and resid 69 through 78 removed outlier: 4.597A pdb=" N MET B 73 " --> pdb=" O GLU B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 85 removed outlier: 3.547A pdb=" N PHE B 85 " --> pdb=" O GLY B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 88 No H-bonds generated for 'chain 'B' and resid 86 through 88' Processing helix chain 'B' and resid 100 through 106 Processing helix chain 'B' and resid 106 through 127 removed outlier: 4.257A pdb=" N GLU B 111 " --> pdb=" O THR B 107 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 159 Processing helix chain 'B' and resid 180 through 196 removed outlier: 4.126A pdb=" N HIS B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N GLN B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 214 Processing helix chain 'B' and resid 221 through 236 removed outlier: 3.519A pdb=" N LEU B 228 " --> pdb=" O ASP B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 242 removed outlier: 3.687A pdb=" N ARG B 241 " --> pdb=" O THR B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 258 removed outlier: 3.525A pdb=" N ASN B 256 " --> pdb=" O LYS B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 295 Processing helix chain 'B' and resid 296 through 299 Processing helix chain 'B' and resid 304 through 308 Processing helix chain 'B' and resid 322 through 337 Processing helix chain 'B' and resid 338 through 341 Processing helix chain 'B' and resid 374 through 390 removed outlier: 4.231A pdb=" N PHE B 378 " --> pdb=" O ILE B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 400 Processing helix chain 'B' and resid 401 through 403 No H-bonds generated for 'chain 'B' and resid 401 through 403' Processing helix chain 'B' and resid 404 through 428 removed outlier: 4.524A pdb=" N PHE B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N THR B 409 " --> pdb=" O GLU B 405 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N TYR B 425 " --> pdb=" O GLU B 421 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLN B 426 " --> pdb=" O TYR B 422 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP B 427 " --> pdb=" O GLN B 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 29 Processing helix chain 'D' and resid 40 through 46 removed outlier: 4.029A pdb=" N LEU D 44 " --> pdb=" O SER D 40 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ARG D 46 " --> pdb=" O LEU D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 49 No H-bonds generated for 'chain 'D' and resid 47 through 49' Processing helix chain 'D' and resid 55 through 57 No H-bonds generated for 'chain 'D' and resid 55 through 57' Processing helix chain 'D' and resid 70 through 78 Processing helix chain 'D' and resid 81 through 85 removed outlier: 3.677A pdb=" N PHE D 85 " --> pdb=" O GLY D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 88 No H-bonds generated for 'chain 'D' and resid 86 through 88' Processing helix chain 'D' and resid 100 through 107 Processing helix chain 'D' and resid 107 through 127 removed outlier: 4.541A pdb=" N ASP D 114 " --> pdb=" O ALA D 110 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N SER D 115 " --> pdb=" O GLU D 111 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP D 118 " --> pdb=" O ASP D 114 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL D 119 " --> pdb=" O SER D 115 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N CYS D 127 " --> pdb=" O GLU D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 159 Processing helix chain 'D' and resid 180 through 196 removed outlier: 3.932A pdb=" N HIS D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N GLN D 191 " --> pdb=" O LEU D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 214 Processing helix chain 'D' and resid 221 through 236 removed outlier: 3.593A pdb=" N LEU D 225 " --> pdb=" O THR D 221 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR D 232 " --> pdb=" O LEU D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 242 removed outlier: 3.557A pdb=" N ARG D 241 " --> pdb=" O THR D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 258 Processing helix chain 'D' and resid 285 through 295 Processing helix chain 'D' and resid 296 through 299 Processing helix chain 'D' and resid 304 through 308 removed outlier: 3.535A pdb=" N HIS D 307 " --> pdb=" O ASP D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 337 Processing helix chain 'D' and resid 338 through 341 removed outlier: 3.510A pdb=" N PHE D 341 " --> pdb=" O SER D 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 338 through 341' Processing helix chain 'D' and resid 373 through 392 removed outlier: 4.304A pdb=" N LEU D 377 " --> pdb=" O ALA D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 401 removed outlier: 3.932A pdb=" N TYR D 398 " --> pdb=" O PHE D 394 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU D 401 " --> pdb=" O TRP D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 428 removed outlier: 3.933A pdb=" N PHE D 408 " --> pdb=" O ASP D 404 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N TYR D 425 " --> pdb=" O GLU D 421 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN D 426 " --> pdb=" O TYR D 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 29 removed outlier: 3.587A pdb=" N LYS F 19 " --> pdb=" O GLN F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 46 removed outlier: 4.331A pdb=" N LEU F 44 " --> pdb=" O SER F 40 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ARG F 46 " --> pdb=" O LEU F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 49 No H-bonds generated for 'chain 'F' and resid 47 through 49' Processing helix chain 'F' and resid 69 through 78 removed outlier: 4.277A pdb=" N MET F 73 " --> pdb=" O GLU F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 85 removed outlier: 3.562A pdb=" N PHE F 85 " --> pdb=" O GLY F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 106 Processing helix chain 'F' and resid 106 through 127 removed outlier: 3.673A pdb=" N ALA F 110 " --> pdb=" O TYR F 106 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU F 111 " --> pdb=" O THR F 107 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU F 112 " --> pdb=" O GLU F 108 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ASP F 114 " --> pdb=" O ALA F 110 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N SER F 115 " --> pdb=" O GLU F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 159 removed outlier: 3.670A pdb=" N SER F 145 " --> pdb=" O GLY F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 195 removed outlier: 3.978A pdb=" N HIS F 190 " --> pdb=" O THR F 186 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLN F 191 " --> pdb=" O LEU F 187 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU F 194 " --> pdb=" O HIS F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 214 Processing helix chain 'F' and resid 221 through 236 removed outlier: 3.876A pdb=" N LEU F 228 " --> pdb=" O ASP F 224 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL F 229 " --> pdb=" O LEU F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 242 removed outlier: 3.858A pdb=" N ARG F 241 " --> pdb=" O THR F 237 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 258 Processing helix chain 'F' and resid 275 through 280 removed outlier: 4.276A pdb=" N GLN F 280 " --> pdb=" O ARG F 276 " (cutoff:3.500A) Processing helix chain 'F' and resid 285 through 294 removed outlier: 3.562A pdb=" N PHE F 294 " --> pdb=" O THR F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 299 removed outlier: 3.661A pdb=" N MET F 299 " --> pdb=" O ALA F 296 " (cutoff:3.500A) Processing helix chain 'F' and resid 304 through 308 Processing helix chain 'F' and resid 322 through 337 Processing helix chain 'F' and resid 338 through 341 removed outlier: 3.537A pdb=" N PHE F 341 " --> pdb=" O SER F 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 338 through 341' Processing helix chain 'F' and resid 374 through 391 removed outlier: 4.008A pdb=" N PHE F 378 " --> pdb=" O ILE F 374 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ARG F 391 " --> pdb=" O ALA F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 through 401 removed outlier: 4.052A pdb=" N TYR F 398 " --> pdb=" O PHE F 394 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU F 401 " --> pdb=" O TRP F 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 404 through 428 removed outlier: 3.910A pdb=" N PHE F 408 " --> pdb=" O ASP F 404 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N TYR F 425 " --> pdb=" O GLU F 421 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLN F 426 " --> pdb=" O TYR F 422 " (cutoff:3.500A) Processing helix chain 'Q' and resid 10 through 29 removed outlier: 3.564A pdb=" N LYS Q 19 " --> pdb=" O GLN Q 15 " (cutoff:3.500A) Processing helix chain 'Q' and resid 40 through 46 removed outlier: 4.178A pdb=" N LEU Q 44 " --> pdb=" O SER Q 40 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ARG Q 46 " --> pdb=" O LEU Q 42 " (cutoff:3.500A) Processing helix chain 'Q' and resid 47 through 49 No H-bonds generated for 'chain 'Q' and resid 47 through 49' Processing helix chain 'Q' and resid 69 through 78 removed outlier: 4.516A pdb=" N MET Q 73 " --> pdb=" O GLU Q 69 " (cutoff:3.500A) Processing helix chain 'Q' and resid 81 through 85 removed outlier: 3.556A pdb=" N PHE Q 85 " --> pdb=" O GLY Q 82 " (cutoff:3.500A) Processing helix chain 'Q' and resid 86 through 88 No H-bonds generated for 'chain 'Q' and resid 86 through 88' Processing helix chain 'Q' and resid 100 through 106 Processing helix chain 'Q' and resid 108 through 127 removed outlier: 3.901A pdb=" N LEU Q 112 " --> pdb=" O GLU Q 108 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ASP Q 114 " --> pdb=" O ALA Q 110 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N SER Q 115 " --> pdb=" O GLU Q 111 " (cutoff:3.500A) Processing helix chain 'Q' and resid 142 through 159 Processing helix chain 'Q' and resid 180 through 195 removed outlier: 3.926A pdb=" N HIS Q 190 " --> pdb=" O THR Q 186 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLN Q 191 " --> pdb=" O LEU Q 187 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU Q 194 " --> pdb=" O HIS Q 190 " (cutoff:3.500A) Processing helix chain 'Q' and resid 204 through 214 Processing helix chain 'Q' and resid 221 through 237 removed outlier: 3.775A pdb=" N HIS Q 227 " --> pdb=" O GLY Q 223 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LEU Q 228 " --> pdb=" O ASP Q 224 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL Q 229 " --> pdb=" O LEU Q 225 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR Q 237 " --> pdb=" O MET Q 233 " (cutoff:3.500A) Processing helix chain 'Q' and resid 237 through 242 removed outlier: 3.801A pdb=" N ARG Q 241 " --> pdb=" O THR Q 237 " (cutoff:3.500A) Processing helix chain 'Q' and resid 249 through 258 Processing helix chain 'Q' and resid 285 through 295 Processing helix chain 'Q' and resid 296 through 299 Processing helix chain 'Q' and resid 304 through 308 Processing helix chain 'Q' and resid 322 through 337 Processing helix chain 'Q' and resid 338 through 341 Processing helix chain 'Q' and resid 374 through 390 removed outlier: 4.150A pdb=" N PHE Q 378 " --> pdb=" O ILE Q 374 " (cutoff:3.500A) Processing helix chain 'Q' and resid 394 through 401 removed outlier: 4.156A pdb=" N TYR Q 398 " --> pdb=" O PHE Q 394 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU Q 401 " --> pdb=" O TRP Q 397 " (cutoff:3.500A) Processing helix chain 'Q' and resid 405 through 428 removed outlier: 3.778A pdb=" N THR Q 409 " --> pdb=" O GLU Q 405 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TYR Q 425 " --> pdb=" O GLU Q 421 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN Q 426 " --> pdb=" O TYR Q 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 29 removed outlier: 3.736A pdb=" N ALA A 19 " --> pdb=" O GLN A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 51 removed outlier: 3.830A pdb=" N THR A 51 " --> pdb=" O ASP A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 81 removed outlier: 4.722A pdb=" N ILE A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 85 removed outlier: 4.578A pdb=" N GLN A 85 " --> pdb=" O THR A 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 82 through 85' Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 111 through 129 removed outlier: 4.602A pdb=" N ASP A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N LEU A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 161 Processing helix chain 'A' and resid 182 through 190 removed outlier: 3.665A pdb=" N ASN A 186 " --> pdb=" O VAL A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 197 Processing helix chain 'A' and resid 206 through 216 Processing helix chain 'A' and resid 223 through 244 removed outlier: 3.594A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG A 243 " --> pdb=" O THR A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 Processing helix chain 'A' and resid 277 through 284 removed outlier: 3.881A pdb=" N TYR A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N HIS A 283 " --> pdb=" O GLU A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 removed outlier: 3.990A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 302 removed outlier: 3.613A pdb=" N GLN A 301 " --> pdb=" O PRO A 298 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N MET A 302 " --> pdb=" O ALA A 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 298 through 302' Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 338 removed outlier: 3.556A pdb=" N VAL A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR A 337 " --> pdb=" O ALA A 333 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS A 338 " --> pdb=" O THR A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 401 removed outlier: 3.851A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG A 390 " --> pdb=" O GLU A 386 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LYS A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.989A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 436 removed outlier: 4.083A pdb=" N PHE A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY A 436 " --> pdb=" O TYR A 432 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 29 removed outlier: 3.774A pdb=" N ALA I 19 " --> pdb=" O GLN I 15 " (cutoff:3.500A) Processing helix chain 'I' and resid 44 through 48 Processing helix chain 'I' and resid 49 through 51 No H-bonds generated for 'chain 'I' and resid 49 through 51' Processing helix chain 'I' and resid 72 through 80 Processing helix chain 'I' and resid 102 through 108 Processing helix chain 'I' and resid 111 through 129 removed outlier: 4.665A pdb=" N ASP I 116 " --> pdb=" O LYS I 112 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N LEU I 117 " --> pdb=" O GLU I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 143 through 161 Processing helix chain 'I' and resid 182 through 190 Processing helix chain 'I' and resid 190 through 198 Processing helix chain 'I' and resid 206 through 216 Processing helix chain 'I' and resid 223 through 244 removed outlier: 3.756A pdb=" N ARG I 229 " --> pdb=" O THR I 225 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU I 230 " --> pdb=" O ASN I 226 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N SER I 241 " --> pdb=" O SER I 237 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N LEU I 242 " --> pdb=" O ILE I 238 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG I 243 " --> pdb=" O THR I 239 " (cutoff:3.500A) Processing helix chain 'I' and resid 251 through 260 Processing helix chain 'I' and resid 277 through 282 removed outlier: 4.099A pdb=" N TYR I 282 " --> pdb=" O ALA I 278 " (cutoff:3.500A) Processing helix chain 'I' and resid 287 through 297 Processing helix chain 'I' and resid 298 through 301 removed outlier: 3.501A pdb=" N GLN I 301 " --> pdb=" O PRO I 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 298 through 301' Processing helix chain 'I' and resid 306 through 310 removed outlier: 3.625A pdb=" N HIS I 309 " --> pdb=" O ASP I 306 " (cutoff:3.500A) Processing helix chain 'I' and resid 324 through 337 removed outlier: 3.724A pdb=" N THR I 337 " --> pdb=" O ALA I 333 " (cutoff:3.500A) Processing helix chain 'I' and resid 384 through 400 removed outlier: 3.824A pdb=" N TRP I 388 " --> pdb=" O ILE I 384 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N MET I 398 " --> pdb=" O LYS I 394 " (cutoff:3.500A) Processing helix chain 'I' and resid 404 through 410 removed outlier: 4.036A pdb=" N TYR I 408 " --> pdb=" O PHE I 404 " (cutoff:3.500A) Processing helix chain 'I' and resid 415 through 436 removed outlier: 4.061A pdb=" N SER I 419 " --> pdb=" O GLU I 415 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY I 436 " --> pdb=" O TYR I 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 29 removed outlier: 3.752A pdb=" N ALA C 19 " --> pdb=" O GLN C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 51 removed outlier: 3.602A pdb=" N THR C 51 " --> pdb=" O ASP C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 81 removed outlier: 4.652A pdb=" N ILE C 75 " --> pdb=" O GLU C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 85 removed outlier: 4.659A pdb=" N GLN C 85 " --> pdb=" O THR C 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 82 through 85' Processing helix chain 'C' and resid 88 through 90 No H-bonds generated for 'chain 'C' and resid 88 through 90' Processing helix chain 'C' and resid 102 through 108 Processing helix chain 'C' and resid 110 through 129 removed outlier: 4.310A pdb=" N ILE C 114 " --> pdb=" O ILE C 110 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASP C 116 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N LEU C 117 " --> pdb=" O GLU C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 161 Processing helix chain 'C' and resid 182 through 197 removed outlier: 4.627A pdb=" N HIS C 192 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N THR C 193 " --> pdb=" O LEU C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 216 Processing helix chain 'C' and resid 223 through 244 removed outlier: 3.806A pdb=" N LEU C 227 " --> pdb=" O THR C 223 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N SER C 241 " --> pdb=" O SER C 237 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N LEU C 242 " --> pdb=" O ILE C 238 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG C 243 " --> pdb=" O THR C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 260 Processing helix chain 'C' and resid 277 through 282 removed outlier: 4.064A pdb=" N TYR C 282 " --> pdb=" O ALA C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 296 removed outlier: 3.912A pdb=" N PHE C 296 " --> pdb=" O THR C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 309 Processing helix chain 'C' and resid 324 through 339 removed outlier: 3.688A pdb=" N ARG C 339 " --> pdb=" O ILE C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 401 removed outlier: 3.701A pdb=" N TRP C 388 " --> pdb=" O ILE C 384 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N LYS C 401 " --> pdb=" O LEU C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 411 removed outlier: 3.948A pdb=" N TYR C 408 " --> pdb=" O PHE C 404 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU C 411 " --> pdb=" O TRP C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 435 removed outlier: 3.733A pdb=" N SER C 419 " --> pdb=" O GLU C 415 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL C 435 " --> pdb=" O ASP C 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 29 removed outlier: 3.768A pdb=" N ALA E 19 " --> pdb=" O GLN E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 51 removed outlier: 3.700A pdb=" N ASP E 46 " --> pdb=" O GLY E 43 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N SER E 48 " --> pdb=" O GLY E 45 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N PHE E 49 " --> pdb=" O ASP E 46 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR E 51 " --> pdb=" O SER E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 80 removed outlier: 4.448A pdb=" N ILE E 75 " --> pdb=" O GLU E 71 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU E 77 " --> pdb=" O THR E 73 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL E 78 " --> pdb=" O VAL E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 86 removed outlier: 4.590A pdb=" N GLN E 85 " --> pdb=" O THR E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 108 Processing helix chain 'E' and resid 110 through 129 removed outlier: 4.129A pdb=" N ILE E 114 " --> pdb=" O ILE E 110 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ASP E 116 " --> pdb=" O LYS E 112 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N LEU E 117 " --> pdb=" O GLU E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 161 Processing helix chain 'E' and resid 182 through 190 Processing helix chain 'E' and resid 190 through 198 Processing helix chain 'E' and resid 206 through 216 Processing helix chain 'E' and resid 223 through 244 removed outlier: 3.883A pdb=" N LEU E 227 " --> pdb=" O THR E 223 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N SER E 241 " --> pdb=" O SER E 237 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N LEU E 242 " --> pdb=" O ILE E 238 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG E 243 " --> pdb=" O THR E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 260 Processing helix chain 'E' and resid 277 through 282 removed outlier: 4.208A pdb=" N TYR E 282 " --> pdb=" O ALA E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 296 removed outlier: 3.744A pdb=" N PHE E 296 " --> pdb=" O THR E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 301 removed outlier: 3.530A pdb=" N ASN E 300 " --> pdb=" O GLU E 297 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN E 301 " --> pdb=" O PRO E 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 297 through 301' Processing helix chain 'E' and resid 306 through 310 removed outlier: 3.529A pdb=" N HIS E 309 " --> pdb=" O ASP E 306 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 338 removed outlier: 3.505A pdb=" N LYS E 338 " --> pdb=" O THR E 334 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 400 removed outlier: 4.114A pdb=" N ALA E 387 " --> pdb=" O ALA E 383 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS E 394 " --> pdb=" O ARG E 390 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N MET E 398 " --> pdb=" O LYS E 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 411 removed outlier: 4.072A pdb=" N TYR E 408 " --> pdb=" O PHE E 404 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU E 411 " --> pdb=" O TRP E 407 " (cutoff:3.500A) Processing helix chain 'E' and resid 415 through 438 removed outlier: 4.263A pdb=" N SER E 419 " --> pdb=" O GLU E 415 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLY E 436 " --> pdb=" O TYR E 432 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ASP E 438 " --> pdb=" O GLU E 434 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 90 through 92 removed outlier: 8.240A pdb=" N VAL B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU B 65 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N GLU B 3 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY B 132 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N SER B 138 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N GLN B 131 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N ASN B 165 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N PHE B 133 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N PHE B 167 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU B 135 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N VAL B 169 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N HIS B 137 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N THR B 199 " --> pdb=" O PHE B 266 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N CYS B 201 " --> pdb=" O PRO B 268 " (cutoff:3.500A) removed outlier: 10.460A pdb=" N PHE B 270 " --> pdb=" O CYS B 201 " (cutoff:3.500A) removed outlier: 13.744A pdb=" N ASP B 203 " --> pdb=" O PHE B 270 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N PHE B 265 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N SER B 371 " --> pdb=" O PHE B 265 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 51 through 53 Processing sheet with id=AA3, first strand: chain 'D' and resid 90 through 92 removed outlier: 8.321A pdb=" N VAL D 91 " --> pdb=" O ALA D 63 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU D 65 " --> pdb=" O VAL D 91 " (cutoff:3.500A) removed outlier: 8.532A pdb=" N ILE D 64 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N HIS D 6 " --> pdb=" O ILE D 64 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N VAL D 66 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N GLN D 8 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N GLU D 3 " --> pdb=" O GLN D 131 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N PHE D 133 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N VAL D 5 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N LEU D 135 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE D 7 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N HIS D 137 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N ALA D 9 " --> pdb=" O HIS D 137 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N HIS D 137 " --> pdb=" O PHE D 167 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N THR D 199 " --> pdb=" O PHE D 266 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N CYS D 201 " --> pdb=" O PRO D 268 " (cutoff:3.500A) removed outlier: 10.783A pdb=" N PHE D 270 " --> pdb=" O CYS D 201 " (cutoff:3.500A) removed outlier: 13.811A pdb=" N ASP D 203 " --> pdb=" O PHE D 270 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N PHE D 265 " --> pdb=" O SER D 371 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N SER D 371 " --> pdb=" O PHE D 265 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 51 through 53 Processing sheet with id=AA5, first strand: chain 'F' and resid 90 through 92 removed outlier: 8.191A pdb=" N VAL F 91 " --> pdb=" O ALA F 63 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LEU F 65 " --> pdb=" O VAL F 91 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N ILE F 64 " --> pdb=" O ILE F 4 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N HIS F 6 " --> pdb=" O ILE F 64 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N VAL F 66 " --> pdb=" O HIS F 6 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N GLN F 8 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N GLU F 3 " --> pdb=" O GLN F 131 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N PHE F 133 " --> pdb=" O GLU F 3 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VAL F 5 " --> pdb=" O PHE F 133 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N LEU F 135 " --> pdb=" O VAL F 5 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE F 7 " --> pdb=" O LEU F 135 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N HIS F 137 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N ALA F 9 " --> pdb=" O HIS F 137 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLN F 131 " --> pdb=" O ILE F 163 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N ASN F 165 " --> pdb=" O GLN F 131 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N PHE F 133 " --> pdb=" O ASN F 165 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N PHE F 167 " --> pdb=" O PHE F 133 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU F 135 " --> pdb=" O PHE F 167 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N VAL F 169 " --> pdb=" O LEU F 135 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N HIS F 137 " --> pdb=" O VAL F 169 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU F 198 " --> pdb=" O MET F 164 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N THR F 199 " --> pdb=" O PHE F 266 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N CYS F 201 " --> pdb=" O PRO F 268 " (cutoff:3.500A) removed outlier: 10.446A pdb=" N PHE F 270 " --> pdb=" O CYS F 201 " (cutoff:3.500A) removed outlier: 13.534A pdb=" N ASP F 203 " --> pdb=" O PHE F 270 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N PHE F 265 " --> pdb=" O SER F 371 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N SER F 371 " --> pdb=" O PHE F 265 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 51 through 53 Processing sheet with id=AA7, first strand: chain 'Q' and resid 90 through 92 removed outlier: 8.066A pdb=" N VAL Q 91 " --> pdb=" O ALA Q 63 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LEU Q 65 " --> pdb=" O VAL Q 91 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N ILE Q 64 " --> pdb=" O ILE Q 4 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N HIS Q 6 " --> pdb=" O ILE Q 64 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N VAL Q 66 " --> pdb=" O HIS Q 6 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N GLN Q 8 " --> pdb=" O VAL Q 66 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N GLU Q 3 " --> pdb=" O GLN Q 131 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N PHE Q 133 " --> pdb=" O GLU Q 3 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL Q 5 " --> pdb=" O PHE Q 133 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N LEU Q 135 " --> pdb=" O VAL Q 5 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE Q 7 " --> pdb=" O LEU Q 135 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N HIS Q 137 " --> pdb=" O ILE Q 7 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N ALA Q 9 " --> pdb=" O HIS Q 137 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N GLN Q 131 " --> pdb=" O ILE Q 163 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N ASN Q 165 " --> pdb=" O GLN Q 131 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N PHE Q 133 " --> pdb=" O ASN Q 165 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N PHE Q 167 " --> pdb=" O PHE Q 133 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LEU Q 135 " --> pdb=" O PHE Q 167 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N VAL Q 169 " --> pdb=" O LEU Q 135 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N HIS Q 137 " --> pdb=" O VAL Q 169 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N THR Q 199 " --> pdb=" O PHE Q 266 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N CYS Q 201 " --> pdb=" O PRO Q 268 " (cutoff:3.500A) removed outlier: 10.250A pdb=" N PHE Q 270 " --> pdb=" O CYS Q 201 " (cutoff:3.500A) removed outlier: 13.511A pdb=" N ASP Q 203 " --> pdb=" O PHE Q 270 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N PHE Q 265 " --> pdb=" O SER Q 371 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N SER Q 371 " --> pdb=" O PHE Q 265 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ALA Q 364 " --> pdb=" O PHE Q 317 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N PHE Q 317 " --> pdb=" O ALA Q 364 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N THR Q 366 " --> pdb=" O ALA Q 315 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ALA Q 315 " --> pdb=" O THR Q 366 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ILE Q 368 " --> pdb=" O VAL Q 313 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N VAL Q 313 " --> pdb=" O ILE Q 368 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ASN Q 370 " --> pdb=" O LEU Q 311 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'Q' and resid 51 through 54 removed outlier: 3.768A pdb=" N LYS Q 58 " --> pdb=" O ALA Q 54 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 92 through 94 removed outlier: 7.898A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N SER A 140 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N PHE A 135 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N PHE A 169 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL A 137 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N ILE A 171 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N HIS A 139 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N CYS A 200 " --> pdb=" O LYS A 166 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AB2, first strand: chain 'A' and resid 269 through 270 Processing sheet with id=AB3, first strand: chain 'I' and resid 92 through 94 removed outlier: 7.766A pdb=" N ILE I 93 " --> pdb=" O ALA I 65 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N PHE I 67 " --> pdb=" O ILE I 93 " (cutoff:3.500A) removed outlier: 8.607A pdb=" N VAL I 66 " --> pdb=" O CYS I 4 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N SER I 6 " --> pdb=" O VAL I 66 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N VAL I 68 " --> pdb=" O SER I 6 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N HIS I 8 " --> pdb=" O VAL I 68 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLU I 3 " --> pdb=" O LEU I 132 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLY I 134 " --> pdb=" O GLU I 3 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N SER I 140 " --> pdb=" O VAL I 9 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N GLN I 133 " --> pdb=" O SER I 165 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N LEU I 167 " --> pdb=" O GLN I 133 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N PHE I 135 " --> pdb=" O LEU I 167 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N PHE I 169 " --> pdb=" O PHE I 135 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N VAL I 137 " --> pdb=" O PHE I 169 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N ILE I 171 " --> pdb=" O VAL I 137 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N HIS I 139 " --> pdb=" O ILE I 171 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N CYS I 200 " --> pdb=" O LYS I 166 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 53 through 55 Processing sheet with id=AB5, first strand: chain 'I' and resid 269 through 273 removed outlier: 3.592A pdb=" N ALA I 314 " --> pdb=" O ASN I 380 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 92 through 94 removed outlier: 7.909A pdb=" N ILE C 93 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N PHE C 67 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N SER C 6 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N VAL C 68 " --> pdb=" O SER C 6 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N HIS C 8 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ILE C 5 " --> pdb=" O LEU C 136 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N PHE C 138 " --> pdb=" O ILE C 5 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE C 7 " --> pdb=" O PHE C 138 " (cutoff:3.500A) removed outlier: 8.845A pdb=" N SER C 140 " --> pdb=" O ILE C 7 " (cutoff:3.500A) removed outlier: 8.703A pdb=" N VAL C 9 " --> pdb=" O SER C 140 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N PHE C 135 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N PHE C 169 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL C 137 " --> pdb=" O PHE C 169 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N ILE C 171 " --> pdb=" O VAL C 137 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N HIS C 139 " --> pdb=" O ILE C 171 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AB8, first strand: chain 'C' and resid 268 through 270 Processing sheet with id=AB9, first strand: chain 'C' and resid 268 through 270 Processing sheet with id=AC1, first strand: chain 'E' and resid 92 through 94 removed outlier: 8.037A pdb=" N ILE E 93 " --> pdb=" O ALA E 65 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N PHE E 67 " --> pdb=" O ILE E 93 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N VAL E 66 " --> pdb=" O CYS E 4 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N SER E 6 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N VAL E 68 " --> pdb=" O SER E 6 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N HIS E 8 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N GLU E 3 " --> pdb=" O GLY E 134 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N LEU E 136 " --> pdb=" O GLU E 3 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ILE E 5 " --> pdb=" O LEU E 136 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N PHE E 138 " --> pdb=" O ILE E 5 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE E 7 " --> pdb=" O PHE E 138 " (cutoff:3.500A) removed outlier: 9.015A pdb=" N SER E 140 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 8.751A pdb=" N VAL E 9 " --> pdb=" O SER E 140 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N GLN E 133 " --> pdb=" O SER E 165 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N LEU E 167 " --> pdb=" O GLN E 133 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N PHE E 135 " --> pdb=" O LEU E 167 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N PHE E 169 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N VAL E 137 " --> pdb=" O PHE E 169 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N ILE E 171 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N HIS E 139 " --> pdb=" O ILE E 171 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N CYS E 200 " --> pdb=" O LYS E 166 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AC3, first strand: chain 'E' and resid 269 through 273 removed outlier: 6.984A pdb=" N ALA E 374 " --> pdb=" O TYR E 319 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N TYR E 319 " --> pdb=" O ALA E 374 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N CYS E 376 " --> pdb=" O LEU E 317 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N LEU E 317 " --> pdb=" O CYS E 376 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU E 378 " --> pdb=" O CYS E 315 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N CYS E 315 " --> pdb=" O LEU E 378 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ASN E 380 " --> pdb=" O MET E 313 " (cutoff:3.500A) 1341 hydrogen bonds defined for protein. 3909 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: 5.24 Time building geometry restraints manager: 2.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4831 1.32 - 1.45: 7785 1.45 - 1.59: 14919 1.59 - 1.72: 32 1.72 - 1.85: 298 Bond restraints: 27865 Sorted by residual: bond pdb=" C MET B 406 " pdb=" O MET B 406 " ideal model delta sigma weight residual 1.236 1.285 -0.048 1.26e-02 6.30e+03 1.48e+01 bond pdb=" C THR B 409 " pdb=" O THR B 409 " ideal model delta sigma weight residual 1.236 1.192 0.044 1.25e-02 6.40e+03 1.25e+01 bond pdb=" N LEU Q 361 " pdb=" CA LEU Q 361 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.21e-02 6.83e+03 7.92e+00 bond pdb=" N LEU B 361 " pdb=" CA LEU B 361 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.16e-02 7.43e+03 7.19e+00 bond pdb=" N LEU F 361 " pdb=" CA LEU F 361 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.29e-02 6.01e+03 7.17e+00 ... (remaining 27860 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.93: 37379 2.93 - 5.85: 439 5.85 - 8.78: 56 8.78 - 11.70: 5 11.70 - 14.63: 5 Bond angle restraints: 37884 Sorted by residual: angle pdb=" N GLU B 407 " pdb=" CA GLU B 407 " pdb=" C GLU B 407 " ideal model delta sigma weight residual 111.71 104.93 6.78 1.15e+00 7.56e-01 3.48e+01 angle pdb=" C MET B 406 " pdb=" N GLU B 407 " pdb=" CA GLU B 407 " ideal model delta sigma weight residual 120.28 113.02 7.26 1.44e+00 4.82e-01 2.54e+01 angle pdb=" CB MET D 406 " pdb=" CG MET D 406 " pdb=" SD MET D 406 " ideal model delta sigma weight residual 112.70 127.33 -14.63 3.00e+00 1.11e-01 2.38e+01 angle pdb=" CB MET D 321 " pdb=" CG MET D 321 " pdb=" SD MET D 321 " ideal model delta sigma weight residual 112.70 126.74 -14.04 3.00e+00 1.11e-01 2.19e+01 angle pdb=" CB MET B 299 " pdb=" CG MET B 299 " pdb=" SD MET B 299 " ideal model delta sigma weight residual 112.70 125.80 -13.10 3.00e+00 1.11e-01 1.91e+01 ... (remaining 37879 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.85: 16189 35.85 - 71.70: 352 71.70 - 107.55: 37 107.55 - 143.40: 5 143.40 - 179.25: 7 Dihedral angle restraints: 16590 sinusoidal: 6610 harmonic: 9980 Sorted by residual: dihedral pdb=" C5' GTP C 501 " pdb=" O5' GTP C 501 " pdb=" PA GTP C 501 " pdb=" O3A GTP C 501 " ideal model delta sinusoidal sigma weight residual 69.27 -109.98 179.25 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' GTP I 501 " pdb=" O5' GTP I 501 " pdb=" PA GTP I 501 " pdb=" O3A GTP I 501 " ideal model delta sinusoidal sigma weight residual 69.27 -108.12 177.39 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' GTP E 501 " pdb=" O5' GTP E 501 " pdb=" PA GTP E 501 " pdb=" O3A GTP E 501 " ideal model delta sinusoidal sigma weight residual 69.27 -113.53 -177.20 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 16587 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 3625 0.069 - 0.138: 491 0.138 - 0.207: 39 0.207 - 0.276: 0 0.276 - 0.345: 1 Chirality restraints: 4156 Sorted by residual: chirality pdb=" CB THR A 150 " pdb=" CA THR A 150 " pdb=" OG1 THR A 150 " pdb=" CG2 THR A 150 " both_signs ideal model delta sigma weight residual False 2.55 2.21 0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" CB ILE B 155 " pdb=" CA ILE B 155 " pdb=" CG1 ILE B 155 " pdb=" CG2 ILE B 155 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.19 2.00e-01 2.50e+01 9.26e-01 chirality pdb=" CA ILE F 345 " pdb=" N ILE F 345 " pdb=" C ILE F 345 " pdb=" CB ILE F 345 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.36e-01 ... (remaining 4153 not shown) Planarity restraints: 4935 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 363 " -0.053 5.00e-02 4.00e+02 7.96e-02 1.01e+01 pdb=" N PRO A 364 " 0.138 5.00e-02 4.00e+02 pdb=" CA PRO A 364 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 364 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 390 " -0.014 2.00e-02 2.50e+03 2.85e-02 8.12e+00 pdb=" C ARG B 390 " 0.049 2.00e-02 2.50e+03 pdb=" O ARG B 390 " -0.018 2.00e-02 2.50e+03 pdb=" N ARG B 391 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 106 " -0.011 2.00e-02 2.50e+03 2.28e-02 5.20e+00 pdb=" C TYR B 106 " 0.039 2.00e-02 2.50e+03 pdb=" O TYR B 106 " -0.015 2.00e-02 2.50e+03 pdb=" N THR B 107 " -0.013 2.00e-02 2.50e+03 ... (remaining 4932 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 44 2.42 - 3.04: 16289 3.04 - 3.66: 40979 3.66 - 4.28: 62374 4.28 - 4.90: 107318 Nonbonded interactions: 227004 Sorted by model distance: nonbonded pdb=" O1G GTP C 501 " pdb="MG MG C 502 " model vdw 1.803 2.170 nonbonded pdb=" O1G GTP A 501 " pdb="MG MG A 502 " model vdw 1.878 2.170 nonbonded pdb=" O1G GTP E 501 " pdb="MG MG E 502 " model vdw 1.944 2.170 nonbonded pdb=" O2B G2P Q 501 " pdb="MG MG Q 502 " model vdw 1.959 2.170 nonbonded pdb=" O3G G2P B 501 " pdb="MG MG B 502 " model vdw 1.965 2.170 ... (remaining 226999 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 120 or (resid 121 and (name N or name CA or name \ C or name O or name CB )) or resid 122 through 162 or (resid 163 and (name N or \ name CA or name C or name O or name CB )) or resid 164 through 220 or (resid 22 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 222 through \ 502)) selection = (chain 'C' and (resid 1 through 120 or (resid 121 and (name N or name CA or name \ C or name O or name CB )) or resid 122 through 162 or (resid 163 and (name N or \ name CA or name C or name O or name CB )) or resid 164 through 220 or (resid 22 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 222 through \ 502)) selection = chain 'E' selection = (chain 'I' and (resid 1 through 120 or (resid 121 and (name N or name CA or name \ C or name O or name CB )) or resid 122 through 502)) } ncs_group { reference = (chain 'B' and (resid 1 through 322 or (resid 323 and (name N or name CA or name \ C or name O or name CB )) or resid 324 through 502)) selection = chain 'D' selection = (chain 'F' and ((resid 1 and (name N or name CA or name C or name O or name CB ) \ ) or resid 2 through 281 or (resid 282 through 283 and (name N or name CA or nam \ e C or name O or name CB )) or resid 284 through 322 or (resid 323 and (name N o \ r name CA or name C or name O or name CB )) or resid 324 through 502)) selection = (chain 'Q' and ((resid 1 and (name N or name CA or name C or name O or name CB ) \ ) or resid 2 through 281 or (resid 282 through 283 and (name N or name CA or nam \ e C or name O or name CB )) or resid 284 through 322 or (resid 323 and (name N o \ r name CA or name C or name O or name CB )) or resid 324 through 502)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 14.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 24.200 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6679 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 : 0.005 0.055 27865 Z= 0.222 Angle : 0.818 14.626 37884 Z= 0.429 Chirality : 0.047 0.345 4156 Planarity : 0.005 0.088 4935 Dihedral : 15.790 179.247 10198 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.34 % Allowed : 8.19 % Favored : 91.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.14), residues: 3440 helix: 1.17 (0.13), residues: 1572 sheet: 0.22 (0.23), residues: 496 loop : -0.87 (0.16), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 214 TYR 0.013 0.001 TYR C 312 PHE 0.026 0.001 PHE E 255 TRP 0.037 0.002 TRP E 388 HIS 0.006 0.001 HIS C 266 Details of bonding type rmsd covalent geometry : bond 0.00476 (27865) covalent geometry : angle 0.81849 (37884) hydrogen bonds : bond 0.12821 ( 1331) hydrogen bonds : angle 5.75008 ( 3909) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 803 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 793 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 PHE cc_start: 0.7400 (p90) cc_final: 0.7199 (p90) REVERT: B 157 GLU cc_start: 0.7435 (mm-30) cc_final: 0.7196 (mt-10) REVERT: B 164 MET cc_start: 0.6789 (ttm) cc_final: 0.6561 (ttp) REVERT: B 186 THR cc_start: 0.8442 (m) cc_final: 0.8153 (p) REVERT: B 227 HIS cc_start: 0.7753 (t-90) cc_final: 0.7349 (t70) REVERT: B 298 ASN cc_start: 0.8430 (t0) cc_final: 0.8218 (t0) REVERT: B 328 GLU cc_start: 0.6807 (tp30) cc_final: 0.6040 (tm-30) REVERT: B 332 ASN cc_start: 0.7092 (t0) cc_final: 0.6788 (m-40) REVERT: B 379 LYS cc_start: 0.8103 (mtpp) cc_final: 0.7815 (mtpt) REVERT: B 404 ASP cc_start: 0.7421 (m-30) cc_final: 0.7146 (t0) REVERT: D 94 GLN cc_start: 0.7130 (mt0) cc_final: 0.6848 (mm-40) REVERT: D 155 ILE cc_start: 0.7984 (mt) cc_final: 0.7536 (mt) REVERT: D 159 TYR cc_start: 0.7201 (m-80) cc_final: 0.6850 (m-80) REVERT: D 178 THR cc_start: 0.7015 (m) cc_final: 0.6671 (p) REVERT: D 280 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.8103 (pt0) REVERT: D 320 ARG cc_start: 0.7528 (mmm-85) cc_final: 0.7174 (mmt-90) REVERT: D 328 GLU cc_start: 0.7082 (tp30) cc_final: 0.6607 (mm-30) REVERT: D 332 ASN cc_start: 0.7130 (t0) cc_final: 0.6425 (m-40) REVERT: D 378 PHE cc_start: 0.7793 (m-10) cc_final: 0.7575 (m-10) REVERT: D 422 TYR cc_start: 0.7548 (m-80) cc_final: 0.7256 (m-80) REVERT: D 425 TYR cc_start: 0.6941 (m-80) cc_final: 0.6531 (m-80) REVERT: F 33 THR cc_start: 0.7005 (m) cc_final: 0.6637 (t) REVERT: F 190 HIS cc_start: 0.7046 (t70) cc_final: 0.6835 (t-170) REVERT: F 209 ASP cc_start: 0.6715 (m-30) cc_final: 0.6478 (m-30) REVERT: F 245 GLN cc_start: 0.7360 (mt0) cc_final: 0.6155 (tp40) REVERT: F 267 MET cc_start: 0.7962 (ttp) cc_final: 0.7527 (ttm) REVERT: F 320 ARG cc_start: 0.7902 (mmm160) cc_final: 0.7505 (mmt180) REVERT: F 332 ASN cc_start: 0.7098 (m-40) cc_final: 0.6727 (m-40) REVERT: F 362 LYS cc_start: 0.8133 (ttpp) cc_final: 0.7803 (tttt) REVERT: F 376 GLU cc_start: 0.7238 (mm-30) cc_final: 0.6958 (mt-10) REVERT: Q 8 GLN cc_start: 0.8289 (mt0) cc_final: 0.8032 (mt0) REVERT: Q 190 HIS cc_start: 0.7426 (t70) cc_final: 0.7098 (t70) REVERT: Q 191 GLN cc_start: 0.7520 (mm-40) cc_final: 0.7183 (mp10) REVERT: Q 216 LYS cc_start: 0.7987 (mppt) cc_final: 0.7785 (mmtt) REVERT: Q 291 GLN cc_start: 0.7942 (tt0) cc_final: 0.7199 (mm-40) REVERT: Q 332 ASN cc_start: 0.7171 (t0) cc_final: 0.6568 (m-40) REVERT: Q 425 TYR cc_start: 0.7332 (m-80) cc_final: 0.6911 (m-80) REVERT: A 55 GLU cc_start: 0.7896 (tt0) cc_final: 0.7639 (tp30) REVERT: A 123 ARG cc_start: 0.6466 (tpp-160) cc_final: 0.5712 (tpp-160) REVERT: A 168 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7378 (mt-10) REVERT: A 170 SER cc_start: 0.8340 (m) cc_final: 0.7995 (p) REVERT: A 297 GLU cc_start: 0.6863 (mm-30) cc_final: 0.6379 (mt-10) REVERT: A 373 ARG cc_start: 0.7708 (mtm-85) cc_final: 0.7351 (ttm110) REVERT: A 377 MET cc_start: 0.8307 (ttp) cc_final: 0.8050 (ttp) REVERT: A 386 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7400 (tt0) REVERT: A 417 GLU cc_start: 0.7143 (mm-30) cc_final: 0.6891 (mt-10) REVERT: I 1 MET cc_start: 0.6674 (mmm) cc_final: 0.5952 (tpp) REVERT: I 112 LYS cc_start: 0.6943 (ptmt) cc_final: 0.6531 (mptt) REVERT: I 130 THR cc_start: 0.7109 (m) cc_final: 0.6573 (p) REVERT: I 241 SER cc_start: 0.8194 (m) cc_final: 0.7721 (t) REVERT: I 254 GLU cc_start: 0.3190 (mm-30) cc_final: 0.1836 (pt0) REVERT: I 297 GLU cc_start: 0.6710 (pt0) cc_final: 0.6303 (tp30) REVERT: I 425 MET cc_start: 0.6770 (tpt) cc_final: 0.6245 (tpp) REVERT: C 31 GLN cc_start: 0.7006 (mt0) cc_final: 0.6701 (mm-40) REVERT: C 55 GLU cc_start: 0.7637 (tt0) cc_final: 0.7167 (mm-30) REVERT: C 199 ASP cc_start: 0.6555 (m-30) cc_final: 0.6023 (m-30) REVERT: C 290 GLU cc_start: 0.6991 (mm-30) cc_final: 0.6790 (tt0) REVERT: C 398 MET cc_start: 0.5871 (OUTLIER) cc_final: 0.4905 (mpp) REVERT: E 85 GLN cc_start: 0.7359 (mt0) cc_final: 0.6953 (mp10) REVERT: E 192 HIS cc_start: 0.7232 (OUTLIER) cc_final: 0.6926 (t70) REVERT: E 232 SER cc_start: 0.7759 (m) cc_final: 0.7094 (p) REVERT: E 254 GLU cc_start: 0.2461 (mm-30) cc_final: 0.1474 (tt0) outliers start: 10 outliers final: 3 residues processed: 798 average time/residue: 0.2032 time to fit residues: 245.5496 Evaluate side-chains 408 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 402 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 280 GLN Chi-restraints excluded: chain Q residue 159 TYR Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain I residue 378 LEU Chi-restraints excluded: chain C residue 398 MET Chi-restraints excluded: chain E residue 192 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 0.4980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 414 ASN D 89 ASN D 137 HIS ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 256 ASN D 298 ASN D 334 GLN D 348 ASN F 43 GLN F 307 HIS Q 6 HIS Q 8 GLN Q 307 HIS Q 347 ASN A 50 ASN A 309 HIS I 50 ASN C 61 HIS C 88 HIS C 91 GLN C 256 GLN C 309 HIS E 28 HIS E 31 GLN E 88 HIS ** E 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 139 HIS E 380 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.111005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.093191 restraints weight = 38635.177| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.92 r_work: 0.3190 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.4335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 27865 Z= 0.178 Angle : 0.613 9.383 37884 Z= 0.323 Chirality : 0.046 0.154 4156 Planarity : 0.005 0.070 4935 Dihedral : 11.648 179.514 3953 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.41 % Allowed : 9.88 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.14), residues: 3440 helix: 1.30 (0.13), residues: 1564 sheet: 0.49 (0.23), residues: 500 loop : -0.68 (0.16), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 162 TYR 0.021 0.002 TYR E 224 PHE 0.019 0.002 PHE D 242 TRP 0.017 0.002 TRP I 21 HIS 0.009 0.001 HIS C 406 Details of bonding type rmsd covalent geometry : bond 0.00395 (27865) covalent geometry : angle 0.61292 (37884) hydrogen bonds : bond 0.04895 ( 1331) hydrogen bonds : angle 4.73124 ( 3909) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 423 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 108 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8114 (mp0) REVERT: B 164 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.8060 (mtp) REVERT: B 257 MET cc_start: 0.9063 (mmm) cc_final: 0.8638 (mmm) REVERT: B 321 MET cc_start: 0.8652 (mmp) cc_final: 0.8283 (mmt) REVERT: B 328 GLU cc_start: 0.8028 (tp30) cc_final: 0.7642 (tm-30) REVERT: D 40 SER cc_start: 0.8265 (OUTLIER) cc_final: 0.8005 (p) REVERT: D 65 LEU cc_start: 0.8755 (mp) cc_final: 0.8551 (mp) REVERT: D 312 THR cc_start: 0.8559 (p) cc_final: 0.8344 (p) REVERT: D 328 GLU cc_start: 0.7948 (tp30) cc_final: 0.7631 (tm-30) REVERT: F 33 THR cc_start: 0.8451 (m) cc_final: 0.8220 (t) REVERT: F 35 THR cc_start: 0.7933 (p) cc_final: 0.7470 (t) REVERT: F 281 TYR cc_start: 0.8736 (m-80) cc_final: 0.8483 (m-80) REVERT: F 299 MET cc_start: 0.9123 (mmp) cc_final: 0.8763 (mmt) REVERT: Q 328 GLU cc_start: 0.7779 (pt0) cc_final: 0.7441 (pt0) REVERT: A 1 MET cc_start: 0.8529 (tpp) cc_final: 0.8285 (mmm) REVERT: A 98 ASP cc_start: 0.8480 (p0) cc_final: 0.8237 (p0) REVERT: A 116 ASP cc_start: 0.8136 (m-30) cc_final: 0.7879 (m-30) REVERT: A 334 THR cc_start: 0.8837 (m) cc_final: 0.8558 (p) REVERT: A 338 LYS cc_start: 0.8179 (mtpm) cc_final: 0.7921 (mtpt) REVERT: A 402 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.7695 (mmt180) REVERT: A 425 MET cc_start: 0.8270 (tpp) cc_final: 0.8059 (tpp) REVERT: I 1 MET cc_start: 0.7849 (mmm) cc_final: 0.7630 (mmt) REVERT: I 47 ASP cc_start: 0.7472 (t70) cc_final: 0.6773 (p0) REVERT: I 90 GLU cc_start: 0.8707 (mm-30) cc_final: 0.8471 (mm-30) REVERT: I 123 ARG cc_start: 0.7582 (ttp-110) cc_final: 0.7308 (tpm170) REVERT: I 203 MET cc_start: 0.8972 (OUTLIER) cc_final: 0.8682 (mtt) REVERT: I 215 ARG cc_start: 0.8184 (mtm-85) cc_final: 0.7868 (mtp85) REVERT: I 254 GLU cc_start: 0.6196 (mm-30) cc_final: 0.4678 (pt0) REVERT: C 94 THR cc_start: 0.7055 (OUTLIER) cc_final: 0.6822 (t) REVERT: C 124 LYS cc_start: 0.8534 (mtpp) cc_final: 0.8331 (mttt) REVERT: C 398 MET cc_start: 0.8040 (OUTLIER) cc_final: 0.7681 (mtp) REVERT: C 432 TYR cc_start: 0.8611 (OUTLIER) cc_final: 0.7625 (m-80) REVERT: E 123 ARG cc_start: 0.8458 (ttt180) cc_final: 0.7928 (tpp-160) REVERT: E 254 GLU cc_start: 0.5479 (mm-30) cc_final: 0.3748 (pt0) REVERT: E 345 ASP cc_start: 0.8370 (p0) cc_final: 0.8151 (p0) outliers start: 70 outliers final: 32 residues processed: 473 average time/residue: 0.1835 time to fit residues: 136.6761 Evaluate side-chains 329 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 289 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 334 GLN Chi-restraints excluded: chain D residue 344 TRP Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 288 GLU Chi-restraints excluded: chain Q residue 35 THR Chi-restraints excluded: chain Q residue 136 THR Chi-restraints excluded: chain Q residue 159 TYR Chi-restraints excluded: chain Q residue 172 SER Chi-restraints excluded: chain Q residue 363 MET Chi-restraints excluded: chain Q residue 409 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain I residue 203 MET Chi-restraints excluded: chain I residue 225 THR Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 398 MET Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 432 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 54 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 256 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 184 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 260 optimal weight: 0.5980 chunk 222 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 323 optimal weight: 0.6980 chunk 314 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 HIS B 298 ASN D 37 HIS D 256 ASN D 334 GLN D 348 ASN D 414 ASN D 423 GLN F 6 HIS F 8 GLN F 15 GLN F 279 GLN F 347 ASN F 414 ASN Q 332 ASN A 50 ASN A 329 ASN I 28 HIS C 11 GLN C 61 HIS C 88 HIS C 101 ASN C 406 HIS E 101 ASN ** E 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 139 HIS E 266 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.104643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.086417 restraints weight = 38724.941| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.91 r_work: 0.3073 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.5713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 27865 Z= 0.166 Angle : 0.557 8.189 37884 Z= 0.293 Chirality : 0.045 0.193 4156 Planarity : 0.004 0.053 4935 Dihedral : 11.569 178.750 3946 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.86 % Allowed : 10.32 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.14), residues: 3440 helix: 1.50 (0.13), residues: 1548 sheet: 0.95 (0.24), residues: 484 loop : -0.80 (0.16), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 221 TYR 0.013 0.001 TYR F 310 PHE 0.018 0.001 PHE C 255 TRP 0.019 0.001 TRP I 21 HIS 0.011 0.001 HIS D 190 Details of bonding type rmsd covalent geometry : bond 0.00391 (27865) covalent geometry : angle 0.55723 (37884) hydrogen bonds : bond 0.04786 ( 1331) hydrogen bonds : angle 4.58879 ( 3909) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 307 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 108 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.7186 (mp0) REVERT: B 114 ASP cc_start: 0.7962 (m-30) cc_final: 0.7738 (p0) REVERT: B 131 GLN cc_start: 0.9234 (OUTLIER) cc_final: 0.8766 (tt0) REVERT: B 164 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.8398 (ttt) REVERT: B 257 MET cc_start: 0.9047 (mmm) cc_final: 0.8720 (mmm) REVERT: B 328 GLU cc_start: 0.7934 (tp30) cc_final: 0.7656 (tt0) REVERT: B 332 ASN cc_start: 0.8367 (m-40) cc_final: 0.8070 (m-40) REVERT: D 40 SER cc_start: 0.8209 (OUTLIER) cc_final: 0.7985 (p) REVERT: D 65 LEU cc_start: 0.8923 (mp) cc_final: 0.8693 (mp) REVERT: D 159 TYR cc_start: 0.8711 (m-80) cc_final: 0.8455 (m-80) REVERT: D 312 THR cc_start: 0.8680 (OUTLIER) cc_final: 0.8452 (p) REVERT: D 401 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7945 (mp0) REVERT: F 190 HIS cc_start: 0.8433 (t70) cc_final: 0.8224 (t-90) REVERT: F 250 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8685 (mp) REVERT: F 320 ARG cc_start: 0.8303 (mmm160) cc_final: 0.8006 (mmt180) REVERT: A 168 GLU cc_start: 0.8895 (mt-10) cc_final: 0.8563 (mt-10) REVERT: A 338 LYS cc_start: 0.8312 (mtpm) cc_final: 0.8109 (mtpt) REVERT: I 1 MET cc_start: 0.8497 (mmm) cc_final: 0.8037 (mmt) REVERT: I 47 ASP cc_start: 0.7760 (t70) cc_final: 0.7030 (p0) REVERT: I 90 GLU cc_start: 0.8641 (mm-30) cc_final: 0.8441 (mm-30) REVERT: I 123 ARG cc_start: 0.7699 (ttp-110) cc_final: 0.7488 (tpt170) REVERT: I 203 MET cc_start: 0.9041 (OUTLIER) cc_final: 0.8726 (mtt) REVERT: I 215 ARG cc_start: 0.8388 (mtm-85) cc_final: 0.7977 (mtp85) REVERT: I 254 GLU cc_start: 0.6102 (mm-30) cc_final: 0.4600 (pt0) REVERT: C 124 LYS cc_start: 0.8621 (mtpp) cc_final: 0.8391 (mttt) REVERT: C 432 TYR cc_start: 0.8834 (OUTLIER) cc_final: 0.7987 (m-80) REVERT: E 120 ASP cc_start: 0.8036 (m-30) cc_final: 0.7669 (m-30) REVERT: E 123 ARG cc_start: 0.8614 (ttt180) cc_final: 0.8130 (tpp-160) REVERT: E 254 GLU cc_start: 0.5142 (mm-30) cc_final: 0.3691 (pt0) REVERT: E 255 PHE cc_start: 0.8974 (OUTLIER) cc_final: 0.8462 (t80) outliers start: 83 outliers final: 47 residues processed: 371 average time/residue: 0.1908 time to fit residues: 110.3198 Evaluate side-chains 321 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 265 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 288 GLU Chi-restraints excluded: chain F residue 312 THR Chi-restraints excluded: chain F residue 382 SER Chi-restraints excluded: chain Q residue 135 LEU Chi-restraints excluded: chain Q residue 172 SER Chi-restraints excluded: chain Q residue 363 MET Chi-restraints excluded: chain Q residue 409 THR Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain I residue 3 GLU Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 194 THR Chi-restraints excluded: chain I residue 203 MET Chi-restraints excluded: chain I residue 324 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 88 HIS Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain E residue 3 GLU Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 255 PHE Chi-restraints excluded: chain E residue 337 THR Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 432 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 173 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 280 optimal weight: 0.1980 chunk 76 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 338 optimal weight: 1.9990 chunk 247 optimal weight: 2.9990 chunk 174 optimal weight: 0.1980 chunk 286 optimal weight: 1.9990 chunk 163 optimal weight: 0.8980 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 298 ASN B 329 GLN ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 414 ASN C 31 GLN C 88 HIS C 133 GLN C 139 HIS E 101 ASN E 258 ASN E 266 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.104663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.086574 restraints weight = 38600.367| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 1.86 r_work: 0.3072 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.6099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27865 Z= 0.131 Angle : 0.509 7.347 37884 Z= 0.267 Chirality : 0.043 0.186 4156 Planarity : 0.004 0.051 4935 Dihedral : 11.336 177.279 3941 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.48 % Allowed : 11.29 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.14), residues: 3440 helix: 1.63 (0.13), residues: 1552 sheet: 0.87 (0.25), residues: 432 loop : -0.80 (0.15), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 221 TYR 0.011 0.001 TYR F 310 PHE 0.015 0.001 PHE B 408 TRP 0.020 0.001 TRP I 21 HIS 0.018 0.001 HIS C 88 Details of bonding type rmsd covalent geometry : bond 0.00305 (27865) covalent geometry : angle 0.50854 (37884) hydrogen bonds : bond 0.04188 ( 1331) hydrogen bonds : angle 4.47077 ( 3909) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 287 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 108 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.7171 (mp0) REVERT: B 114 ASP cc_start: 0.7978 (m-30) cc_final: 0.7775 (p0) REVERT: B 164 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.8160 (mtp) REVERT: B 257 MET cc_start: 0.9113 (mmm) cc_final: 0.8678 (mmm) REVERT: B 321 MET cc_start: 0.8804 (mmt) cc_final: 0.8430 (mmt) REVERT: D 40 SER cc_start: 0.8166 (OUTLIER) cc_final: 0.7903 (p) REVERT: D 65 LEU cc_start: 0.8933 (mp) cc_final: 0.8704 (mp) REVERT: D 203 ASP cc_start: 0.8503 (t0) cc_final: 0.8066 (m-30) REVERT: D 377 LEU cc_start: 0.8719 (mp) cc_final: 0.8484 (mp) REVERT: D 401 GLU cc_start: 0.8313 (mm-30) cc_final: 0.8058 (mp0) REVERT: F 257 MET cc_start: 0.8520 (mmm) cc_final: 0.8313 (mmm) REVERT: F 299 MET cc_start: 0.9193 (mmp) cc_final: 0.8839 (mmt) REVERT: F 320 ARG cc_start: 0.8274 (mmm160) cc_final: 0.8004 (mmt180) REVERT: I 47 ASP cc_start: 0.7861 (t70) cc_final: 0.7129 (p0) REVERT: I 123 ARG cc_start: 0.7688 (ttp-110) cc_final: 0.7424 (tpt170) REVERT: I 203 MET cc_start: 0.9016 (OUTLIER) cc_final: 0.8731 (mtt) REVERT: I 215 ARG cc_start: 0.8414 (mtm-85) cc_final: 0.7992 (mtp85) REVERT: I 254 GLU cc_start: 0.6011 (mm-30) cc_final: 0.4553 (pt0) REVERT: C 36 MET cc_start: 0.8516 (mtp) cc_final: 0.8089 (mtm) REVERT: C 90 GLU cc_start: 0.8955 (tp30) cc_final: 0.8719 (mt-10) REVERT: C 203 MET cc_start: 0.9089 (mmt) cc_final: 0.8874 (mmt) REVERT: C 432 TYR cc_start: 0.8827 (OUTLIER) cc_final: 0.8190 (m-80) REVERT: E 120 ASP cc_start: 0.7968 (m-30) cc_final: 0.7589 (m-30) REVERT: E 123 ARG cc_start: 0.8605 (ttt180) cc_final: 0.8130 (tpp-160) REVERT: E 128 GLN cc_start: 0.7175 (pt0) cc_final: 0.6776 (pp30) REVERT: E 254 GLU cc_start: 0.5161 (mm-30) cc_final: 0.3772 (pt0) REVERT: E 255 PHE cc_start: 0.8957 (OUTLIER) cc_final: 0.8413 (t80) REVERT: E 432 TYR cc_start: 0.8713 (OUTLIER) cc_final: 0.7536 (t80) outliers start: 72 outliers final: 44 residues processed: 342 average time/residue: 0.1897 time to fit residues: 101.7852 Evaluate side-chains 300 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 249 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 328 GLU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 288 GLU Chi-restraints excluded: chain F residue 312 THR Chi-restraints excluded: chain Q residue 88 ASP Chi-restraints excluded: chain Q residue 135 LEU Chi-restraints excluded: chain Q residue 136 THR Chi-restraints excluded: chain Q residue 172 SER Chi-restraints excluded: chain Q residue 409 THR Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain I residue 3 GLU Chi-restraints excluded: chain I residue 194 THR Chi-restraints excluded: chain I residue 203 MET Chi-restraints excluded: chain I residue 324 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 96 LYS Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain E residue 3 GLU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 101 ASN Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 255 PHE Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 432 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 102 optimal weight: 2.9990 chunk 228 optimal weight: 0.0770 chunk 43 optimal weight: 1.9990 chunk 3 optimal weight: 0.4980 chunk 122 optimal weight: 0.7980 chunk 209 optimal weight: 0.3980 chunk 20 optimal weight: 0.6980 chunk 233 optimal weight: 0.9980 chunk 154 optimal weight: 1.9990 chunk 322 optimal weight: 0.9980 chunk 188 optimal weight: 0.9980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 ASN D 6 HIS ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 133 GLN C 133 GLN E 31 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.104568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.086823 restraints weight = 38514.197| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.80 r_work: 0.3076 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.6333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27865 Z= 0.121 Angle : 0.492 6.859 37884 Z= 0.257 Chirality : 0.042 0.183 4156 Planarity : 0.004 0.049 4935 Dihedral : 11.198 177.880 3941 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.68 % Allowed : 11.73 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.14), residues: 3440 helix: 1.69 (0.13), residues: 1556 sheet: 0.89 (0.25), residues: 432 loop : -0.82 (0.15), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 221 TYR 0.010 0.001 TYR F 310 PHE 0.015 0.001 PHE C 255 TRP 0.018 0.001 TRP I 21 HIS 0.010 0.001 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00280 (27865) covalent geometry : angle 0.49185 (37884) hydrogen bonds : bond 0.03984 ( 1331) hydrogen bonds : angle 4.36311 ( 3909) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 271 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 50 TYR cc_start: 0.9413 (m-80) cc_final: 0.9210 (m-80) REVERT: B 108 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8191 (mm-30) REVERT: B 131 GLN cc_start: 0.9180 (OUTLIER) cc_final: 0.8722 (tt0) REVERT: B 164 MET cc_start: 0.8552 (OUTLIER) cc_final: 0.8245 (mtp) REVERT: B 257 MET cc_start: 0.9028 (mmm) cc_final: 0.8605 (mmm) REVERT: B 321 MET cc_start: 0.8750 (mmt) cc_final: 0.8351 (mmt) REVERT: B 332 ASN cc_start: 0.8405 (m-40) cc_final: 0.8111 (m-40) REVERT: B 375 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.7501 (pp30) REVERT: D 65 LEU cc_start: 0.8931 (mp) cc_final: 0.8713 (mp) REVERT: D 203 ASP cc_start: 0.8564 (t0) cc_final: 0.8189 (m-30) REVERT: D 401 GLU cc_start: 0.8320 (mm-30) cc_final: 0.8112 (mp0) REVERT: F 299 MET cc_start: 0.9148 (mmp) cc_final: 0.8873 (mmt) REVERT: F 320 ARG cc_start: 0.8264 (mmm160) cc_final: 0.8005 (mmt180) REVERT: A 85 GLN cc_start: 0.8649 (mm-40) cc_final: 0.8335 (mt0) REVERT: A 377 MET cc_start: 0.9195 (tmm) cc_final: 0.8858 (ttp) REVERT: I 47 ASP cc_start: 0.7927 (t70) cc_final: 0.7205 (p0) REVERT: I 123 ARG cc_start: 0.7686 (ttp-110) cc_final: 0.7430 (tpt170) REVERT: I 215 ARG cc_start: 0.8416 (mtm-85) cc_final: 0.7992 (mtp85) REVERT: I 254 GLU cc_start: 0.6008 (mm-30) cc_final: 0.4586 (pt0) REVERT: I 398 MET cc_start: 0.9055 (ptm) cc_final: 0.8709 (ttp) REVERT: C 432 TYR cc_start: 0.8825 (OUTLIER) cc_final: 0.8237 (m-80) REVERT: E 123 ARG cc_start: 0.8599 (ttt180) cc_final: 0.8094 (tpp-160) REVERT: E 254 GLU cc_start: 0.5163 (mm-30) cc_final: 0.3921 (pt0) REVERT: E 255 PHE cc_start: 0.8955 (OUTLIER) cc_final: 0.8370 (t80) REVERT: E 432 TYR cc_start: 0.8757 (OUTLIER) cc_final: 0.7588 (t80) outliers start: 78 outliers final: 56 residues processed: 336 average time/residue: 0.1880 time to fit residues: 99.3311 Evaluate side-chains 319 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 256 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 375 GLN Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 328 GLU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 288 GLU Chi-restraints excluded: chain F residue 312 THR Chi-restraints excluded: chain F residue 382 SER Chi-restraints excluded: chain Q residue 88 ASP Chi-restraints excluded: chain Q residue 135 LEU Chi-restraints excluded: chain Q residue 136 THR Chi-restraints excluded: chain Q residue 172 SER Chi-restraints excluded: chain Q residue 409 THR Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain I residue 3 GLU Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 204 VAL Chi-restraints excluded: chain I residue 324 VAL Chi-restraints excluded: chain I residue 434 GLU Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 96 LYS Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 356 ASN Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain E residue 3 GLU Chi-restraints excluded: chain E residue 31 GLN Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 255 PHE Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 384 ILE Chi-restraints excluded: chain E residue 432 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 227 optimal weight: 0.0670 chunk 2 optimal weight: 2.9990 chunk 275 optimal weight: 0.0270 chunk 237 optimal weight: 0.6980 chunk 192 optimal weight: 2.9990 chunk 225 optimal weight: 2.9990 chunk 205 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 48 optimal weight: 0.3980 chunk 139 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 overall best weight: 0.3976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 329 GLN ** D 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 426 GLN C 133 GLN C 300 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.105407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.087889 restraints weight = 38752.168| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.81 r_work: 0.3087 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.6476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27865 Z= 0.109 Angle : 0.477 7.592 37884 Z= 0.248 Chirality : 0.042 0.184 4156 Planarity : 0.004 0.048 4935 Dihedral : 11.032 177.028 3941 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.31 % Allowed : 12.28 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.14), residues: 3440 helix: 1.74 (0.13), residues: 1564 sheet: 0.92 (0.24), residues: 456 loop : -0.81 (0.15), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 221 TYR 0.010 0.001 TYR C 432 PHE 0.014 0.001 PHE C 255 TRP 0.017 0.001 TRP I 21 HIS 0.011 0.001 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00251 (27865) covalent geometry : angle 0.47738 (37884) hydrogen bonds : bond 0.03779 ( 1331) hydrogen bonds : angle 4.28998 ( 3909) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 276 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 50 TYR cc_start: 0.9401 (m-80) cc_final: 0.9189 (m-80) REVERT: B 108 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.8047 (mp0) REVERT: B 131 GLN cc_start: 0.9177 (OUTLIER) cc_final: 0.8734 (tt0) REVERT: B 164 MET cc_start: 0.8561 (OUTLIER) cc_final: 0.8316 (mtp) REVERT: B 257 MET cc_start: 0.8978 (mmm) cc_final: 0.8604 (mmm) REVERT: B 321 MET cc_start: 0.8788 (mmt) cc_final: 0.8558 (mmt) REVERT: B 332 ASN cc_start: 0.8361 (m-40) cc_final: 0.8053 (m-40) REVERT: B 375 GLN cc_start: 0.8857 (OUTLIER) cc_final: 0.7470 (pp30) REVERT: D 65 LEU cc_start: 0.8897 (mp) cc_final: 0.8692 (mp) REVERT: D 203 ASP cc_start: 0.8587 (t0) cc_final: 0.8199 (m-30) REVERT: F 299 MET cc_start: 0.9145 (mmp) cc_final: 0.8904 (mmt) REVERT: F 320 ARG cc_start: 0.8255 (mmm160) cc_final: 0.7980 (mmt180) REVERT: Q 41 ASP cc_start: 0.8425 (m-30) cc_final: 0.8206 (m-30) REVERT: A 154 MET cc_start: 0.8947 (mmm) cc_final: 0.8489 (mtm) REVERT: A 377 MET cc_start: 0.9208 (tmm) cc_final: 0.8830 (ttp) REVERT: I 47 ASP cc_start: 0.7906 (t70) cc_final: 0.7320 (p0) REVERT: I 123 ARG cc_start: 0.7711 (ttp-110) cc_final: 0.7433 (tpt170) REVERT: I 215 ARG cc_start: 0.8407 (mtm-85) cc_final: 0.7989 (mtp85) REVERT: I 254 GLU cc_start: 0.5953 (mm-30) cc_final: 0.4571 (pt0) REVERT: I 398 MET cc_start: 0.9057 (ptm) cc_final: 0.8690 (ttp) REVERT: I 425 MET cc_start: 0.8756 (tpt) cc_final: 0.8452 (tpt) REVERT: C 36 MET cc_start: 0.8479 (mtp) cc_final: 0.8250 (mtm) REVERT: C 398 MET cc_start: 0.8358 (mmm) cc_final: 0.8075 (mtp) REVERT: C 432 TYR cc_start: 0.8804 (OUTLIER) cc_final: 0.8345 (m-80) REVERT: E 123 ARG cc_start: 0.8599 (ttt180) cc_final: 0.8141 (tpp-160) REVERT: E 254 GLU cc_start: 0.5098 (mm-30) cc_final: 0.3916 (pt0) REVERT: E 255 PHE cc_start: 0.8888 (OUTLIER) cc_final: 0.8265 (t80) REVERT: E 432 TYR cc_start: 0.8751 (OUTLIER) cc_final: 0.7581 (t80) outliers start: 67 outliers final: 54 residues processed: 334 average time/residue: 0.1929 time to fit residues: 99.4712 Evaluate side-chains 315 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 254 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 375 GLN Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 328 GLU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 288 GLU Chi-restraints excluded: chain F residue 312 THR Chi-restraints excluded: chain F residue 382 SER Chi-restraints excluded: chain Q residue 88 ASP Chi-restraints excluded: chain Q residue 135 LEU Chi-restraints excluded: chain Q residue 136 THR Chi-restraints excluded: chain Q residue 157 GLU Chi-restraints excluded: chain Q residue 172 SER Chi-restraints excluded: chain Q residue 409 THR Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain I residue 3 GLU Chi-restraints excluded: chain I residue 204 VAL Chi-restraints excluded: chain I residue 324 VAL Chi-restraints excluded: chain I residue 434 GLU Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 96 LYS Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 356 ASN Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain E residue 3 GLU Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 255 PHE Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 337 THR Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 384 ILE Chi-restraints excluded: chain E residue 432 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 294 optimal weight: 1.9990 chunk 233 optimal weight: 0.9980 chunk 283 optimal weight: 0.6980 chunk 231 optimal weight: 0.6980 chunk 15 optimal weight: 0.0870 chunk 286 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 63 optimal weight: 0.7980 chunk 339 optimal weight: 2.9990 chunk 180 optimal weight: 2.9990 chunk 59 optimal weight: 0.0980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 329 GLN ** F 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 309 HIS C 133 GLN C 300 ASN C 309 HIS E 107 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.105138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.087521 restraints weight = 38620.591| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.82 r_work: 0.3082 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.6659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27865 Z= 0.113 Angle : 0.484 9.594 37884 Z= 0.251 Chirality : 0.042 0.177 4156 Planarity : 0.004 0.047 4935 Dihedral : 10.920 176.757 3941 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.58 % Allowed : 12.28 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.14), residues: 3440 helix: 1.79 (0.13), residues: 1564 sheet: 0.96 (0.25), residues: 432 loop : -0.80 (0.15), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 339 TYR 0.009 0.001 TYR F 310 PHE 0.014 0.001 PHE C 255 TRP 0.017 0.001 TRP I 21 HIS 0.011 0.001 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00261 (27865) covalent geometry : angle 0.48386 (37884) hydrogen bonds : bond 0.03776 ( 1331) hydrogen bonds : angle 4.25912 ( 3909) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 269 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 50 TYR cc_start: 0.9379 (m-80) cc_final: 0.9160 (m-80) REVERT: B 108 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8026 (mp0) REVERT: B 131 GLN cc_start: 0.9171 (OUTLIER) cc_final: 0.8732 (tt0) REVERT: B 164 MET cc_start: 0.8552 (OUTLIER) cc_final: 0.8326 (mtp) REVERT: B 257 MET cc_start: 0.8941 (mmm) cc_final: 0.8632 (mmm) REVERT: B 321 MET cc_start: 0.8752 (mmt) cc_final: 0.8520 (mmt) REVERT: B 332 ASN cc_start: 0.8341 (m-40) cc_final: 0.8036 (m-40) REVERT: B 375 GLN cc_start: 0.8853 (OUTLIER) cc_final: 0.7409 (pp30) REVERT: D 203 ASP cc_start: 0.8607 (t0) cc_final: 0.8203 (m-30) REVERT: F 320 ARG cc_start: 0.8285 (mmm160) cc_final: 0.7981 (mmt180) REVERT: Q 41 ASP cc_start: 0.8441 (m-30) cc_final: 0.8219 (m-30) REVERT: A 154 MET cc_start: 0.8959 (mmm) cc_final: 0.8510 (mtm) REVERT: I 47 ASP cc_start: 0.7854 (t70) cc_final: 0.7290 (p0) REVERT: I 123 ARG cc_start: 0.7705 (ttp-110) cc_final: 0.7440 (tpt170) REVERT: I 215 ARG cc_start: 0.8415 (mtm-85) cc_final: 0.7979 (mtp85) REVERT: I 254 GLU cc_start: 0.5918 (mm-30) cc_final: 0.4585 (pt0) REVERT: I 398 MET cc_start: 0.9065 (ptm) cc_final: 0.8685 (ttp) REVERT: I 425 MET cc_start: 0.8792 (tpt) cc_final: 0.8485 (tpt) REVERT: C 36 MET cc_start: 0.8490 (mtp) cc_final: 0.8258 (mtm) REVERT: C 203 MET cc_start: 0.9103 (mmt) cc_final: 0.8840 (mmt) REVERT: C 393 HIS cc_start: 0.8323 (t70) cc_final: 0.8075 (t70) REVERT: C 398 MET cc_start: 0.8385 (mmm) cc_final: 0.8088 (mtp) REVERT: E 120 ASP cc_start: 0.8037 (m-30) cc_final: 0.7640 (m-30) REVERT: E 123 ARG cc_start: 0.8628 (ttt180) cc_final: 0.8142 (tpp-160) REVERT: E 254 GLU cc_start: 0.5034 (mm-30) cc_final: 0.3921 (pt0) REVERT: E 255 PHE cc_start: 0.8903 (OUTLIER) cc_final: 0.8285 (t80) REVERT: E 279 GLU cc_start: 0.7834 (mp0) cc_final: 0.7593 (mp0) REVERT: E 432 TYR cc_start: 0.8833 (OUTLIER) cc_final: 0.7736 (t80) outliers start: 75 outliers final: 59 residues processed: 332 average time/residue: 0.1873 time to fit residues: 97.5611 Evaluate side-chains 315 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 250 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 375 GLN Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 328 GLU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 288 GLU Chi-restraints excluded: chain F residue 312 THR Chi-restraints excluded: chain F residue 382 SER Chi-restraints excluded: chain Q residue 88 ASP Chi-restraints excluded: chain Q residue 135 LEU Chi-restraints excluded: chain Q residue 136 THR Chi-restraints excluded: chain Q residue 172 SER Chi-restraints excluded: chain Q residue 409 THR Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain I residue 3 GLU Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 204 VAL Chi-restraints excluded: chain I residue 324 VAL Chi-restraints excluded: chain I residue 434 GLU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 96 LYS Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain E residue 3 GLU Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 255 PHE Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 337 THR Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 384 ILE Chi-restraints excluded: chain E residue 432 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 336 optimal weight: 0.6980 chunk 168 optimal weight: 3.9990 chunk 278 optimal weight: 0.0980 chunk 287 optimal weight: 0.0970 chunk 157 optimal weight: 3.9990 chunk 194 optimal weight: 0.9980 chunk 102 optimal weight: 0.7980 chunk 175 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 217 optimal weight: 0.8980 chunk 130 optimal weight: 0.2980 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 ASN ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 190 HIS C 133 GLN C 300 ASN C 356 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.105756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.087844 restraints weight = 38750.142| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.84 r_work: 0.3084 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.6765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27865 Z= 0.109 Angle : 0.480 10.380 37884 Z= 0.249 Chirality : 0.042 0.192 4156 Planarity : 0.004 0.046 4935 Dihedral : 10.806 178.899 3941 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.51 % Allowed : 12.46 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.14), residues: 3440 helix: 1.82 (0.13), residues: 1564 sheet: 0.97 (0.24), residues: 456 loop : -0.76 (0.15), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Q 213 TYR 0.009 0.001 TYR I 161 PHE 0.014 0.001 PHE C 255 TRP 0.017 0.001 TRP I 21 HIS 0.012 0.001 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00250 (27865) covalent geometry : angle 0.48038 (37884) hydrogen bonds : bond 0.03670 ( 1331) hydrogen bonds : angle 4.22290 ( 3909) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 262 time to evaluate : 1.180 Fit side-chains revert: symmetry clash REVERT: B 50 TYR cc_start: 0.9364 (m-80) cc_final: 0.9146 (m-80) REVERT: B 108 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8032 (mp0) REVERT: B 131 GLN cc_start: 0.9159 (OUTLIER) cc_final: 0.8712 (tt0) REVERT: B 257 MET cc_start: 0.8900 (mmm) cc_final: 0.8580 (mmm) REVERT: B 321 MET cc_start: 0.8877 (mmt) cc_final: 0.8589 (mmt) REVERT: B 332 ASN cc_start: 0.8331 (m-40) cc_final: 0.8024 (m-40) REVERT: B 375 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.7419 (pp30) REVERT: D 203 ASP cc_start: 0.8702 (t0) cc_final: 0.8354 (m-30) REVERT: F 299 MET cc_start: 0.9213 (mmt) cc_final: 0.8999 (mmp) REVERT: F 320 ARG cc_start: 0.8278 (mmm160) cc_final: 0.7976 (mmt180) REVERT: Q 41 ASP cc_start: 0.8460 (m-30) cc_final: 0.8216 (m-30) REVERT: Q 190 HIS cc_start: 0.8271 (OUTLIER) cc_final: 0.7682 (t-90) REVERT: A 154 MET cc_start: 0.8860 (mmm) cc_final: 0.8549 (mtm) REVERT: I 47 ASP cc_start: 0.7871 (t70) cc_final: 0.7261 (p0) REVERT: I 123 ARG cc_start: 0.7733 (ttp-110) cc_final: 0.7496 (tpt170) REVERT: I 215 ARG cc_start: 0.8394 (mtm-85) cc_final: 0.7966 (mtp85) REVERT: I 254 GLU cc_start: 0.5900 (mm-30) cc_final: 0.4574 (pt0) REVERT: I 398 MET cc_start: 0.9061 (ptm) cc_final: 0.8778 (ttp) REVERT: C 36 MET cc_start: 0.8480 (mtp) cc_final: 0.8255 (mtm) REVERT: C 203 MET cc_start: 0.9111 (mmt) cc_final: 0.8842 (mmt) REVERT: C 393 HIS cc_start: 0.8328 (t70) cc_final: 0.8081 (t70) REVERT: E 120 ASP cc_start: 0.8063 (m-30) cc_final: 0.7689 (m-30) REVERT: E 123 ARG cc_start: 0.8632 (ttt180) cc_final: 0.8161 (tpp-160) REVERT: E 254 GLU cc_start: 0.5019 (mm-30) cc_final: 0.3925 (pt0) REVERT: E 255 PHE cc_start: 0.8899 (OUTLIER) cc_final: 0.8268 (t80) REVERT: E 279 GLU cc_start: 0.7913 (mp0) cc_final: 0.7590 (mp0) REVERT: E 432 TYR cc_start: 0.8810 (OUTLIER) cc_final: 0.7726 (t80) outliers start: 73 outliers final: 57 residues processed: 320 average time/residue: 0.1950 time to fit residues: 97.9549 Evaluate side-chains 309 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 246 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 375 GLN Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 328 GLU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 312 THR Chi-restraints excluded: chain F residue 382 SER Chi-restraints excluded: chain Q residue 88 ASP Chi-restraints excluded: chain Q residue 135 LEU Chi-restraints excluded: chain Q residue 136 THR Chi-restraints excluded: chain Q residue 157 GLU Chi-restraints excluded: chain Q residue 172 SER Chi-restraints excluded: chain Q residue 190 HIS Chi-restraints excluded: chain Q residue 409 THR Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain I residue 3 GLU Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain I residue 204 VAL Chi-restraints excluded: chain I residue 324 VAL Chi-restraints excluded: chain I residue 434 GLU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 96 LYS Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain E residue 3 GLU Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 255 PHE Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 337 THR Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 384 ILE Chi-restraints excluded: chain E residue 432 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 227 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 314 optimal weight: 0.4980 chunk 151 optimal weight: 1.9990 chunk 245 optimal weight: 0.2980 chunk 291 optimal weight: 3.9990 chunk 246 optimal weight: 0.7980 chunk 161 optimal weight: 0.9980 chunk 155 optimal weight: 1.9990 chunk 259 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 190 HIS Q 414 ASN C 133 GLN C 356 ASN E 61 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.103402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.085308 restraints weight = 38643.908| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.91 r_work: 0.3050 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.6875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27865 Z= 0.142 Angle : 0.512 10.939 37884 Z= 0.266 Chirality : 0.043 0.195 4156 Planarity : 0.004 0.045 4935 Dihedral : 10.963 179.275 3941 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.37 % Allowed : 12.63 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.14), residues: 3440 helix: 1.73 (0.13), residues: 1564 sheet: 0.94 (0.25), residues: 432 loop : -0.81 (0.15), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 221 TYR 0.010 0.001 TYR F 310 PHE 0.017 0.001 PHE C 255 TRP 0.017 0.001 TRP I 21 HIS 0.019 0.001 HIS Q 190 Details of bonding type rmsd covalent geometry : bond 0.00338 (27865) covalent geometry : angle 0.51177 (37884) hydrogen bonds : bond 0.04129 ( 1331) hydrogen bonds : angle 4.31911 ( 3909) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 252 time to evaluate : 1.055 Fit side-chains REVERT: B 108 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8023 (mp0) REVERT: B 131 GLN cc_start: 0.9198 (OUTLIER) cc_final: 0.8778 (tt0) REVERT: B 257 MET cc_start: 0.8926 (mmm) cc_final: 0.8660 (mmm) REVERT: B 332 ASN cc_start: 0.8346 (m-40) cc_final: 0.8026 (m-40) REVERT: B 375 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.7411 (pp30) REVERT: D 122 LYS cc_start: 0.8572 (mtpp) cc_final: 0.8176 (mtpt) REVERT: D 203 ASP cc_start: 0.8686 (t0) cc_final: 0.8360 (m-30) REVERT: F 320 ARG cc_start: 0.8311 (mmm160) cc_final: 0.8014 (mmt180) REVERT: Q 41 ASP cc_start: 0.8477 (m-30) cc_final: 0.8244 (m-30) REVERT: Q 190 HIS cc_start: 0.8289 (OUTLIER) cc_final: 0.7833 (t-90) REVERT: A 154 MET cc_start: 0.8904 (mmm) cc_final: 0.8519 (mtm) REVERT: A 377 MET cc_start: 0.9206 (tmm) cc_final: 0.8826 (ttp) REVERT: I 47 ASP cc_start: 0.7965 (t70) cc_final: 0.7368 (p0) REVERT: I 123 ARG cc_start: 0.7785 (ttp-110) cc_final: 0.7547 (tpt170) REVERT: I 215 ARG cc_start: 0.8413 (mtm-85) cc_final: 0.7990 (mtp85) REVERT: I 254 GLU cc_start: 0.6002 (mm-30) cc_final: 0.4612 (pt0) REVERT: I 284 GLU cc_start: 0.7455 (mt-10) cc_final: 0.7110 (mt-10) REVERT: I 398 MET cc_start: 0.9116 (ptm) cc_final: 0.8687 (ttp) REVERT: C 36 MET cc_start: 0.8507 (mtp) cc_final: 0.8285 (mtm) REVERT: C 393 HIS cc_start: 0.8345 (t70) cc_final: 0.8098 (t70) REVERT: E 120 ASP cc_start: 0.8080 (m-30) cc_final: 0.7689 (m-30) REVERT: E 123 ARG cc_start: 0.8629 (ttt180) cc_final: 0.8176 (tpp-160) REVERT: E 254 GLU cc_start: 0.5187 (mm-30) cc_final: 0.4026 (pt0) REVERT: E 255 PHE cc_start: 0.8999 (OUTLIER) cc_final: 0.8411 (t80) REVERT: E 432 TYR cc_start: 0.8866 (OUTLIER) cc_final: 0.7854 (t80) outliers start: 69 outliers final: 54 residues processed: 311 average time/residue: 0.1918 time to fit residues: 93.4898 Evaluate side-chains 298 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 238 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 375 GLN Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 328 GLU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 312 THR Chi-restraints excluded: chain F residue 382 SER Chi-restraints excluded: chain Q residue 26 ASP Chi-restraints excluded: chain Q residue 88 ASP Chi-restraints excluded: chain Q residue 135 LEU Chi-restraints excluded: chain Q residue 136 THR Chi-restraints excluded: chain Q residue 157 GLU Chi-restraints excluded: chain Q residue 172 SER Chi-restraints excluded: chain Q residue 190 HIS Chi-restraints excluded: chain Q residue 409 THR Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain I residue 3 GLU Chi-restraints excluded: chain I residue 6 SER Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain I residue 204 VAL Chi-restraints excluded: chain I residue 324 VAL Chi-restraints excluded: chain I residue 434 GLU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 96 LYS Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain E residue 3 GLU Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 255 PHE Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 337 THR Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 384 ILE Chi-restraints excluded: chain E residue 432 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 219 optimal weight: 0.0070 chunk 228 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 321 optimal weight: 0.6980 chunk 278 optimal weight: 2.9990 chunk 294 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 257 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 423 GLN ** F 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 134 GLN Q 190 HIS Q 414 ASN C 35 GLN ** C 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 356 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.102242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.084233 restraints weight = 38998.705| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 1.87 r_work: 0.3019 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.6999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 27865 Z= 0.170 Angle : 0.540 11.442 37884 Z= 0.281 Chirality : 0.044 0.192 4156 Planarity : 0.004 0.045 4935 Dihedral : 11.206 179.346 3941 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.10 % Allowed : 12.97 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.14), residues: 3440 helix: 1.64 (0.13), residues: 1540 sheet: 0.88 (0.24), residues: 432 loop : -0.87 (0.15), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Q 213 TYR 0.011 0.001 TYR F 310 PHE 0.018 0.001 PHE C 255 TRP 0.018 0.002 TRP I 21 HIS 0.016 0.001 HIS Q 190 Details of bonding type rmsd covalent geometry : bond 0.00409 (27865) covalent geometry : angle 0.54031 (37884) hydrogen bonds : bond 0.04510 ( 1331) hydrogen bonds : angle 4.44013 ( 3909) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 249 time to evaluate : 0.910 Fit side-chains REVERT: B 108 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.8036 (mp0) REVERT: B 131 GLN cc_start: 0.9221 (OUTLIER) cc_final: 0.8997 (tt0) REVERT: B 257 MET cc_start: 0.8966 (mmm) cc_final: 0.8679 (mmm) REVERT: B 332 ASN cc_start: 0.8406 (m-40) cc_final: 0.7982 (m110) REVERT: B 375 GLN cc_start: 0.8881 (OUTLIER) cc_final: 0.7476 (pp30) REVERT: D 203 ASP cc_start: 0.8645 (OUTLIER) cc_final: 0.8271 (m-30) REVERT: F 320 ARG cc_start: 0.8299 (mmm160) cc_final: 0.7999 (mmt180) REVERT: Q 41 ASP cc_start: 0.8469 (m-30) cc_final: 0.8256 (m-30) REVERT: Q 46 ARG cc_start: 0.9272 (OUTLIER) cc_final: 0.7093 (mtm-85) REVERT: A 1 MET cc_start: 0.8652 (mmm) cc_final: 0.8228 (mmt) REVERT: A 154 MET cc_start: 0.8852 (mmm) cc_final: 0.8650 (mtm) REVERT: A 377 MET cc_start: 0.9212 (tmm) cc_final: 0.8868 (ttp) REVERT: I 123 ARG cc_start: 0.7798 (ttp-110) cc_final: 0.7596 (tpt170) REVERT: I 215 ARG cc_start: 0.8448 (mtm-85) cc_final: 0.8035 (mtp85) REVERT: I 254 GLU cc_start: 0.6023 (mm-30) cc_final: 0.4571 (pt0) REVERT: I 284 GLU cc_start: 0.7421 (mt-10) cc_final: 0.7072 (mt-10) REVERT: I 398 MET cc_start: 0.9135 (ptm) cc_final: 0.8697 (ttp) REVERT: C 393 HIS cc_start: 0.8319 (t70) cc_final: 0.8048 (t70) REVERT: E 120 ASP cc_start: 0.8098 (m-30) cc_final: 0.7712 (m-30) REVERT: E 123 ARG cc_start: 0.8618 (ttt180) cc_final: 0.8183 (tpp-160) REVERT: E 254 GLU cc_start: 0.5167 (mm-30) cc_final: 0.3990 (pt0) REVERT: E 255 PHE cc_start: 0.9046 (OUTLIER) cc_final: 0.8487 (t80) REVERT: E 279 GLU cc_start: 0.7961 (mp0) cc_final: 0.7670 (mp0) REVERT: E 432 TYR cc_start: 0.8874 (OUTLIER) cc_final: 0.7788 (t80) outliers start: 61 outliers final: 49 residues processed: 302 average time/residue: 0.1920 time to fit residues: 90.9172 Evaluate side-chains 297 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 241 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 375 GLN Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 203 ASP Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 312 THR Chi-restraints excluded: chain F residue 382 SER Chi-restraints excluded: chain Q residue 26 ASP Chi-restraints excluded: chain Q residue 46 ARG Chi-restraints excluded: chain Q residue 88 ASP Chi-restraints excluded: chain Q residue 135 LEU Chi-restraints excluded: chain Q residue 136 THR Chi-restraints excluded: chain Q residue 157 GLU Chi-restraints excluded: chain Q residue 409 THR Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain I residue 3 GLU Chi-restraints excluded: chain I residue 6 SER Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 204 VAL Chi-restraints excluded: chain I residue 324 VAL Chi-restraints excluded: chain I residue 434 GLU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 96 LYS Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain E residue 3 GLU Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 255 PHE Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 337 THR Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 384 ILE Chi-restraints excluded: chain E residue 432 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 19 optimal weight: 2.9990 chunk 159 optimal weight: 0.3980 chunk 147 optimal weight: 0.5980 chunk 88 optimal weight: 0.0050 chunk 22 optimal weight: 0.4980 chunk 133 optimal weight: 0.8980 chunk 166 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 146 optimal weight: 0.7980 chunk 150 optimal weight: 0.9980 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 GLN C 256 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.104395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.086266 restraints weight = 38505.428| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.91 r_work: 0.3058 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.7042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27865 Z= 0.118 Angle : 0.495 11.202 37884 Z= 0.257 Chirality : 0.042 0.184 4156 Planarity : 0.004 0.045 4935 Dihedral : 11.004 179.868 3941 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.06 % Allowed : 13.45 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.14), residues: 3440 helix: 1.75 (0.13), residues: 1540 sheet: 0.92 (0.24), residues: 456 loop : -0.84 (0.15), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Q 213 TYR 0.010 0.001 TYR F 310 PHE 0.015 0.001 PHE C 255 TRP 0.018 0.002 TRP I 388 HIS 0.014 0.001 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00274 (27865) covalent geometry : angle 0.49471 (37884) hydrogen bonds : bond 0.03878 ( 1331) hydrogen bonds : angle 4.31822 ( 3909) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6533.24 seconds wall clock time: 112 minutes 55.48 seconds (6775.48 seconds total)