Starting phenix.real_space_refine on Thu Nov 20 23:52:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6dpv_7974/11_2025/6dpv_7974.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dpv_7974/11_2025/6dpv_7974.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6dpv_7974/11_2025/6dpv_7974.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dpv_7974/11_2025/6dpv_7974.map" model { file = "/net/cci-nas-00/data/ceres_data/6dpv_7974/11_2025/6dpv_7974.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dpv_7974/11_2025/6dpv_7974.cif" } resolution = 3.3 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= -0.007 sd= 0.925 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 30 5.49 5 Mg 6 5.21 5 S 276 5.16 5 C 25464 2.51 5 N 6924 2.21 5 O 7806 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 96 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 40506 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3350 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 3340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3340 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "C" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3350 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 3340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3340 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "E" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3350 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 3340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3340 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "G" Number of atoms: 3340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3340 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "H" Number of atoms: 3340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3340 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "I" Number of atoms: 3340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3340 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "J" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3350 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "K" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3350 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3350 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 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: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 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: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 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} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "J" 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: "K" 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: "L" 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: 8.89, per 1000 atoms: 0.22 Number of scatterers: 40506 At special positions: 0 Unit cell: (170.482, 86.32, 209.326, 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 276 16.00 P 30 15.00 Mg 6 11.99 O 7806 8.00 N 6924 7.00 C 25464 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: 3.49 Conformation dependent library (CDL) restraints added in 1.8 seconds 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9492 Finding SS restraints... Secondary structure from input PDB file: 252 helices and 30 sheets defined 56.2% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'A' and resid 10 through 29 Processing helix chain 'A' and resid 47 through 51 Processing helix chain 'A' and resid 72 through 81 removed outlier: 3.635A pdb=" N VAL A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 90 No H-bonds generated for 'chain 'A' and resid 88 through 90' Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 110 through 113 Processing helix chain 'A' and resid 114 through 128 removed outlier: 3.594A pdb=" N GLN A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 161 removed outlier: 4.093A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 195 Processing helix chain 'A' and resid 196 through 198 No H-bonds generated for 'chain 'A' and resid 196 through 198' Processing helix chain 'A' and resid 206 through 218 Processing helix chain 'A' and resid 223 through 244 removed outlier: 4.584A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 removed outlier: 3.991A pdb=" N PHE A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLN A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N THR A 257 " --> pdb=" O THR A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 283 removed outlier: 3.706A pdb=" N TYR A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N HIS A 283 " --> pdb=" O GLU A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 removed outlier: 3.846A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 338 removed outlier: 3.562A pdb=" N VAL A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 401 removed outlier: 3.750A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 411 removed outlier: 3.894A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 437 removed outlier: 3.873A pdb=" N PHE A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 29 Processing helix chain 'B' and resid 41 through 48 removed outlier: 4.450A pdb=" N ARG B 48 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 51 No H-bonds generated for 'chain 'B' and resid 49 through 51' Processing helix chain 'B' and resid 71 through 81 removed outlier: 4.574A pdb=" N MET B 75 " --> pdb=" O GLU B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 87 removed outlier: 3.745A pdb=" N PHE B 87 " --> pdb=" O GLY B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 90 No H-bonds generated for 'chain 'B' and resid 88 through 90' Processing helix chain 'B' and resid 102 through 108 Processing helix chain 'B' and resid 109 through 129 removed outlier: 4.474A pdb=" N ASP B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N SER B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 161 Processing helix chain 'B' and resid 182 through 198 removed outlier: 3.886A pdb=" N GLU B 196 " --> pdb=" O HIS B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 216 Processing helix chain 'B' and resid 223 through 244 removed outlier: 5.198A pdb=" N CYS B 241 " --> pdb=" O GLY B 237 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU B 242 " --> pdb=" O VAL B 238 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG B 243 " --> pdb=" O THR B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 260 Processing helix chain 'B' and resid 287 through 296 Processing helix chain 'B' and resid 297 through 301 Processing helix chain 'B' and resid 306 through 310 Processing helix chain 'B' and resid 324 through 339 Processing helix chain 'B' and resid 340 through 343 Processing helix chain 'B' and resid 384 through 401 removed outlier: 3.631A pdb=" N ARG B 401 " --> pdb=" O ALA B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 4.075A pdb=" N TYR B 408 " --> pdb=" O PHE B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 436 removed outlier: 3.951A pdb=" N PHE B 418 " --> pdb=" O ASP B 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 29 Processing helix chain 'C' and resid 47 through 51 Processing helix chain 'C' and resid 72 through 81 removed outlier: 3.634A pdb=" N VAL C 78 " --> pdb=" O VAL C 74 " (cutoff:3.500A) 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 113 Processing helix chain 'C' and resid 114 through 128 removed outlier: 3.594A pdb=" N GLN C 128 " --> pdb=" O LYS C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 161 removed outlier: 4.094A pdb=" N THR C 150 " --> pdb=" O GLY C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 195 Processing helix chain 'C' and resid 196 through 198 No H-bonds generated for 'chain 'C' and resid 196 through 198' Processing helix chain 'C' and resid 206 through 218 Processing helix chain 'C' and resid 223 through 244 removed outlier: 4.583A pdb=" N SER C 241 " --> pdb=" O SER C 237 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N LEU C 242 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 260 removed outlier: 3.991A pdb=" N PHE C 255 " --> pdb=" O ASP C 251 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLN C 256 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N THR C 257 " --> pdb=" O THR C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 283 removed outlier: 3.705A pdb=" N TYR C 282 " --> pdb=" O ALA C 278 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N HIS C 283 " --> pdb=" O GLU C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 296 removed outlier: 3.847A pdb=" N PHE C 296 " --> pdb=" O THR C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 301 Processing helix chain 'C' and resid 306 through 310 Processing helix chain 'C' and resid 324 through 338 removed outlier: 3.562A pdb=" N VAL C 328 " --> pdb=" O VAL C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 401 removed outlier: 3.750A pdb=" N ALA C 387 " --> pdb=" O ALA C 383 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS C 401 " --> pdb=" O LEU C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 411 removed outlier: 3.893A pdb=" N TYR C 408 " --> pdb=" O PHE C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 437 removed outlier: 3.872A pdb=" N PHE C 418 " --> pdb=" O GLU C 414 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL C 437 " --> pdb=" O GLU C 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 29 Processing helix chain 'D' and resid 41 through 48 removed outlier: 4.450A pdb=" N ARG D 48 " --> pdb=" O LEU D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 51 No H-bonds generated for 'chain 'D' and resid 49 through 51' Processing helix chain 'D' and resid 71 through 81 removed outlier: 4.573A pdb=" N MET D 75 " --> pdb=" O GLU D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 87 removed outlier: 3.744A pdb=" N PHE D 87 " --> pdb=" O GLY D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 90 No H-bonds generated for 'chain 'D' and resid 88 through 90' Processing helix chain 'D' and resid 102 through 108 Processing helix chain 'D' and resid 109 through 129 removed outlier: 4.473A pdb=" N ASP D 116 " --> pdb=" O ALA D 112 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N SER D 117 " --> pdb=" O GLU D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 161 Processing helix chain 'D' and resid 182 through 198 removed outlier: 3.886A pdb=" N GLU D 196 " --> pdb=" O HIS D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 216 Processing helix chain 'D' and resid 223 through 244 removed outlier: 5.198A pdb=" N CYS D 241 " --> pdb=" O GLY D 237 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU D 242 " --> pdb=" O VAL D 238 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG D 243 " --> pdb=" O THR D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 260 Processing helix chain 'D' and resid 287 through 296 Processing helix chain 'D' and resid 297 through 301 Processing helix chain 'D' and resid 306 through 310 Processing helix chain 'D' and resid 324 through 339 Processing helix chain 'D' and resid 340 through 343 Processing helix chain 'D' and resid 384 through 401 removed outlier: 3.632A pdb=" N ARG D 401 " --> pdb=" O ALA D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 410 removed outlier: 4.074A pdb=" N TYR D 408 " --> pdb=" O PHE D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 436 removed outlier: 3.950A pdb=" N PHE D 418 " --> pdb=" O ASP D 414 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 29 Processing helix chain 'E' and resid 47 through 51 Processing helix chain 'E' and resid 72 through 81 removed outlier: 3.633A pdb=" N VAL E 78 " --> pdb=" O VAL E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing helix chain 'E' and resid 102 through 108 Processing helix chain 'E' and resid 110 through 113 Processing helix chain 'E' and resid 114 through 128 removed outlier: 3.594A pdb=" N GLN E 128 " --> pdb=" O LYS E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 161 removed outlier: 4.093A pdb=" N THR E 150 " --> pdb=" O GLY E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 195 Processing helix chain 'E' and resid 196 through 198 No H-bonds generated for 'chain 'E' and resid 196 through 198' Processing helix chain 'E' and resid 206 through 218 Processing helix chain 'E' and resid 223 through 244 removed outlier: 4.584A pdb=" N SER E 241 " --> pdb=" O SER E 237 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N LEU E 242 " --> pdb=" O ILE E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 260 removed outlier: 3.991A pdb=" N PHE E 255 " --> pdb=" O ASP E 251 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLN E 256 " --> pdb=" O LEU E 252 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N THR E 257 " --> pdb=" O THR E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 277 through 283 removed outlier: 3.706A pdb=" N TYR E 282 " --> pdb=" O ALA E 278 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N HIS E 283 " --> pdb=" O GLU E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 296 removed outlier: 3.846A pdb=" N PHE E 296 " --> pdb=" O THR E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 301 Processing helix chain 'E' and resid 306 through 310 Processing helix chain 'E' and resid 324 through 338 removed outlier: 3.563A pdb=" N VAL E 328 " --> pdb=" O VAL E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 401 removed outlier: 3.750A pdb=" N ALA E 387 " --> pdb=" O ALA E 383 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS E 401 " --> pdb=" O LEU E 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 411 removed outlier: 3.894A pdb=" N TYR E 408 " --> pdb=" O PHE E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 437 removed outlier: 3.873A pdb=" N PHE E 418 " --> pdb=" O GLU E 414 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL E 437 " --> pdb=" O GLU E 433 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 29 Processing helix chain 'F' and resid 41 through 48 removed outlier: 4.449A pdb=" N ARG F 48 " --> pdb=" O LEU F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 51 No H-bonds generated for 'chain 'F' and resid 49 through 51' Processing helix chain 'F' and resid 71 through 81 removed outlier: 4.573A pdb=" N MET F 75 " --> pdb=" O GLU F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 87 removed outlier: 3.744A pdb=" N PHE F 87 " --> pdb=" O GLY F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 90 No H-bonds generated for 'chain 'F' and resid 88 through 90' Processing helix chain 'F' and resid 102 through 108 Processing helix chain 'F' and resid 109 through 129 removed outlier: 4.474A pdb=" N ASP F 116 " --> pdb=" O ALA F 112 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N SER F 117 " --> pdb=" O GLU F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 161 Processing helix chain 'F' and resid 182 through 198 removed outlier: 3.885A pdb=" N GLU F 196 " --> pdb=" O HIS F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 216 Processing helix chain 'F' and resid 223 through 244 removed outlier: 5.199A pdb=" N CYS F 241 " --> pdb=" O GLY F 237 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU F 242 " --> pdb=" O VAL F 238 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG F 243 " --> pdb=" O THR F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 251 through 260 Processing helix chain 'F' and resid 287 through 296 Processing helix chain 'F' and resid 297 through 301 Processing helix chain 'F' and resid 306 through 310 Processing helix chain 'F' and resid 324 through 339 Processing helix chain 'F' and resid 340 through 343 Processing helix chain 'F' and resid 384 through 401 removed outlier: 3.632A pdb=" N ARG F 401 " --> pdb=" O ALA F 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 404 through 410 removed outlier: 4.074A pdb=" N TYR F 408 " --> pdb=" O PHE F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 436 removed outlier: 3.950A pdb=" N PHE F 418 " --> pdb=" O ASP F 414 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 29 Processing helix chain 'G' and resid 41 through 48 removed outlier: 4.449A pdb=" N ARG G 48 " --> pdb=" O LEU G 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 51 No H-bonds generated for 'chain 'G' and resid 49 through 51' Processing helix chain 'G' and resid 71 through 81 removed outlier: 4.573A pdb=" N MET G 75 " --> pdb=" O GLU G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 87 removed outlier: 3.745A pdb=" N PHE G 87 " --> pdb=" O GLY G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 90 No H-bonds generated for 'chain 'G' and resid 88 through 90' Processing helix chain 'G' and resid 102 through 108 Processing helix chain 'G' and resid 109 through 129 removed outlier: 4.474A pdb=" N ASP G 116 " --> pdb=" O ALA G 112 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N SER G 117 " --> pdb=" O GLU G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 144 through 161 Processing helix chain 'G' and resid 182 through 198 removed outlier: 3.885A pdb=" N GLU G 196 " --> pdb=" O HIS G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 216 Processing helix chain 'G' and resid 223 through 244 removed outlier: 5.198A pdb=" N CYS G 241 " --> pdb=" O GLY G 237 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LEU G 242 " --> pdb=" O VAL G 238 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG G 243 " --> pdb=" O THR G 239 " (cutoff:3.500A) Processing helix chain 'G' and resid 251 through 260 Processing helix chain 'G' and resid 287 through 296 Processing helix chain 'G' and resid 297 through 301 Processing helix chain 'G' and resid 306 through 310 Processing helix chain 'G' and resid 324 through 339 Processing helix chain 'G' and resid 340 through 343 Processing helix chain 'G' and resid 384 through 401 removed outlier: 3.630A pdb=" N ARG G 401 " --> pdb=" O ALA G 397 " (cutoff:3.500A) Processing helix chain 'G' and resid 404 through 410 removed outlier: 4.073A pdb=" N TYR G 408 " --> pdb=" O PHE G 404 " (cutoff:3.500A) Processing helix chain 'G' and resid 414 through 436 removed outlier: 3.950A pdb=" N PHE G 418 " --> pdb=" O ASP G 414 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 29 Processing helix chain 'H' and resid 41 through 48 removed outlier: 4.450A pdb=" N ARG H 48 " --> pdb=" O LEU H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 51 No H-bonds generated for 'chain 'H' and resid 49 through 51' Processing helix chain 'H' and resid 71 through 81 removed outlier: 4.574A pdb=" N MET H 75 " --> pdb=" O GLU H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.744A pdb=" N PHE H 87 " --> pdb=" O GLY H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 90 No H-bonds generated for 'chain 'H' and resid 88 through 90' Processing helix chain 'H' and resid 102 through 108 Processing helix chain 'H' and resid 109 through 129 removed outlier: 4.474A pdb=" N ASP H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N SER H 117 " --> pdb=" O GLU H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 144 through 161 Processing helix chain 'H' and resid 182 through 198 removed outlier: 3.885A pdb=" N GLU H 196 " --> pdb=" O HIS H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 206 through 216 Processing helix chain 'H' and resid 223 through 244 removed outlier: 5.197A pdb=" N CYS H 241 " --> pdb=" O GLY H 237 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LEU H 242 " --> pdb=" O VAL H 238 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG H 243 " --> pdb=" O THR H 239 " (cutoff:3.500A) Processing helix chain 'H' and resid 251 through 260 Processing helix chain 'H' and resid 287 through 296 Processing helix chain 'H' and resid 297 through 301 Processing helix chain 'H' and resid 306 through 310 Processing helix chain 'H' and resid 324 through 339 Processing helix chain 'H' and resid 340 through 343 Processing helix chain 'H' and resid 384 through 401 removed outlier: 3.631A pdb=" N ARG H 401 " --> pdb=" O ALA H 397 " (cutoff:3.500A) Processing helix chain 'H' and resid 404 through 410 removed outlier: 4.073A pdb=" N TYR H 408 " --> pdb=" O PHE H 404 " (cutoff:3.500A) Processing helix chain 'H' and resid 414 through 436 removed outlier: 3.950A pdb=" N PHE H 418 " --> pdb=" O ASP H 414 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 29 Processing helix chain 'I' and resid 41 through 48 removed outlier: 4.450A pdb=" N ARG I 48 " --> pdb=" O LEU I 42 " (cutoff:3.500A) 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 71 through 81 removed outlier: 4.574A pdb=" N MET I 75 " --> pdb=" O GLU I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 87 removed outlier: 3.744A pdb=" N PHE I 87 " --> pdb=" O GLY I 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 90 No H-bonds generated for 'chain 'I' and resid 88 through 90' Processing helix chain 'I' and resid 102 through 108 Processing helix chain 'I' and resid 109 through 129 removed outlier: 4.474A pdb=" N ASP I 116 " --> pdb=" O ALA I 112 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N SER I 117 " --> pdb=" O GLU I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 144 through 161 Processing helix chain 'I' and resid 182 through 198 removed outlier: 3.885A pdb=" N GLU I 196 " --> pdb=" O HIS I 192 " (cutoff:3.500A) Processing helix chain 'I' and resid 206 through 216 Processing helix chain 'I' and resid 223 through 244 removed outlier: 5.198A pdb=" N CYS I 241 " --> pdb=" O GLY I 237 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LEU I 242 " --> pdb=" O VAL I 238 " (cutoff:3.500A) removed outlier: 3.616A 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 287 through 296 Processing helix chain 'I' and resid 297 through 301 Processing helix chain 'I' and resid 306 through 310 Processing helix chain 'I' and resid 324 through 339 Processing helix chain 'I' and resid 340 through 343 Processing helix chain 'I' and resid 384 through 401 removed outlier: 3.631A pdb=" N ARG I 401 " --> pdb=" O ALA I 397 " (cutoff:3.500A) Processing helix chain 'I' and resid 404 through 410 removed outlier: 4.073A pdb=" N TYR I 408 " --> pdb=" O PHE I 404 " (cutoff:3.500A) Processing helix chain 'I' and resid 414 through 436 removed outlier: 3.950A pdb=" N PHE I 418 " --> pdb=" O ASP I 414 " (cutoff:3.500A) Processing helix chain 'J' and resid 10 through 29 Processing helix chain 'J' and resid 47 through 51 Processing helix chain 'J' and resid 72 through 81 removed outlier: 3.634A pdb=" N VAL J 78 " --> pdb=" O VAL J 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 90 No H-bonds generated for 'chain 'J' and resid 88 through 90' Processing helix chain 'J' and resid 102 through 108 Processing helix chain 'J' and resid 110 through 113 Processing helix chain 'J' and resid 114 through 128 removed outlier: 3.594A pdb=" N GLN J 128 " --> pdb=" O LYS J 124 " (cutoff:3.500A) Processing helix chain 'J' and resid 143 through 161 removed outlier: 4.093A pdb=" N THR J 150 " --> pdb=" O GLY J 146 " (cutoff:3.500A) Processing helix chain 'J' and resid 182 through 195 Processing helix chain 'J' and resid 196 through 198 No H-bonds generated for 'chain 'J' and resid 196 through 198' Processing helix chain 'J' and resid 206 through 218 Processing helix chain 'J' and resid 223 through 244 removed outlier: 4.584A pdb=" N SER J 241 " --> pdb=" O SER J 237 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N LEU J 242 " --> pdb=" O ILE J 238 " (cutoff:3.500A) Processing helix chain 'J' and resid 251 through 260 removed outlier: 3.990A pdb=" N PHE J 255 " --> pdb=" O ASP J 251 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLN J 256 " --> pdb=" O LEU J 252 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N THR J 257 " --> pdb=" O THR J 253 " (cutoff:3.500A) Processing helix chain 'J' and resid 277 through 283 removed outlier: 3.705A pdb=" N TYR J 282 " --> pdb=" O ALA J 278 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N HIS J 283 " --> pdb=" O GLU J 279 " (cutoff:3.500A) Processing helix chain 'J' and resid 287 through 296 removed outlier: 3.847A pdb=" N PHE J 296 " --> pdb=" O THR J 292 " (cutoff:3.500A) Processing helix chain 'J' and resid 297 through 301 Processing helix chain 'J' and resid 306 through 310 Processing helix chain 'J' and resid 324 through 338 removed outlier: 3.562A pdb=" N VAL J 328 " --> pdb=" O VAL J 324 " (cutoff:3.500A) Processing helix chain 'J' and resid 383 through 401 removed outlier: 3.750A pdb=" N ALA J 387 " --> pdb=" O ALA J 383 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS J 401 " --> pdb=" O LEU J 397 " (cutoff:3.500A) Processing helix chain 'J' and resid 404 through 411 removed outlier: 3.895A pdb=" N TYR J 408 " --> pdb=" O PHE J 404 " (cutoff:3.500A) Processing helix chain 'J' and resid 414 through 437 removed outlier: 3.872A pdb=" N PHE J 418 " --> pdb=" O GLU J 414 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL J 437 " --> pdb=" O GLU J 433 " (cutoff:3.500A) Processing helix chain 'K' and resid 10 through 29 Processing helix chain 'K' and resid 47 through 51 Processing helix chain 'K' and resid 72 through 81 removed outlier: 3.635A pdb=" N VAL K 78 " --> pdb=" O VAL K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 88 through 90 No H-bonds generated for 'chain 'K' and resid 88 through 90' Processing helix chain 'K' and resid 102 through 108 Processing helix chain 'K' and resid 110 through 113 Processing helix chain 'K' and resid 114 through 128 removed outlier: 3.595A pdb=" N GLN K 128 " --> pdb=" O LYS K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 143 through 161 removed outlier: 4.094A pdb=" N THR K 150 " --> pdb=" O GLY K 146 " (cutoff:3.500A) Processing helix chain 'K' and resid 182 through 195 Processing helix chain 'K' and resid 196 through 198 No H-bonds generated for 'chain 'K' and resid 196 through 198' Processing helix chain 'K' and resid 206 through 218 Processing helix chain 'K' and resid 223 through 244 removed outlier: 4.584A pdb=" N SER K 241 " --> pdb=" O SER K 237 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N LEU K 242 " --> pdb=" O ILE K 238 " (cutoff:3.500A) Processing helix chain 'K' and resid 251 through 260 removed outlier: 3.990A pdb=" N PHE K 255 " --> pdb=" O ASP K 251 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLN K 256 " --> pdb=" O LEU K 252 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N THR K 257 " --> pdb=" O THR K 253 " (cutoff:3.500A) Processing helix chain 'K' and resid 277 through 283 removed outlier: 3.705A pdb=" N TYR K 282 " --> pdb=" O ALA K 278 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N HIS K 283 " --> pdb=" O GLU K 279 " (cutoff:3.500A) Processing helix chain 'K' and resid 287 through 296 removed outlier: 3.846A pdb=" N PHE K 296 " --> pdb=" O THR K 292 " (cutoff:3.500A) Processing helix chain 'K' and resid 297 through 301 Processing helix chain 'K' and resid 306 through 310 Processing helix chain 'K' and resid 324 through 338 removed outlier: 3.562A pdb=" N VAL K 328 " --> pdb=" O VAL K 324 " (cutoff:3.500A) Processing helix chain 'K' and resid 383 through 401 removed outlier: 3.750A pdb=" N ALA K 387 " --> pdb=" O ALA K 383 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS K 401 " --> pdb=" O LEU K 397 " (cutoff:3.500A) Processing helix chain 'K' and resid 404 through 411 removed outlier: 3.895A pdb=" N TYR K 408 " --> pdb=" O PHE K 404 " (cutoff:3.500A) Processing helix chain 'K' and resid 414 through 437 removed outlier: 3.872A pdb=" N PHE K 418 " --> pdb=" O GLU K 414 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL K 437 " --> pdb=" O GLU K 433 " (cutoff:3.500A) Processing helix chain 'L' and resid 10 through 29 Processing helix chain 'L' and resid 47 through 51 Processing helix chain 'L' and resid 72 through 81 removed outlier: 3.635A pdb=" N VAL L 78 " --> pdb=" O VAL L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 88 through 90 No H-bonds generated for 'chain 'L' and resid 88 through 90' Processing helix chain 'L' and resid 102 through 108 Processing helix chain 'L' and resid 110 through 113 Processing helix chain 'L' and resid 114 through 128 removed outlier: 3.594A pdb=" N GLN L 128 " --> pdb=" O LYS L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 143 through 161 removed outlier: 4.093A pdb=" N THR L 150 " --> pdb=" O GLY L 146 " (cutoff:3.500A) Processing helix chain 'L' and resid 182 through 195 Processing helix chain 'L' and resid 196 through 198 No H-bonds generated for 'chain 'L' and resid 196 through 198' Processing helix chain 'L' and resid 206 through 218 Processing helix chain 'L' and resid 223 through 244 removed outlier: 4.584A pdb=" N SER L 241 " --> pdb=" O SER L 237 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N LEU L 242 " --> pdb=" O ILE L 238 " (cutoff:3.500A) Processing helix chain 'L' and resid 251 through 260 removed outlier: 3.990A pdb=" N PHE L 255 " --> pdb=" O ASP L 251 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLN L 256 " --> pdb=" O LEU L 252 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N THR L 257 " --> pdb=" O THR L 253 " (cutoff:3.500A) Processing helix chain 'L' and resid 277 through 283 removed outlier: 3.704A pdb=" N TYR L 282 " --> pdb=" O ALA L 278 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N HIS L 283 " --> pdb=" O GLU L 279 " (cutoff:3.500A) Processing helix chain 'L' and resid 287 through 296 removed outlier: 3.845A pdb=" N PHE L 296 " --> pdb=" O THR L 292 " (cutoff:3.500A) Processing helix chain 'L' and resid 297 through 301 Processing helix chain 'L' and resid 306 through 310 Processing helix chain 'L' and resid 324 through 338 removed outlier: 3.563A pdb=" N VAL L 328 " --> pdb=" O VAL L 324 " (cutoff:3.500A) Processing helix chain 'L' and resid 383 through 401 removed outlier: 3.751A pdb=" N ALA L 387 " --> pdb=" O ALA L 383 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS L 401 " --> pdb=" O LEU L 397 " (cutoff:3.500A) Processing helix chain 'L' and resid 404 through 411 removed outlier: 3.893A pdb=" N TYR L 408 " --> pdb=" O PHE L 404 " (cutoff:3.500A) Processing helix chain 'L' and resid 414 through 437 removed outlier: 3.873A pdb=" N PHE L 418 " --> pdb=" O GLU L 414 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL L 437 " --> pdb=" O GLU L 433 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 94 removed outlier: 8.051A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N GLU A 3 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLY A 134 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N SER A 140 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER A 165 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE A 171 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LYS A 166 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N PHE A 202 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N GLU A 168 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N VAL A 204 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N SER A 170 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 269 through 273 removed outlier: 3.622A pdb=" N ALA A 314 " --> pdb=" O ASN A 380 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 92 through 94 removed outlier: 7.870A pdb=" N VAL B 93 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N LEU B 67 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N ILE B 66 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N HIS B 6 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N VAL B 68 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N GLN B 8 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N GLU B 3 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N PHE B 135 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL B 5 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N LEU B 137 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE B 7 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N HIS B 139 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ALA B 9 " --> pdb=" O HIS B 139 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N GLN B 133 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ASN B 167 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N PHE B 135 " --> pdb=" O ASN B 167 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N PHE B 169 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LEU B 137 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N VAL B 171 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N HIS B 139 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N MET B 166 " --> pdb=" O GLU B 200 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N TYR B 202 " --> pdb=" O MET B 166 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N THR B 168 " --> pdb=" O TYR B 202 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ILE B 204 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N SER B 170 " --> pdb=" O ILE B 204 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N THR B 201 " --> pdb=" O PHE B 268 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N CYS B 203 " --> pdb=" O PRO B 270 " (cutoff:3.500A) removed outlier: 10.259A pdb=" N PHE B 272 " --> pdb=" O CYS B 203 " (cutoff:3.500A) removed outlier: 13.237A pdb=" N ASP B 205 " --> pdb=" O PHE B 272 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N PHE B 267 " --> pdb=" O SER B 381 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N SER B 381 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N LYS B 352 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL B 315 " --> pdb=" O LYS B 352 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N ALA B 354 " --> pdb=" O VAL B 315 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA B 317 " --> pdb=" O ALA B 354 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N CYS B 356 " --> pdb=" O ALA B 317 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N PHE B 319 " --> pdb=" O CYS B 356 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU B 248 " --> pdb=" O VAL B 355 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 53 through 55 Processing sheet with id=AA6, first strand: chain 'C' and resid 92 through 94 removed outlier: 8.052A pdb=" N ILE C 93 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N PHE C 67 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N VAL C 66 " --> pdb=" O CYS C 4 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N SER C 6 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N VAL C 68 " --> pdb=" O SER C 6 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N HIS C 8 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N GLU C 3 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLY C 134 " --> pdb=" O GLU C 3 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N SER C 140 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER C 165 " --> pdb=" O GLN C 133 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE C 171 " --> pdb=" O HIS C 139 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LYS C 166 " --> pdb=" O CYS C 200 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N PHE C 202 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLU C 168 " --> pdb=" O PHE C 202 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N VAL C 204 " --> pdb=" O GLU C 168 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N SER C 170 " --> pdb=" O VAL C 204 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AA8, first strand: chain 'C' and resid 269 through 273 removed outlier: 3.621A pdb=" N ALA C 314 " --> pdb=" O ASN C 380 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 92 through 94 removed outlier: 7.870A pdb=" N VAL D 93 " --> pdb=" O ALA D 65 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N LEU D 67 " --> pdb=" O VAL D 93 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N ILE D 66 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N HIS D 6 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N VAL D 68 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N GLN D 8 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N GLU D 3 " --> pdb=" O GLN D 133 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N PHE D 135 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL D 5 " --> pdb=" O PHE D 135 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N LEU D 137 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE D 7 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N HIS D 139 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ALA D 9 " --> pdb=" O HIS D 139 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N GLN D 133 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N ASN D 167 " --> pdb=" O GLN D 133 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N PHE D 135 " --> pdb=" O ASN D 167 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N PHE D 169 " --> pdb=" O PHE D 135 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU D 137 " --> pdb=" O PHE D 169 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N VAL D 171 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N HIS D 139 " --> pdb=" O VAL D 171 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N MET D 166 " --> pdb=" O GLU D 200 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N TYR D 202 " --> pdb=" O MET D 166 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N THR D 168 " --> pdb=" O TYR D 202 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N ILE D 204 " --> pdb=" O THR D 168 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N SER D 170 " --> pdb=" O ILE D 204 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N THR D 201 " --> pdb=" O PHE D 268 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N CYS D 203 " --> pdb=" O PRO D 270 " (cutoff:3.500A) removed outlier: 10.259A pdb=" N PHE D 272 " --> pdb=" O CYS D 203 " (cutoff:3.500A) removed outlier: 13.238A pdb=" N ASP D 205 " --> pdb=" O PHE D 272 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N PHE D 267 " --> pdb=" O SER D 381 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N SER D 381 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N LYS D 352 " --> pdb=" O LEU D 313 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL D 315 " --> pdb=" O LYS D 352 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N ALA D 354 " --> pdb=" O VAL D 315 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ALA D 317 " --> pdb=" O ALA D 354 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N CYS D 356 " --> pdb=" O ALA D 317 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N PHE D 319 " --> pdb=" O CYS D 356 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU D 248 " --> pdb=" O VAL D 355 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 53 through 55 Processing sheet with id=AB2, first strand: chain 'E' and resid 92 through 94 removed outlier: 8.052A pdb=" N ILE E 93 " --> pdb=" O ALA E 65 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N PHE E 67 " --> pdb=" O ILE E 93 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N VAL E 66 " --> pdb=" O CYS E 4 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N SER E 6 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N VAL E 68 " --> pdb=" O SER E 6 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N HIS E 8 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N GLU E 3 " --> pdb=" O LEU E 132 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLY E 134 " --> pdb=" O GLU E 3 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N SER E 140 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER E 165 " --> pdb=" O GLN E 133 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE E 171 " --> pdb=" O HIS E 139 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LYS E 166 " --> pdb=" O CYS E 200 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N PHE E 202 " --> pdb=" O LYS E 166 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N GLU E 168 " --> pdb=" O PHE E 202 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N VAL E 204 " --> pdb=" O GLU E 168 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N SER E 170 " --> pdb=" O VAL E 204 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AB4, first strand: chain 'E' and resid 269 through 273 removed outlier: 3.622A pdb=" N ALA E 314 " --> pdb=" O ASN E 380 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 92 through 94 removed outlier: 7.870A pdb=" N VAL F 93 " --> pdb=" O ALA F 65 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N LEU F 67 " --> pdb=" O VAL F 93 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N ILE F 66 " --> pdb=" O ILE F 4 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N HIS F 6 " --> pdb=" O ILE F 66 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N VAL F 68 " --> pdb=" O HIS F 6 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N GLN F 8 " --> pdb=" O VAL F 68 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N GLU F 3 " --> pdb=" O GLN F 133 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N PHE F 135 " --> pdb=" O GLU F 3 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL F 5 " --> pdb=" O PHE F 135 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N LEU F 137 " --> pdb=" O VAL F 5 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE F 7 " --> pdb=" O LEU F 137 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N HIS F 139 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ALA F 9 " --> pdb=" O HIS F 139 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N GLN F 133 " --> pdb=" O ILE F 165 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N ASN F 167 " --> pdb=" O GLN F 133 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N PHE F 135 " --> pdb=" O ASN F 167 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N PHE F 169 " --> pdb=" O PHE F 135 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU F 137 " --> pdb=" O PHE F 169 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N VAL F 171 " --> pdb=" O LEU F 137 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N HIS F 139 " --> pdb=" O VAL F 171 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N MET F 166 " --> pdb=" O GLU F 200 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N TYR F 202 " --> pdb=" O MET F 166 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N THR F 168 " --> pdb=" O TYR F 202 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ILE F 204 " --> pdb=" O THR F 168 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N SER F 170 " --> pdb=" O ILE F 204 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N THR F 201 " --> pdb=" O PHE F 268 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N CYS F 203 " --> pdb=" O PRO F 270 " (cutoff:3.500A) removed outlier: 10.258A pdb=" N PHE F 272 " --> pdb=" O CYS F 203 " (cutoff:3.500A) removed outlier: 13.237A pdb=" N ASP F 205 " --> pdb=" O PHE F 272 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N PHE F 267 " --> pdb=" O SER F 381 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N SER F 381 " --> pdb=" O PHE F 267 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N LYS F 352 " --> pdb=" O LEU F 313 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL F 315 " --> pdb=" O LYS F 352 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N ALA F 354 " --> pdb=" O VAL F 315 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA F 317 " --> pdb=" O ALA F 354 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N CYS F 356 " --> pdb=" O ALA F 317 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N PHE F 319 " --> pdb=" O CYS F 356 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU F 248 " --> pdb=" O VAL F 355 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 53 through 55 Processing sheet with id=AB7, first strand: chain 'G' and resid 92 through 94 removed outlier: 7.870A pdb=" N VAL G 93 " --> pdb=" O ALA G 65 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N LEU G 67 " --> pdb=" O VAL G 93 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N ILE G 66 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N HIS G 6 " --> pdb=" O ILE G 66 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N VAL G 68 " --> pdb=" O HIS G 6 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N GLN G 8 " --> pdb=" O VAL G 68 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N GLU G 3 " --> pdb=" O GLN G 133 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N PHE G 135 " --> pdb=" O GLU G 3 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL G 5 " --> pdb=" O PHE G 135 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N LEU G 137 " --> pdb=" O VAL G 5 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE G 7 " --> pdb=" O LEU G 137 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N HIS G 139 " --> pdb=" O ILE G 7 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ALA G 9 " --> pdb=" O HIS G 139 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N GLN G 133 " --> pdb=" O ILE G 165 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N ASN G 167 " --> pdb=" O GLN G 133 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N PHE G 135 " --> pdb=" O ASN G 167 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N PHE G 169 " --> pdb=" O PHE G 135 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LEU G 137 " --> pdb=" O PHE G 169 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N VAL G 171 " --> pdb=" O LEU G 137 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N HIS G 139 " --> pdb=" O VAL G 171 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N MET G 166 " --> pdb=" O GLU G 200 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N TYR G 202 " --> pdb=" O MET G 166 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N THR G 168 " --> pdb=" O TYR G 202 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ILE G 204 " --> pdb=" O THR G 168 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N SER G 170 " --> pdb=" O ILE G 204 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR G 201 " --> pdb=" O PHE G 268 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N CYS G 203 " --> pdb=" O PRO G 270 " (cutoff:3.500A) removed outlier: 10.259A pdb=" N PHE G 272 " --> pdb=" O CYS G 203 " (cutoff:3.500A) removed outlier: 13.238A pdb=" N ASP G 205 " --> pdb=" O PHE G 272 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N PHE G 267 " --> pdb=" O SER G 381 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N SER G 381 " --> pdb=" O PHE G 267 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N LYS G 352 " --> pdb=" O LEU G 313 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL G 315 " --> pdb=" O LYS G 352 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N ALA G 354 " --> pdb=" O VAL G 315 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ALA G 317 " --> pdb=" O ALA G 354 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N CYS G 356 " --> pdb=" O ALA G 317 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N PHE G 319 " --> pdb=" O CYS G 356 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU G 248 " --> pdb=" O VAL G 355 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 53 through 55 Processing sheet with id=AB9, first strand: chain 'H' and resid 92 through 94 removed outlier: 7.870A pdb=" N VAL H 93 " --> pdb=" O ALA H 65 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N LEU H 67 " --> pdb=" O VAL H 93 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N ILE H 66 " --> pdb=" O ILE H 4 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N HIS H 6 " --> pdb=" O ILE H 66 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N VAL H 68 " --> pdb=" O HIS H 6 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N GLN H 8 " --> pdb=" O VAL H 68 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N GLU H 3 " --> pdb=" O GLN H 133 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N PHE H 135 " --> pdb=" O GLU H 3 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL H 5 " --> pdb=" O PHE H 135 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N LEU H 137 " --> pdb=" O VAL H 5 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE H 7 " --> pdb=" O LEU H 137 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N HIS H 139 " --> pdb=" O ILE H 7 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ALA H 9 " --> pdb=" O HIS H 139 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N GLN H 133 " --> pdb=" O ILE H 165 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N ASN H 167 " --> pdb=" O GLN H 133 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N PHE H 135 " --> pdb=" O ASN H 167 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N PHE H 169 " --> pdb=" O PHE H 135 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LEU H 137 " --> pdb=" O PHE H 169 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N VAL H 171 " --> pdb=" O LEU H 137 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N HIS H 139 " --> pdb=" O VAL H 171 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N MET H 166 " --> pdb=" O GLU H 200 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N TYR H 202 " --> pdb=" O MET H 166 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N THR H 168 " --> pdb=" O TYR H 202 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ILE H 204 " --> pdb=" O THR H 168 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N SER H 170 " --> pdb=" O ILE H 204 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR H 201 " --> pdb=" O PHE H 268 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N CYS H 203 " --> pdb=" O PRO H 270 " (cutoff:3.500A) removed outlier: 10.259A pdb=" N PHE H 272 " --> pdb=" O CYS H 203 " (cutoff:3.500A) removed outlier: 13.237A pdb=" N ASP H 205 " --> pdb=" O PHE H 272 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N PHE H 267 " --> pdb=" O SER H 381 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N SER H 381 " --> pdb=" O PHE H 267 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N LYS H 352 " --> pdb=" O LEU H 313 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL H 315 " --> pdb=" O LYS H 352 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N ALA H 354 " --> pdb=" O VAL H 315 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ALA H 317 " --> pdb=" O ALA H 354 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N CYS H 356 " --> pdb=" O ALA H 317 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N PHE H 319 " --> pdb=" O CYS H 356 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU H 248 " --> pdb=" O VAL H 355 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 53 through 55 Processing sheet with id=AC2, first strand: chain 'I' and resid 92 through 94 removed outlier: 7.871A pdb=" N VAL I 93 " --> pdb=" O ALA I 65 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N LEU I 67 " --> pdb=" O VAL I 93 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N ILE I 66 " --> pdb=" O ILE I 4 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N HIS I 6 " --> pdb=" O ILE I 66 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N VAL I 68 " --> pdb=" O HIS I 6 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N GLN I 8 " --> pdb=" O VAL I 68 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N GLU I 3 " --> pdb=" O GLN I 133 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N PHE I 135 " --> pdb=" O GLU I 3 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VAL I 5 " --> pdb=" O PHE I 135 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N LEU I 137 " --> pdb=" O VAL I 5 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE I 7 " --> pdb=" O LEU I 137 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N HIS I 139 " --> pdb=" O ILE I 7 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N ALA I 9 " --> pdb=" O HIS I 139 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N GLN I 133 " --> pdb=" O ILE I 165 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N ASN I 167 " --> pdb=" O GLN I 133 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N PHE I 135 " --> pdb=" O ASN I 167 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N PHE I 169 " --> pdb=" O PHE I 135 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LEU I 137 " --> pdb=" O PHE I 169 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N VAL I 171 " --> pdb=" O LEU I 137 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N HIS I 139 " --> pdb=" O VAL I 171 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N MET I 166 " --> pdb=" O GLU I 200 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N TYR I 202 " --> pdb=" O MET I 166 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N THR I 168 " --> pdb=" O TYR I 202 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N ILE I 204 " --> pdb=" O THR I 168 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N SER I 170 " --> pdb=" O ILE I 204 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR I 201 " --> pdb=" O PHE I 268 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N CYS I 203 " --> pdb=" O PRO I 270 " (cutoff:3.500A) removed outlier: 10.259A pdb=" N PHE I 272 " --> pdb=" O CYS I 203 " (cutoff:3.500A) removed outlier: 13.238A pdb=" N ASP I 205 " --> pdb=" O PHE I 272 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N PHE I 267 " --> pdb=" O SER I 381 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N SER I 381 " --> pdb=" O PHE I 267 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N LYS I 352 " --> pdb=" O LEU I 313 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL I 315 " --> pdb=" O LYS I 352 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N ALA I 354 " --> pdb=" O VAL I 315 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA I 317 " --> pdb=" O ALA I 354 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N CYS I 356 " --> pdb=" O ALA I 317 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N PHE I 319 " --> pdb=" O CYS I 356 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU I 248 " --> pdb=" O VAL I 355 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 53 through 55 Processing sheet with id=AC4, first strand: chain 'J' and resid 92 through 94 removed outlier: 8.052A pdb=" N ILE J 93 " --> pdb=" O ALA J 65 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N PHE J 67 " --> pdb=" O ILE J 93 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N VAL J 66 " --> pdb=" O CYS J 4 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N SER J 6 " --> pdb=" O VAL J 66 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N VAL J 68 " --> pdb=" O SER J 6 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N HIS J 8 " --> pdb=" O VAL J 68 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N GLU J 3 " --> pdb=" O LEU J 132 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLY J 134 " --> pdb=" O GLU J 3 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N SER J 140 " --> pdb=" O VAL J 9 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER J 165 " --> pdb=" O GLN J 133 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE J 171 " --> pdb=" O HIS J 139 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LYS J 166 " --> pdb=" O CYS J 200 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N PHE J 202 " --> pdb=" O LYS J 166 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLU J 168 " --> pdb=" O PHE J 202 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N VAL J 204 " --> pdb=" O GLU J 168 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N SER J 170 " --> pdb=" O VAL J 204 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 53 through 55 Processing sheet with id=AC6, first strand: chain 'J' and resid 269 through 273 removed outlier: 3.621A pdb=" N ALA J 314 " --> pdb=" O ASN J 380 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 92 through 94 removed outlier: 8.053A pdb=" N ILE K 93 " --> pdb=" O ALA K 65 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N PHE K 67 " --> pdb=" O ILE K 93 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N VAL K 66 " --> pdb=" O CYS K 4 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N SER K 6 " --> pdb=" O VAL K 66 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N VAL K 68 " --> pdb=" O SER K 6 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N HIS K 8 " --> pdb=" O VAL K 68 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N GLU K 3 " --> pdb=" O LEU K 132 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLY K 134 " --> pdb=" O GLU K 3 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N SER K 140 " --> pdb=" O VAL K 9 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N SER K 165 " --> pdb=" O GLN K 133 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE K 171 " --> pdb=" O HIS K 139 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LYS K 166 " --> pdb=" O CYS K 200 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N PHE K 202 " --> pdb=" O LYS K 166 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLU K 168 " --> pdb=" O PHE K 202 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N VAL K 204 " --> pdb=" O GLU K 168 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N SER K 170 " --> pdb=" O VAL K 204 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 53 through 55 Processing sheet with id=AC9, first strand: chain 'K' and resid 269 through 273 removed outlier: 3.621A pdb=" N ALA K 314 " --> pdb=" O ASN K 380 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 92 through 94 removed outlier: 8.052A pdb=" N ILE L 93 " --> pdb=" O ALA L 65 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N PHE L 67 " --> pdb=" O ILE L 93 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N VAL L 66 " --> pdb=" O CYS L 4 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N SER L 6 " --> pdb=" O VAL L 66 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N VAL L 68 " --> pdb=" O SER L 6 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N HIS L 8 " --> pdb=" O VAL L 68 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N GLU L 3 " --> pdb=" O LEU L 132 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLY L 134 " --> pdb=" O GLU L 3 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N SER L 140 " --> pdb=" O VAL L 9 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER L 165 " --> pdb=" O GLN L 133 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE L 171 " --> pdb=" O HIS L 139 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LYS L 166 " --> pdb=" O CYS L 200 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N PHE L 202 " --> pdb=" O LYS L 166 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLU L 168 " --> pdb=" O PHE L 202 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N VAL L 204 " --> pdb=" O GLU L 168 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N SER L 170 " --> pdb=" O VAL L 204 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 53 through 55 Processing sheet with id=AD3, first strand: chain 'L' and resid 269 through 273 removed outlier: 3.622A pdb=" N ALA L 314 " --> pdb=" O ASN L 380 " (cutoff:3.500A) 2058 hydrogen bonds defined for protein. 5904 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: 10.72 Time building geometry restraints manager: 4.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 7181 1.32 - 1.44: 10955 1.44 - 1.57: 22820 1.57 - 1.69: 48 1.69 - 1.81: 432 Bond restraints: 41436 Sorted by residual: bond pdb=" C5 GTP E 501 " pdb=" C6 GTP E 501 " ideal model delta sigma weight residual 1.390 1.489 -0.099 2.00e-02 2.50e+03 2.45e+01 bond pdb=" C5 GTP A 501 " pdb=" C6 GTP A 501 " ideal model delta sigma weight residual 1.390 1.488 -0.098 2.00e-02 2.50e+03 2.39e+01 bond pdb=" C5 GTP C 501 " pdb=" C6 GTP C 501 " ideal model delta sigma weight residual 1.390 1.487 -0.097 2.00e-02 2.50e+03 2.37e+01 bond pdb=" C5 GTP J 501 " pdb=" C6 GTP J 501 " ideal model delta sigma weight residual 1.390 1.486 -0.096 2.00e-02 2.50e+03 2.31e+01 bond pdb=" C5 GTP L 501 " pdb=" C6 GTP L 501 " ideal model delta sigma weight residual 1.390 1.485 -0.095 2.00e-02 2.50e+03 2.24e+01 ... (remaining 41431 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 46491 1.94 - 3.87: 8773 3.87 - 5.81: 877 5.81 - 7.75: 135 7.75 - 9.69: 28 Bond angle restraints: 56304 Sorted by residual: angle pdb=" N THR L 73 " pdb=" CA THR L 73 " pdb=" C THR L 73 " ideal model delta sigma weight residual 111.11 117.45 -6.34 1.20e+00 6.94e-01 2.79e+01 angle pdb=" N THR K 73 " pdb=" CA THR K 73 " pdb=" C THR K 73 " ideal model delta sigma weight residual 111.11 117.42 -6.31 1.20e+00 6.94e-01 2.77e+01 angle pdb=" N THR J 73 " pdb=" CA THR J 73 " pdb=" C THR J 73 " ideal model delta sigma weight residual 111.11 117.40 -6.29 1.20e+00 6.94e-01 2.75e+01 angle pdb=" N THR A 73 " pdb=" CA THR A 73 " pdb=" C THR A 73 " ideal model delta sigma weight residual 111.11 117.38 -6.27 1.20e+00 6.94e-01 2.73e+01 angle pdb=" N THR E 73 " pdb=" CA THR E 73 " pdb=" C THR E 73 " ideal model delta sigma weight residual 111.11 117.37 -6.26 1.20e+00 6.94e-01 2.73e+01 ... (remaining 56299 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.60: 23772 33.60 - 67.20: 780 67.20 - 100.80: 36 100.80 - 134.41: 6 134.41 - 168.01: 18 Dihedral angle restraints: 24612 sinusoidal: 9810 harmonic: 14802 Sorted by residual: dihedral pdb=" C5' GTP K 501 " pdb=" O5' GTP K 501 " pdb=" PA GTP K 501 " pdb=" O3A GTP K 501 " ideal model delta sinusoidal sigma weight residual 69.27 -122.72 -168.01 1 2.00e+01 2.50e-03 4.75e+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 -122.94 -167.79 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " pdb=" O3A GTP A 501 " ideal model delta sinusoidal sigma weight residual 69.27 -122.96 -167.77 1 2.00e+01 2.50e-03 4.75e+01 ... (remaining 24609 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 4016 0.070 - 0.140: 1586 0.140 - 0.210: 439 0.210 - 0.280: 90 0.280 - 0.350: 25 Chirality restraints: 6156 Sorted by residual: chirality pdb=" CA PHE I 83 " pdb=" N PHE I 83 " pdb=" C PHE I 83 " pdb=" CB PHE I 83 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.06e+00 chirality pdb=" CA PHE B 83 " pdb=" N PHE B 83 " pdb=" C PHE B 83 " pdb=" CB PHE B 83 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.06e+00 chirality pdb=" CA PHE D 83 " pdb=" N PHE D 83 " pdb=" C PHE D 83 " pdb=" CB PHE D 83 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.00e+00 ... (remaining 6153 not shown) Planarity restraints: 7338 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL D 288 " 0.050 5.00e-02 4.00e+02 7.64e-02 9.35e+00 pdb=" N PRO D 289 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO D 289 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO D 289 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 288 " 0.050 5.00e-02 4.00e+02 7.62e-02 9.28e+00 pdb=" N PRO B 289 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO B 289 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 289 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL I 288 " 0.050 5.00e-02 4.00e+02 7.61e-02 9.26e+00 pdb=" N PRO I 289 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO I 289 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO I 289 " 0.042 5.00e-02 4.00e+02 ... (remaining 7335 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 84 2.56 - 3.14: 30964 3.14 - 3.73: 64764 3.73 - 4.31: 89611 4.31 - 4.90: 153610 Nonbonded interactions: 339033 Sorted by model distance: nonbonded pdb=" O1B GTP C 501 " pdb="MG MG C 502 " model vdw 1.972 2.170 nonbonded pdb=" O1B GTP E 501 " pdb="MG MG E 502 " model vdw 1.982 2.170 nonbonded pdb=" O1B GTP L 501 " pdb="MG MG L 502 " model vdw 2.007 2.170 nonbonded pdb=" O1B GTP A 501 " pdb="MG MG A 502 " model vdw 2.012 2.170 nonbonded pdb=" O1B GTP J 501 " pdb="MG MG J 502 " model vdw 2.034 2.170 ... (remaining 339028 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: 0.13 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } 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: 13.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.030 Extract box with map and model: 0.520 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 38.070 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:1.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 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 : 0.008 0.099 41436 Z= 0.606 Angle : 1.461 9.685 56304 Z= 1.024 Chirality : 0.082 0.350 6156 Planarity : 0.007 0.076 7338 Dihedral : 16.609 168.007 15120 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.21 % Allowed : 8.99 % Favored : 88.80 % Cbeta Deviations : 0.13 % 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: 0.41 (0.11), residues: 5088 helix: 1.22 (0.10), residues: 2274 sheet: 0.75 (0.19), residues: 714 loop : -0.93 (0.13), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG K 105 TYR 0.019 0.003 TYR I 224 PHE 0.028 0.002 PHE F 92 TRP 0.029 0.004 TRP D 21 HIS 0.012 0.002 HIS E 8 Details of bonding type rmsd covalent geometry : bond 0.00845 (41436) covalent geometry : angle 1.46123 (56304) hydrogen bonds : bond 0.18776 ( 2058) hydrogen bonds : angle 7.14005 ( 5904) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1693 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 1597 time to evaluate : 1.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ASN cc_start: 0.7824 (t0) cc_final: 0.7430 (t0) REVERT: A 71 GLU cc_start: 0.7353 (pt0) cc_final: 0.6977 (pt0) REVERT: A 76 ASP cc_start: 0.7356 (OUTLIER) cc_final: 0.7151 (m-30) REVERT: A 110 ILE cc_start: 0.8850 (mm) cc_final: 0.8592 (mm) REVERT: A 178 SER cc_start: 0.7437 (OUTLIER) cc_final: 0.7216 (p) REVERT: A 251 ASP cc_start: 0.7291 (p0) cc_final: 0.6917 (p0) REVERT: A 401 LYS cc_start: 0.8137 (mmtt) cc_final: 0.7891 (mmtt) REVERT: B 31 ASP cc_start: 0.6891 (p0) cc_final: 0.6491 (p0) REVERT: C 27 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7632 (mt-10) REVERT: C 50 ASN cc_start: 0.7541 (t0) cc_final: 0.7104 (t0) REVERT: C 110 ILE cc_start: 0.8859 (mm) cc_final: 0.8623 (mm) REVERT: C 114 ILE cc_start: 0.8930 (tp) cc_final: 0.8722 (mt) REVERT: C 161 TYR cc_start: 0.8382 (m-80) cc_final: 0.8132 (m-80) REVERT: C 230 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8191 (tt) REVERT: C 311 LYS cc_start: 0.8321 (mtmp) cc_final: 0.8110 (mttp) REVERT: C 396 ASP cc_start: 0.6382 (m-30) cc_final: 0.6127 (m-30) REVERT: D 31 ASP cc_start: 0.6694 (p0) cc_final: 0.6458 (p0) REVERT: D 314 THR cc_start: 0.8290 (p) cc_final: 0.7956 (p) REVERT: D 398 MET cc_start: 0.8277 (mtt) cc_final: 0.8012 (mtt) REVERT: E 50 ASN cc_start: 0.7838 (t0) cc_final: 0.7358 (t0) REVERT: E 110 ILE cc_start: 0.8846 (mm) cc_final: 0.8557 (mm) REVERT: E 172 TYR cc_start: 0.8106 (t80) cc_final: 0.7518 (t80) REVERT: E 230 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.7990 (mp) REVERT: F 31 ASP cc_start: 0.6701 (p0) cc_final: 0.6295 (p0) REVERT: F 224 TYR cc_start: 0.7854 (OUTLIER) cc_final: 0.7253 (m-80) REVERT: F 301 MET cc_start: 0.7695 (mmp) cc_final: 0.7470 (mmp) REVERT: G 88 ARG cc_start: 0.7741 (ttp-110) cc_final: 0.7086 (tpt170) REVERT: H 286 LEU cc_start: 0.7776 (mt) cc_final: 0.7169 (mp) REVERT: H 287 THR cc_start: 0.8390 (p) cc_final: 0.7930 (t) REVERT: H 398 MET cc_start: 0.7603 (mtt) cc_final: 0.7259 (mtp) REVERT: I 27 GLU cc_start: 0.7685 (mt-10) cc_final: 0.7301 (mt-10) REVERT: I 299 LYS cc_start: 0.7753 (ttpp) cc_final: 0.7372 (mtpp) REVERT: I 398 MET cc_start: 0.7791 (mtt) cc_final: 0.7389 (mtp) REVERT: J 71 GLU cc_start: 0.7301 (pt0) cc_final: 0.6937 (pt0) REVERT: J 161 TYR cc_start: 0.8467 (m-80) cc_final: 0.8157 (m-80) REVERT: J 230 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.7979 (mp) REVERT: J 326 LYS cc_start: 0.7406 (ttmt) cc_final: 0.7047 (mttt) REVERT: J 396 ASP cc_start: 0.6435 (m-30) cc_final: 0.6086 (m-30) REVERT: K 161 TYR cc_start: 0.8256 (m-80) cc_final: 0.8005 (m-80) REVERT: K 230 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.7996 (mp) REVERT: K 326 LYS cc_start: 0.7465 (ttmt) cc_final: 0.6778 (mttt) REVERT: L 71 GLU cc_start: 0.7068 (pt0) cc_final: 0.6837 (pt0) REVERT: L 230 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8143 (mp) REVERT: L 252 LEU cc_start: 0.8732 (mt) cc_final: 0.8316 (mt) outliers start: 96 outliers final: 24 residues processed: 1654 average time/residue: 0.2644 time to fit residues: 696.3069 Evaluate side-chains 963 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 931 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain B residue 224 TYR Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain E residue 219 ILE Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain F residue 224 TYR Chi-restraints excluded: chain G residue 356 CYS Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 356 CYS Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain J residue 76 ASP Chi-restraints excluded: chain J residue 219 ILE Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 245 ASP Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 371 VAL Chi-restraints excluded: chain K residue 219 ILE Chi-restraints excluded: chain K residue 230 LEU Chi-restraints excluded: chain K residue 245 ASP Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 371 VAL Chi-restraints excluded: chain L residue 219 ILE Chi-restraints excluded: chain L residue 230 LEU Chi-restraints excluded: chain L residue 245 ASP Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 371 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 432 optimal weight: 0.4980 chunk 197 optimal weight: 8.9990 chunk 388 optimal weight: 2.9990 chunk 455 optimal weight: 4.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 2.9990 chunk 494 optimal weight: 5.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 6.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 HIS A 15 GLN A 18 ASN A 88 HIS A 101 ASN A 300 ASN B 6 HIS B 37 HIS B 91 ASN B 193 GLN B 282 GLN ** B 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 436 GLN C 8 HIS C 15 GLN C 18 ASN C 88 HIS C 283 HIS C 300 ASN C 309 HIS D 6 HIS D 37 HIS D 91 ASN D 139 HIS D 282 GLN E 8 HIS E 15 GLN E 18 ASN E 61 HIS E 88 HIS E 192 HIS E 285 GLN E 300 ASN E 309 HIS F 37 HIS F 85 GLN F 91 ASN F 139 HIS ** F 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 HIS G 91 ASN G 193 GLN G 331 GLN G 350 ASN H 91 ASN H 349 ASN H 350 ASN I 6 HIS I 91 ASN I 331 GLN I 334 ASN I 350 ASN J 8 HIS J 15 GLN J 192 HIS J 197 HIS J 216 ASN J 285 GLN J 300 ASN ** J 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 8 HIS K 15 GLN K 18 ASN K 88 HIS K 101 ASN K 192 HIS K 197 HIS ** K 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 300 ASN L 8 HIS L 15 GLN L 18 ASN L 88 HIS L 101 ASN L 107 HIS L 192 HIS L 197 HIS L 283 HIS L 300 ASN L 301 GLN Total number of N/Q/H flips: 76 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.130065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.111077 restraints weight = 50757.984| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.28 r_work: 0.3300 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 41436 Z= 0.167 Angle : 0.629 9.907 56304 Z= 0.330 Chirality : 0.045 0.221 6156 Planarity : 0.005 0.056 7338 Dihedral : 12.298 171.175 5771 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.76 % Allowed : 15.47 % Favored : 80.77 % 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: 1.35 (0.12), residues: 5088 helix: 2.28 (0.11), residues: 2310 sheet: 0.76 (0.18), residues: 792 loop : -0.74 (0.13), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 369 TYR 0.017 0.001 TYR E 185 PHE 0.023 0.002 PHE B 388 TRP 0.015 0.002 TRP I 346 HIS 0.006 0.001 HIS D 139 Details of bonding type rmsd covalent geometry : bond 0.00360 (41436) covalent geometry : angle 0.62929 (56304) hydrogen bonds : bond 0.05889 ( 2058) hydrogen bonds : angle 5.01797 ( 5904) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1185 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 1022 time to evaluate : 1.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 GLU cc_start: 0.8158 (pt0) cc_final: 0.7791 (pt0) REVERT: A 77 GLU cc_start: 0.7814 (tp30) cc_final: 0.7517 (tp30) REVERT: A 357 TYR cc_start: 0.8077 (m-80) cc_final: 0.7865 (m-80) REVERT: B 123 ARG cc_start: 0.8518 (ttm110) cc_final: 0.8192 (mtm-85) REVERT: B 281 GLN cc_start: 0.8103 (pm20) cc_final: 0.7759 (pm20) REVERT: C 50 ASN cc_start: 0.8202 (t0) cc_final: 0.7933 (t0) REVERT: C 76 ASP cc_start: 0.7957 (OUTLIER) cc_final: 0.7325 (m-30) REVERT: C 396 ASP cc_start: 0.7416 (m-30) cc_final: 0.6966 (m-30) REVERT: C 413 MET cc_start: 0.8055 (ttm) cc_final: 0.7796 (ttm) REVERT: C 433 GLU cc_start: 0.8013 (tm-30) cc_final: 0.7729 (tp30) REVERT: D 123 ARG cc_start: 0.8645 (ttm110) cc_final: 0.8324 (mtm-85) REVERT: D 259 MET cc_start: 0.8627 (mmm) cc_final: 0.8344 (mmm) REVERT: D 281 GLN cc_start: 0.7705 (pm20) cc_final: 0.7456 (pm20) REVERT: D 299 LYS cc_start: 0.8316 (ttpp) cc_final: 0.8102 (ttmm) REVERT: E 50 ASN cc_start: 0.8284 (t0) cc_final: 0.8049 (t0) REVERT: E 76 ASP cc_start: 0.8230 (m-30) cc_final: 0.7710 (m-30) REVERT: E 90 GLU cc_start: 0.8718 (mm-30) cc_final: 0.7735 (tp30) REVERT: E 128 GLN cc_start: 0.8083 (mt0) cc_final: 0.7877 (tt0) REVERT: F 224 TYR cc_start: 0.8033 (OUTLIER) cc_final: 0.7183 (m-80) REVERT: F 282 GLN cc_start: 0.7851 (mm-40) cc_final: 0.7433 (mt0) REVERT: G 74 THR cc_start: 0.7407 (OUTLIER) cc_final: 0.7128 (t) REVERT: G 88 ARG cc_start: 0.8072 (ttp-110) cc_final: 0.6605 (tpt170) REVERT: G 149 MET cc_start: 0.8485 (OUTLIER) cc_final: 0.8228 (ttm) REVERT: G 207 GLU cc_start: 0.7610 (tt0) cc_final: 0.7362 (mt-10) REVERT: G 306 ASP cc_start: 0.7921 (t70) cc_final: 0.7541 (t0) REVERT: G 398 MET cc_start: 0.7960 (mmm) cc_final: 0.7636 (mtp) REVERT: H 125 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7645 (mm-30) REVERT: H 133 GLN cc_start: 0.8013 (tp40) cc_final: 0.7693 (tp40) REVERT: H 213 CYS cc_start: 0.8799 (m) cc_final: 0.8419 (m) REVERT: H 286 LEU cc_start: 0.8162 (mt) cc_final: 0.7677 (mp) REVERT: H 306 ASP cc_start: 0.7925 (t0) cc_final: 0.7483 (t0) REVERT: H 372 LYS cc_start: 0.8712 (ttmm) cc_final: 0.8149 (mmtt) REVERT: H 398 MET cc_start: 0.7808 (mtt) cc_final: 0.7384 (mtp) REVERT: H 405 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8852 (mp) REVERT: I 71 GLU cc_start: 0.7189 (pt0) cc_final: 0.6734 (tt0) REVERT: I 88 ARG cc_start: 0.8405 (ttm110) cc_final: 0.8182 (ttm-80) REVERT: I 90 ASP cc_start: 0.8107 (t0) cc_final: 0.7807 (m-30) REVERT: I 125 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7679 (mm-30) REVERT: I 149 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.8019 (tpp) REVERT: I 151 THR cc_start: 0.8451 (OUTLIER) cc_final: 0.8192 (m) REVERT: I 207 GLU cc_start: 0.7575 (tt0) cc_final: 0.7311 (mt-10) REVERT: I 213 CYS cc_start: 0.8679 (m) cc_final: 0.8440 (m) REVERT: I 306 ASP cc_start: 0.8279 (t70) cc_final: 0.7657 (t0) REVERT: I 331 GLN cc_start: 0.7563 (OUTLIER) cc_final: 0.7344 (mt0) REVERT: I 398 MET cc_start: 0.8110 (mtt) cc_final: 0.7573 (mtp) REVERT: J 71 GLU cc_start: 0.8065 (pt0) cc_final: 0.7577 (pt0) REVERT: J 161 TYR cc_start: 0.8491 (m-80) cc_final: 0.7994 (m-80) REVERT: J 230 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8263 (mp) REVERT: J 254 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7566 (mm-30) REVERT: J 301 GLN cc_start: 0.8218 (pt0) cc_final: 0.7951 (pt0) REVERT: J 302 MET cc_start: 0.8427 (mmt) cc_final: 0.8176 (mmt) REVERT: J 309 HIS cc_start: 0.8128 (m90) cc_final: 0.7901 (m90) REVERT: J 392 ASP cc_start: 0.7584 (m-30) cc_final: 0.7212 (m-30) REVERT: J 396 ASP cc_start: 0.7751 (m-30) cc_final: 0.7078 (m-30) REVERT: K 76 ASP cc_start: 0.8419 (m-30) cc_final: 0.8023 (m-30) REVERT: K 83 TYR cc_start: 0.8513 (m-80) cc_final: 0.8308 (m-10) REVERT: K 254 GLU cc_start: 0.7667 (mm-30) cc_final: 0.7437 (mm-30) REVERT: K 302 MET cc_start: 0.8303 (mmt) cc_final: 0.7971 (mmt) REVERT: K 305 CYS cc_start: 0.7728 (t) cc_final: 0.7251 (p) REVERT: L 71 GLU cc_start: 0.7718 (pt0) cc_final: 0.7068 (pt0) REVERT: L 161 TYR cc_start: 0.8368 (m-80) cc_final: 0.7994 (m-80) REVERT: L 168 GLU cc_start: 0.8394 (mt-10) cc_final: 0.8095 (mt-10) REVERT: L 203 MET cc_start: 0.8426 (mtt) cc_final: 0.8182 (mtt) REVERT: L 300 ASN cc_start: 0.8195 (OUTLIER) cc_final: 0.7911 (t0) REVERT: L 301 GLN cc_start: 0.8184 (pt0) cc_final: 0.7262 (pp30) REVERT: L 431 ASP cc_start: 0.7657 (m-30) cc_final: 0.7452 (m-30) outliers start: 163 outliers final: 72 residues processed: 1131 average time/residue: 0.2351 time to fit residues: 440.0350 Evaluate side-chains 941 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 859 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 224 TYR Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 221 ARG Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 330 GLU Chi-restraints excluded: chain D residue 430 SER Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 219 ILE Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 224 TYR Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 149 MET Chi-restraints excluded: chain G residue 165 ILE Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 324 SER Chi-restraints excluded: chain G residue 330 GLU Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 165 ILE Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain H residue 324 SER Chi-restraints excluded: chain H residue 330 GLU Chi-restraints excluded: chain H residue 405 LEU Chi-restraints excluded: chain I residue 149 MET Chi-restraints excluded: chain I residue 151 THR Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 178 SER Chi-restraints excluded: chain I residue 324 SER Chi-restraints excluded: chain I residue 330 GLU Chi-restraints excluded: chain I residue 331 GLN Chi-restraints excluded: chain J residue 76 ASP Chi-restraints excluded: chain J residue 194 THR Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 245 ASP Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 287 SER Chi-restraints excluded: chain J residue 371 VAL Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 194 THR Chi-restraints excluded: chain K residue 238 ILE Chi-restraints excluded: chain K residue 245 ASP Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 287 SER Chi-restraints excluded: chain K residue 371 VAL Chi-restraints excluded: chain L residue 36 MET Chi-restraints excluded: chain L residue 194 THR Chi-restraints excluded: chain L residue 238 ILE Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 287 SER Chi-restraints excluded: chain L residue 300 ASN Chi-restraints excluded: chain L residue 371 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 170 optimal weight: 8.9990 chunk 36 optimal weight: 9.9990 chunk 441 optimal weight: 3.9990 chunk 171 optimal weight: 3.9990 chunk 306 optimal weight: 9.9990 chunk 282 optimal weight: 9.9990 chunk 447 optimal weight: 6.9990 chunk 156 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 466 optimal weight: 4.9990 chunk 131 optimal weight: 0.0980 overall best weight: 3.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN A 28 HIS A 50 ASN A 88 HIS A 192 HIS A 256 GLN ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN B 37 HIS B 91 ASN ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 HIS B 282 GLN ** B 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 GLN ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 192 HIS C 309 HIS ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 11 GLN D 37 HIS ** D 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 192 HIS ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 HIS F 11 GLN F 192 HIS ** F 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 107 HIS ** G 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 192 HIS H 192 HIS H 293 GLN ** I 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 331 GLN I 334 ASN J 107 HIS J 285 GLN J 300 ASN K 88 HIS K 216 ASN ** K 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 300 ASN L 28 HIS L 50 ASN L 88 HIS Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.129365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.111323 restraints weight = 53188.262| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.21 r_work: 0.3367 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 41436 Z= 0.216 Angle : 0.610 7.091 56304 Z= 0.318 Chirality : 0.046 0.158 6156 Planarity : 0.005 0.051 7338 Dihedral : 11.886 174.362 5746 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.80 % Allowed : 17.82 % Favored : 78.38 % 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: 1.25 (0.12), residues: 5088 helix: 2.16 (0.11), residues: 2304 sheet: 0.85 (0.18), residues: 756 loop : -0.76 (0.13), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 400 TYR 0.020 0.002 TYR I 161 PHE 0.017 0.002 PHE F 20 TRP 0.017 0.002 TRP H 346 HIS 0.016 0.001 HIS B 37 Details of bonding type rmsd covalent geometry : bond 0.00503 (41436) covalent geometry : angle 0.60957 (56304) hydrogen bonds : bond 0.05852 ( 2058) hydrogen bonds : angle 4.81943 ( 5904) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1057 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 892 time to evaluate : 1.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.7952 (mp0) cc_final: 0.7752 (mp0) REVERT: A 77 GLU cc_start: 0.7734 (tp30) cc_final: 0.7514 (tp30) REVERT: A 221 ARG cc_start: 0.8012 (ptp-110) cc_final: 0.7482 (mtt90) REVERT: A 230 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8208 (mp) REVERT: A 254 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7455 (mm-30) REVERT: B 71 GLU cc_start: 0.7133 (pt0) cc_final: 0.6784 (pt0) REVERT: C 76 ASP cc_start: 0.7898 (OUTLIER) cc_final: 0.7401 (m-30) REVERT: C 413 MET cc_start: 0.8383 (ttm) cc_final: 0.8067 (ttm) REVERT: C 425 MET cc_start: 0.8120 (mmm) cc_final: 0.7864 (mmm) REVERT: D 259 MET cc_start: 0.8543 (mmm) cc_final: 0.8135 (mmm) REVERT: D 281 GLN cc_start: 0.7819 (pm20) cc_final: 0.7584 (pm20) REVERT: E 50 ASN cc_start: 0.8629 (t0) cc_final: 0.8377 (m-40) REVERT: E 76 ASP cc_start: 0.8325 (OUTLIER) cc_final: 0.7863 (m-30) REVERT: E 90 GLU cc_start: 0.8647 (mm-30) cc_final: 0.7931 (tp30) REVERT: E 128 GLN cc_start: 0.8196 (mt0) cc_final: 0.7974 (tt0) REVERT: E 413 MET cc_start: 0.8340 (ttm) cc_final: 0.7974 (ttm) REVERT: F 207 GLU cc_start: 0.8038 (tp30) cc_final: 0.7689 (mp0) REVERT: F 235 MET cc_start: 0.8069 (mtp) cc_final: 0.7805 (mtp) REVERT: F 282 GLN cc_start: 0.7861 (mm-40) cc_final: 0.7622 (mt0) REVERT: G 74 THR cc_start: 0.7769 (OUTLIER) cc_final: 0.7451 (t) REVERT: G 88 ARG cc_start: 0.8293 (ttp-110) cc_final: 0.6775 (tpt170) REVERT: G 114 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7590 (tp) REVERT: G 149 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.7972 (ttm) REVERT: G 199 ASP cc_start: 0.8366 (m-30) cc_final: 0.7931 (m-30) REVERT: G 207 GLU cc_start: 0.7665 (tt0) cc_final: 0.7417 (mt-10) REVERT: G 306 ASP cc_start: 0.8007 (t70) cc_final: 0.7723 (t0) REVERT: H 71 GLU cc_start: 0.7085 (pt0) cc_final: 0.6690 (tt0) REVERT: H 125 GLU cc_start: 0.7984 (mm-30) cc_final: 0.7780 (mm-30) REVERT: H 133 GLN cc_start: 0.8189 (tp40) cc_final: 0.7898 (tp40) REVERT: H 213 CYS cc_start: 0.8635 (m) cc_final: 0.8286 (m) REVERT: H 286 LEU cc_start: 0.8231 (mt) cc_final: 0.7682 (mp) REVERT: H 293 GLN cc_start: 0.8036 (pt0) cc_final: 0.7694 (pt0) REVERT: H 306 ASP cc_start: 0.8017 (t0) cc_final: 0.7617 (t0) REVERT: H 327 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7870 (mt-10) REVERT: H 372 LYS cc_start: 0.8795 (ttmm) cc_final: 0.8333 (mmtt) REVERT: H 398 MET cc_start: 0.7961 (mtt) cc_final: 0.7611 (mtp) REVERT: H 405 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8903 (mp) REVERT: I 71 GLU cc_start: 0.7095 (pt0) cc_final: 0.6655 (tt0) REVERT: I 124 LYS cc_start: 0.7957 (tttt) cc_final: 0.7713 (tttp) REVERT: I 125 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7663 (mm-30) REVERT: I 149 MET cc_start: 0.8487 (OUTLIER) cc_final: 0.8042 (tpt) REVERT: I 151 THR cc_start: 0.8579 (OUTLIER) cc_final: 0.8338 (m) REVERT: I 213 CYS cc_start: 0.8492 (m) cc_final: 0.8291 (m) REVERT: I 306 ASP cc_start: 0.8139 (t70) cc_final: 0.7727 (t0) REVERT: I 323 MET cc_start: 0.8781 (mtp) cc_final: 0.8469 (mtm) REVERT: I 398 MET cc_start: 0.8371 (mtt) cc_final: 0.7846 (mtp) REVERT: I 425 MET cc_start: 0.8298 (tpp) cc_final: 0.8083 (tpp) REVERT: J 71 GLU cc_start: 0.8053 (pt0) cc_final: 0.7597 (pt0) REVERT: J 161 TYR cc_start: 0.8646 (m-80) cc_final: 0.8138 (m-80) REVERT: J 230 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8333 (mp) REVERT: J 290 GLU cc_start: 0.7391 (tt0) cc_final: 0.6944 (tm-30) REVERT: J 301 GLN cc_start: 0.8203 (pt0) cc_final: 0.7972 (pt0) REVERT: J 392 ASP cc_start: 0.7485 (m-30) cc_final: 0.7271 (m-30) REVERT: J 396 ASP cc_start: 0.7766 (m-30) cc_final: 0.7179 (m-30) REVERT: K 83 TYR cc_start: 0.8604 (m-80) cc_final: 0.8339 (m-10) REVERT: K 302 MET cc_start: 0.8437 (mmt) cc_final: 0.8185 (mmt) REVERT: L 71 GLU cc_start: 0.7941 (pt0) cc_final: 0.7651 (pt0) REVERT: L 161 TYR cc_start: 0.8590 (m-80) cc_final: 0.8312 (m-80) REVERT: L 301 GLN cc_start: 0.8092 (pt0) cc_final: 0.7793 (mt0) REVERT: L 306 ASP cc_start: 0.8124 (t70) cc_final: 0.7559 (t0) outliers start: 165 outliers final: 103 residues processed: 1004 average time/residue: 0.2370 time to fit residues: 392.8230 Evaluate side-chains 918 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 805 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 221 ARG Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 430 SER Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 256 GLN Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 305 CYS Chi-restraints excluded: chain E residue 420 GLU Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 301 MET Chi-restraints excluded: chain F residue 430 SER Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 129 CYS Chi-restraints excluded: chain G residue 149 MET Chi-restraints excluded: chain G residue 165 ILE Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 276 THR Chi-restraints excluded: chain G residue 324 SER Chi-restraints excluded: chain G residue 330 GLU Chi-restraints excluded: chain G residue 356 CYS Chi-restraints excluded: chain G residue 430 SER Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 129 CYS Chi-restraints excluded: chain H residue 165 ILE Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain H residue 276 THR Chi-restraints excluded: chain H residue 324 SER Chi-restraints excluded: chain H residue 330 GLU Chi-restraints excluded: chain H residue 373 MET Chi-restraints excluded: chain H residue 405 LEU Chi-restraints excluded: chain H residue 430 SER Chi-restraints excluded: chain I residue 129 CYS Chi-restraints excluded: chain I residue 149 MET Chi-restraints excluded: chain I residue 151 THR Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 178 SER Chi-restraints excluded: chain I residue 324 SER Chi-restraints excluded: chain I residue 331 GLN Chi-restraints excluded: chain J residue 76 ASP Chi-restraints excluded: chain J residue 194 THR Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 238 ILE Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 287 SER Chi-restraints excluded: chain J residue 300 ASN Chi-restraints excluded: chain J residue 305 CYS Chi-restraints excluded: chain J residue 338 LYS Chi-restraints excluded: chain J residue 371 VAL Chi-restraints excluded: chain J residue 378 LEU Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 158 SER Chi-restraints excluded: chain K residue 194 THR Chi-restraints excluded: chain K residue 230 LEU Chi-restraints excluded: chain K residue 238 ILE Chi-restraints excluded: chain K residue 253 THR Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 287 SER Chi-restraints excluded: chain K residue 300 ASN Chi-restraints excluded: chain K residue 371 VAL Chi-restraints excluded: chain K residue 378 LEU Chi-restraints excluded: chain L residue 36 MET Chi-restraints excluded: chain L residue 158 SER Chi-restraints excluded: chain L residue 194 THR Chi-restraints excluded: chain L residue 238 ILE Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 287 SER Chi-restraints excluded: chain L residue 371 VAL Chi-restraints excluded: chain L residue 437 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 362 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 262 optimal weight: 9.9990 chunk 437 optimal weight: 4.9990 chunk 58 optimal weight: 7.9990 chunk 108 optimal weight: 0.8980 chunk 255 optimal weight: 0.9980 chunk 494 optimal weight: 5.9990 chunk 419 optimal weight: 7.9990 chunk 23 optimal weight: 0.8980 chunk 407 optimal weight: 6.9990 overall best weight: 2.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN A 107 HIS A 309 HIS B 37 HIS B 258 ASN ** B 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 HIS ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 HIS C 233 GLN C 309 HIS ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 282 GLN E 28 HIS E 258 ASN ** F 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 334 ASN ** I 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 331 GLN J 28 HIS J 285 GLN K 28 HIS K 101 ASN L 50 ASN L 300 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.126498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.107528 restraints weight = 51649.334| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.27 r_work: 0.3220 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 41436 Z= 0.189 Angle : 0.581 7.335 56304 Z= 0.302 Chirality : 0.045 0.258 6156 Planarity : 0.005 0.055 7338 Dihedral : 11.708 175.515 5734 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.80 % Allowed : 19.11 % Favored : 77.09 % 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: 1.13 (0.12), residues: 5088 helix: 2.07 (0.11), residues: 2304 sheet: 0.69 (0.18), residues: 756 loop : -0.80 (0.13), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 88 TYR 0.016 0.001 TYR I 161 PHE 0.021 0.001 PHE L 49 TRP 0.018 0.002 TRP G 346 HIS 0.008 0.001 HIS L 309 Details of bonding type rmsd covalent geometry : bond 0.00436 (41436) covalent geometry : angle 0.58073 (56304) hydrogen bonds : bond 0.05384 ( 2058) hydrogen bonds : angle 4.68146 ( 5904) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 991 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 826 time to evaluate : 1.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.8011 (mp0) cc_final: 0.7704 (mp0) REVERT: A 76 ASP cc_start: 0.8391 (OUTLIER) cc_final: 0.7853 (m-30) REVERT: A 77 GLU cc_start: 0.7815 (tp30) cc_final: 0.7560 (tp30) REVERT: A 221 ARG cc_start: 0.7871 (ptp-110) cc_final: 0.7432 (mtt90) REVERT: A 230 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8195 (mp) REVERT: A 254 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7377 (mm-30) REVERT: B 166 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.8233 (tpp) REVERT: B 282 GLN cc_start: 0.8237 (mm110) cc_final: 0.7592 (mt0) REVERT: B 372 LYS cc_start: 0.8668 (ttmm) cc_final: 0.8200 (mmmt) REVERT: C 76 ASP cc_start: 0.7933 (OUTLIER) cc_final: 0.7386 (m-30) REVERT: C 149 PHE cc_start: 0.8927 (t80) cc_final: 0.8682 (t80) REVERT: C 285 GLN cc_start: 0.2218 (mp10) cc_final: 0.1929 (mm110) REVERT: D 149 MET cc_start: 0.8589 (OUTLIER) cc_final: 0.8216 (ttm) REVERT: D 166 MET cc_start: 0.8534 (mmm) cc_final: 0.8197 (tpp) REVERT: D 281 GLN cc_start: 0.7712 (pm20) cc_final: 0.7495 (pm20) REVERT: E 76 ASP cc_start: 0.8192 (OUTLIER) cc_final: 0.7662 (m-30) REVERT: E 90 GLU cc_start: 0.8584 (mm-30) cc_final: 0.7824 (tp30) REVERT: E 287 SER cc_start: 0.7919 (p) cc_final: 0.7710 (m) REVERT: E 396 ASP cc_start: 0.7793 (m-30) cc_final: 0.7376 (m-30) REVERT: E 413 MET cc_start: 0.8205 (ttm) cc_final: 0.7836 (ttm) REVERT: F 69 ASP cc_start: 0.7619 (t0) cc_final: 0.7400 (t0) REVERT: F 207 GLU cc_start: 0.8218 (tp30) cc_final: 0.7865 (mp0) REVERT: F 282 GLN cc_start: 0.8148 (mm-40) cc_final: 0.7845 (mt0) REVERT: G 42 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8144 (mm) REVERT: G 74 THR cc_start: 0.7718 (OUTLIER) cc_final: 0.7483 (t) REVERT: G 88 ARG cc_start: 0.8276 (ttp-110) cc_final: 0.6677 (tpt170) REVERT: G 110 GLU cc_start: 0.7761 (mm-30) cc_final: 0.7458 (mt-10) REVERT: G 114 LEU cc_start: 0.7550 (OUTLIER) cc_final: 0.7253 (tp) REVERT: G 149 MET cc_start: 0.8331 (ttm) cc_final: 0.7680 (tpt) REVERT: G 199 ASP cc_start: 0.8471 (m-30) cc_final: 0.8052 (m-30) REVERT: G 207 GLU cc_start: 0.7737 (tt0) cc_final: 0.7398 (mt-10) REVERT: G 213 CYS cc_start: 0.8755 (m) cc_final: 0.8541 (m) REVERT: G 306 ASP cc_start: 0.7986 (t70) cc_final: 0.7572 (t0) REVERT: H 71 GLU cc_start: 0.6874 (pt0) cc_final: 0.6619 (tt0) REVERT: H 133 GLN cc_start: 0.8243 (tp40) cc_final: 0.8020 (tp40) REVERT: H 213 CYS cc_start: 0.8710 (m) cc_final: 0.8364 (m) REVERT: H 306 ASP cc_start: 0.7980 (t0) cc_final: 0.7444 (t0) REVERT: H 372 LYS cc_start: 0.8682 (ttmm) cc_final: 0.8137 (mmtt) REVERT: H 398 MET cc_start: 0.7961 (mtt) cc_final: 0.7643 (mtp) REVERT: H 405 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8820 (mp) REVERT: I 71 GLU cc_start: 0.6881 (pt0) cc_final: 0.6568 (tt0) REVERT: I 149 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.7806 (tpt) REVERT: I 213 CYS cc_start: 0.8615 (m) cc_final: 0.8304 (m) REVERT: I 306 ASP cc_start: 0.8161 (t70) cc_final: 0.7572 (t0) REVERT: I 312 TYR cc_start: 0.8999 (m-80) cc_final: 0.7985 (m-80) REVERT: I 323 MET cc_start: 0.9033 (mtp) cc_final: 0.8721 (mtm) REVERT: I 398 MET cc_start: 0.8243 (mtt) cc_final: 0.7834 (mtp) REVERT: I 425 MET cc_start: 0.8253 (tpp) cc_final: 0.7980 (tpp) REVERT: J 71 GLU cc_start: 0.7959 (pt0) cc_final: 0.7578 (pt0) REVERT: J 161 TYR cc_start: 0.8584 (m-80) cc_final: 0.8015 (m-80) REVERT: J 290 GLU cc_start: 0.7583 (tt0) cc_final: 0.7144 (tm-30) REVERT: K 83 TYR cc_start: 0.8534 (m-80) cc_final: 0.8282 (m-10) REVERT: L 76 ASP cc_start: 0.8419 (OUTLIER) cc_final: 0.8049 (m-30) REVERT: L 161 TYR cc_start: 0.8516 (m-80) cc_final: 0.8171 (m-80) REVERT: L 172 TYR cc_start: 0.8204 (t80) cc_final: 0.7561 (t80) REVERT: L 301 GLN cc_start: 0.8140 (pt0) cc_final: 0.7227 (pp30) REVERT: L 413 MET cc_start: 0.8316 (ttm) cc_final: 0.8092 (ttm) outliers start: 165 outliers final: 113 residues processed: 935 average time/residue: 0.2434 time to fit residues: 374.6951 Evaluate side-chains 898 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 773 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 221 ARG Chi-restraints excluded: chain C residue 256 GLN Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 430 SER Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 256 GLN Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 305 CYS Chi-restraints excluded: chain E residue 336 LYS Chi-restraints excluded: chain E residue 420 GLU Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain F residue 37 HIS Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 301 MET Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain F residue 430 SER Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 129 CYS Chi-restraints excluded: chain G residue 165 ILE Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 276 THR Chi-restraints excluded: chain G residue 324 SER Chi-restraints excluded: chain G residue 356 CYS Chi-restraints excluded: chain G residue 430 SER Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 129 CYS Chi-restraints excluded: chain H residue 137 LEU Chi-restraints excluded: chain H residue 165 ILE Chi-restraints excluded: chain H residue 276 THR Chi-restraints excluded: chain H residue 324 SER Chi-restraints excluded: chain H residue 330 GLU Chi-restraints excluded: chain H residue 373 MET Chi-restraints excluded: chain H residue 405 LEU Chi-restraints excluded: chain H residue 430 SER Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 129 CYS Chi-restraints excluded: chain I residue 149 MET Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 293 GLN Chi-restraints excluded: chain I residue 324 SER Chi-restraints excluded: chain I residue 331 GLN Chi-restraints excluded: chain I residue 430 SER Chi-restraints excluded: chain J residue 36 MET Chi-restraints excluded: chain J residue 76 ASP Chi-restraints excluded: chain J residue 238 ILE Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 287 SER Chi-restraints excluded: chain J residue 305 CYS Chi-restraints excluded: chain J residue 371 VAL Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 82 THR Chi-restraints excluded: chain K residue 158 SER Chi-restraints excluded: chain K residue 238 ILE Chi-restraints excluded: chain K residue 253 THR Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 287 SER Chi-restraints excluded: chain K residue 371 VAL Chi-restraints excluded: chain K residue 378 LEU Chi-restraints excluded: chain L residue 76 ASP Chi-restraints excluded: chain L residue 151 SER Chi-restraints excluded: chain L residue 158 SER Chi-restraints excluded: chain L residue 230 LEU Chi-restraints excluded: chain L residue 238 ILE Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 287 SER Chi-restraints excluded: chain L residue 435 VAL Chi-restraints excluded: chain L residue 437 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 42 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 255 optimal weight: 0.0060 chunk 469 optimal weight: 6.9990 chunk 168 optimal weight: 10.0000 chunk 426 optimal weight: 0.6980 chunk 394 optimal weight: 10.0000 chunk 339 optimal weight: 8.9990 chunk 253 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 459 optimal weight: 0.8980 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN A 309 HIS B 37 HIS ** B 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 HIS C 309 HIS ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 258 ASN F 258 ASN ** F 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 334 ASN H 6 HIS ** I 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 192 HIS I 258 ASN I 331 GLN ** I 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 285 GLN K 216 ASN L 18 ASN L 50 ASN L 101 ASN L 300 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.130212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.112703 restraints weight = 52874.639| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.11 r_work: 0.3393 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.4216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 41436 Z= 0.119 Angle : 0.535 9.078 56304 Z= 0.274 Chirality : 0.043 0.275 6156 Planarity : 0.005 0.057 7338 Dihedral : 11.513 179.022 5731 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.18 % Allowed : 20.52 % Favored : 76.30 % 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: 1.19 (0.12), residues: 5088 helix: 2.01 (0.11), residues: 2352 sheet: 0.82 (0.18), residues: 804 loop : -0.76 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 390 TYR 0.014 0.001 TYR K 185 PHE 0.018 0.001 PHE L 49 TRP 0.016 0.002 TRP G 346 HIS 0.014 0.001 HIS J 309 Details of bonding type rmsd covalent geometry : bond 0.00251 (41436) covalent geometry : angle 0.53467 (56304) hydrogen bonds : bond 0.04468 ( 2058) hydrogen bonds : angle 4.47163 ( 5904) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 998 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 860 time to evaluate : 1.478 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.7902 (mp0) cc_final: 0.7531 (mp0) REVERT: A 76 ASP cc_start: 0.8325 (OUTLIER) cc_final: 0.7841 (m-30) REVERT: A 170 SER cc_start: 0.8776 (m) cc_final: 0.8512 (p) REVERT: A 221 ARG cc_start: 0.8041 (ptp-110) cc_final: 0.7610 (mtt90) REVERT: B 207 GLU cc_start: 0.8155 (tp30) cc_final: 0.7886 (mp0) REVERT: B 213 CYS cc_start: 0.7895 (m) cc_final: 0.7599 (m) REVERT: B 282 GLN cc_start: 0.8254 (mm110) cc_final: 0.7708 (mt0) REVERT: B 372 LYS cc_start: 0.8610 (ttmm) cc_final: 0.8222 (mmmt) REVERT: C 76 ASP cc_start: 0.7693 (m-30) cc_final: 0.7245 (m-30) REVERT: C 149 PHE cc_start: 0.8908 (t80) cc_final: 0.8641 (t80) REVERT: C 293 ASN cc_start: 0.8587 (m-40) cc_final: 0.8275 (m110) REVERT: C 413 MET cc_start: 0.8292 (ttm) cc_final: 0.8032 (ttm) REVERT: D 156 LYS cc_start: 0.8885 (mptt) cc_final: 0.8624 (mmtt) REVERT: E 76 ASP cc_start: 0.8145 (OUTLIER) cc_final: 0.7719 (m-30) REVERT: E 90 GLU cc_start: 0.8500 (mm-30) cc_final: 0.8099 (tp30) REVERT: E 259 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8786 (mp) REVERT: E 322 ASP cc_start: 0.8536 (t0) cc_final: 0.8133 (m-30) REVERT: E 396 ASP cc_start: 0.7845 (m-30) cc_final: 0.7508 (m-30) REVERT: F 207 GLU cc_start: 0.7941 (tp30) cc_final: 0.7706 (mp0) REVERT: G 42 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8188 (mm) REVERT: G 74 THR cc_start: 0.7886 (OUTLIER) cc_final: 0.7627 (t) REVERT: G 88 ARG cc_start: 0.8246 (ttp-110) cc_final: 0.6735 (tpt170) REVERT: G 110 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7438 (mt-10) REVERT: G 199 ASP cc_start: 0.8153 (m-30) cc_final: 0.7800 (m-30) REVERT: G 306 ASP cc_start: 0.7956 (t70) cc_final: 0.7681 (t0) REVERT: H 133 GLN cc_start: 0.8298 (tp40) cc_final: 0.8086 (tp40) REVERT: H 306 ASP cc_start: 0.8024 (t0) cc_final: 0.7557 (t0) REVERT: H 372 LYS cc_start: 0.8666 (ttmm) cc_final: 0.8269 (mmtt) REVERT: H 398 MET cc_start: 0.8184 (mtt) cc_final: 0.7976 (mtp) REVERT: I 71 GLU cc_start: 0.6912 (pt0) cc_final: 0.6696 (tt0) REVERT: I 149 MET cc_start: 0.8347 (OUTLIER) cc_final: 0.8040 (tpt) REVERT: I 199 ASP cc_start: 0.8231 (m-30) cc_final: 0.7887 (m-30) REVERT: I 306 ASP cc_start: 0.8050 (t70) cc_final: 0.7648 (t0) REVERT: I 312 TYR cc_start: 0.8874 (m-80) cc_final: 0.7936 (m-80) REVERT: I 398 MET cc_start: 0.8380 (mtt) cc_final: 0.8009 (mtp) REVERT: I 425 MET cc_start: 0.8330 (tpp) cc_final: 0.8092 (tpp) REVERT: J 71 GLU cc_start: 0.7924 (pt0) cc_final: 0.7628 (pt0) REVERT: J 161 TYR cc_start: 0.8466 (m-80) cc_final: 0.7918 (m-80) REVERT: J 290 GLU cc_start: 0.7296 (tt0) cc_final: 0.7086 (tm-30) REVERT: J 301 GLN cc_start: 0.8201 (pt0) cc_final: 0.7964 (pt0) REVERT: J 424 ASP cc_start: 0.7804 (OUTLIER) cc_final: 0.7529 (m-30) REVERT: K 83 TYR cc_start: 0.8570 (m-80) cc_final: 0.8318 (m-10) REVERT: K 212 ILE cc_start: 0.8913 (OUTLIER) cc_final: 0.8674 (mp) REVERT: K 302 MET cc_start: 0.8494 (mmt) cc_final: 0.8095 (mmt) REVERT: L 24 TYR cc_start: 0.8995 (m-10) cc_final: 0.8792 (m-10) REVERT: L 76 ASP cc_start: 0.8241 (OUTLIER) cc_final: 0.7990 (m-30) REVERT: L 161 TYR cc_start: 0.8509 (m-80) cc_final: 0.8282 (m-80) REVERT: L 172 TYR cc_start: 0.8262 (t80) cc_final: 0.7731 (t80) REVERT: L 212 ILE cc_start: 0.8855 (OUTLIER) cc_final: 0.8423 (mp) REVERT: L 254 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.7037 (mm-30) REVERT: L 313 MET cc_start: 0.8764 (mtm) cc_final: 0.8554 (mtp) outliers start: 138 outliers final: 89 residues processed: 944 average time/residue: 0.2408 time to fit residues: 375.6354 Evaluate side-chains 878 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 777 time to evaluate : 2.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 221 ARG Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 256 GLN Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 305 CYS Chi-restraints excluded: chain E residue 413 MET Chi-restraints excluded: chain E residue 420 GLU Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain F residue 37 HIS Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 301 MET Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain F residue 430 SER Chi-restraints excluded: chain G residue 37 HIS Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 110 GLU Chi-restraints excluded: chain G residue 129 CYS Chi-restraints excluded: chain G residue 165 ILE Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 276 THR Chi-restraints excluded: chain G residue 324 SER Chi-restraints excluded: chain G residue 356 CYS Chi-restraints excluded: chain G residue 430 SER Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 129 CYS Chi-restraints excluded: chain H residue 137 LEU Chi-restraints excluded: chain H residue 165 ILE Chi-restraints excluded: chain H residue 276 THR Chi-restraints excluded: chain H residue 293 GLN Chi-restraints excluded: chain H residue 324 SER Chi-restraints excluded: chain H residue 373 MET Chi-restraints excluded: chain H residue 430 SER Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 129 CYS Chi-restraints excluded: chain I residue 149 MET Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 293 GLN Chi-restraints excluded: chain I residue 324 SER Chi-restraints excluded: chain I residue 331 GLN Chi-restraints excluded: chain I residue 338 LYS Chi-restraints excluded: chain J residue 36 MET Chi-restraints excluded: chain J residue 76 ASP Chi-restraints excluded: chain J residue 238 ILE Chi-restraints excluded: chain J residue 254 GLU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 287 SER Chi-restraints excluded: chain J residue 305 CYS Chi-restraints excluded: chain J residue 424 ASP Chi-restraints excluded: chain K residue 36 MET Chi-restraints excluded: chain K residue 212 ILE Chi-restraints excluded: chain K residue 238 ILE Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 287 SER Chi-restraints excluded: chain L residue 76 ASP Chi-restraints excluded: chain L residue 82 THR Chi-restraints excluded: chain L residue 151 SER Chi-restraints excluded: chain L residue 158 SER Chi-restraints excluded: chain L residue 212 ILE Chi-restraints excluded: chain L residue 238 ILE Chi-restraints excluded: chain L residue 254 GLU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 300 ASN Chi-restraints excluded: chain L residue 339 ARG Chi-restraints excluded: chain L residue 437 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 28 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 chunk 406 optimal weight: 7.9990 chunk 413 optimal weight: 3.9990 chunk 404 optimal weight: 5.9990 chunk 144 optimal weight: 0.9990 chunk 342 optimal weight: 0.9990 chunk 293 optimal weight: 0.9980 chunk 304 optimal weight: 9.9990 chunk 468 optimal weight: 1.9990 chunk 327 optimal weight: 10.0000 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 309 HIS B 37 HIS ** B 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 HIS ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 282 GLN D 336 GLN F 282 GLN G 334 ASN H 6 HIS H 136 GLN ** I 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 331 GLN ** I 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 285 GLN ** K 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 342 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.128921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.110788 restraints weight = 53621.553| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.26 r_work: 0.3360 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.4355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 41436 Z= 0.146 Angle : 0.546 7.585 56304 Z= 0.280 Chirality : 0.043 0.284 6156 Planarity : 0.005 0.059 7338 Dihedral : 11.417 177.830 5727 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.62 % Allowed : 20.54 % Favored : 75.84 % 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: 1.12 (0.12), residues: 5088 helix: 1.96 (0.11), residues: 2352 sheet: 0.76 (0.18), residues: 804 loop : -0.81 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 400 TYR 0.020 0.001 TYR G 161 PHE 0.015 0.001 PHE L 49 TRP 0.022 0.002 TRP G 346 HIS 0.006 0.001 HIS K 309 Details of bonding type rmsd covalent geometry : bond 0.00332 (41436) covalent geometry : angle 0.54634 (56304) hydrogen bonds : bond 0.04628 ( 2058) hydrogen bonds : angle 4.45644 ( 5904) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 962 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 805 time to evaluate : 1.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.7895 (mp0) cc_final: 0.7426 (mp0) REVERT: A 76 ASP cc_start: 0.8439 (OUTLIER) cc_final: 0.7986 (m-30) REVERT: A 170 SER cc_start: 0.8859 (m) cc_final: 0.8507 (p) REVERT: A 199 ASP cc_start: 0.8617 (m-30) cc_final: 0.8366 (m-30) REVERT: A 221 ARG cc_start: 0.7951 (ptp-110) cc_final: 0.7542 (mtt90) REVERT: B 207 GLU cc_start: 0.8231 (tp30) cc_final: 0.7930 (mp0) REVERT: B 213 CYS cc_start: 0.8093 (m) cc_final: 0.7770 (m) REVERT: B 282 GLN cc_start: 0.8302 (mm110) cc_final: 0.7790 (mt0) REVERT: B 372 LYS cc_start: 0.8615 (ttmm) cc_final: 0.8201 (mmmt) REVERT: C 76 ASP cc_start: 0.7724 (OUTLIER) cc_final: 0.7221 (m-30) REVERT: C 77 GLU cc_start: 0.8063 (tp30) cc_final: 0.7663 (tp30) REVERT: C 149 PHE cc_start: 0.8907 (t80) cc_final: 0.8662 (t80) REVERT: C 322 ASP cc_start: 0.8458 (t0) cc_final: 0.8150 (m-30) REVERT: D 156 LYS cc_start: 0.8839 (mptt) cc_final: 0.8596 (mmtt) REVERT: D 290 GLU cc_start: 0.7258 (mp0) cc_final: 0.7047 (mp0) REVERT: E 76 ASP cc_start: 0.8171 (OUTLIER) cc_final: 0.7736 (m-30) REVERT: E 90 GLU cc_start: 0.8598 (mm-30) cc_final: 0.8123 (tp30) REVERT: E 322 ASP cc_start: 0.8581 (t0) cc_final: 0.8106 (m-30) REVERT: E 396 ASP cc_start: 0.7947 (m-30) cc_final: 0.7571 (m-30) REVERT: F 113 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7868 (mm-30) REVERT: F 207 GLU cc_start: 0.8004 (tp30) cc_final: 0.7726 (mp0) REVERT: G 42 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8195 (mm) REVERT: G 88 ARG cc_start: 0.8348 (ttp-110) cc_final: 0.6799 (tpt170) REVERT: G 110 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7434 (mt-10) REVERT: G 199 ASP cc_start: 0.8235 (m-30) cc_final: 0.7909 (m-30) REVERT: G 306 ASP cc_start: 0.8011 (t70) cc_final: 0.7647 (t0) REVERT: H 133 GLN cc_start: 0.8300 (tp40) cc_final: 0.8095 (tp40) REVERT: H 372 LYS cc_start: 0.8682 (ttmm) cc_final: 0.8250 (mmtt) REVERT: H 398 MET cc_start: 0.8187 (mtt) cc_final: 0.7951 (mtp) REVERT: H 405 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8869 (mp) REVERT: I 149 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.7982 (tpt) REVERT: I 199 ASP cc_start: 0.8308 (m-30) cc_final: 0.7944 (m-30) REVERT: I 248 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8479 (tt) REVERT: I 306 ASP cc_start: 0.8087 (t70) cc_final: 0.7584 (t0) REVERT: I 312 TYR cc_start: 0.8940 (m-80) cc_final: 0.7971 (m-80) REVERT: I 398 MET cc_start: 0.8316 (mtt) cc_final: 0.7953 (mtp) REVERT: I 425 MET cc_start: 0.8332 (tpp) cc_final: 0.8090 (tpp) REVERT: J 4 CYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7978 (t) REVERT: J 60 LYS cc_start: 0.7496 (OUTLIER) cc_final: 0.7277 (tttm) REVERT: J 71 GLU cc_start: 0.7950 (pt0) cc_final: 0.7625 (pt0) REVERT: J 161 TYR cc_start: 0.8509 (m-80) cc_final: 0.8020 (m-80) REVERT: J 290 GLU cc_start: 0.7435 (tt0) cc_final: 0.7159 (tm-30) REVERT: J 301 GLN cc_start: 0.8206 (pt0) cc_final: 0.7926 (pt0) REVERT: K 76 ASP cc_start: 0.8396 (OUTLIER) cc_final: 0.8122 (m-30) REVERT: K 83 TYR cc_start: 0.8605 (m-80) cc_final: 0.8354 (m-10) REVERT: K 212 ILE cc_start: 0.8780 (OUTLIER) cc_final: 0.8554 (mp) REVERT: K 302 MET cc_start: 0.8443 (mmt) cc_final: 0.8086 (mmt) REVERT: K 309 HIS cc_start: 0.8161 (m-70) cc_final: 0.7626 (m90) REVERT: L 76 ASP cc_start: 0.8284 (OUTLIER) cc_final: 0.7984 (m-30) REVERT: L 172 TYR cc_start: 0.8331 (t80) cc_final: 0.7717 (t80) REVERT: L 212 ILE cc_start: 0.8781 (OUTLIER) cc_final: 0.8397 (mp) REVERT: L 254 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.7076 (mm-30) REVERT: L 413 MET cc_start: 0.8164 (ttm) cc_final: 0.7933 (ttm) outliers start: 157 outliers final: 111 residues processed: 907 average time/residue: 0.2447 time to fit residues: 365.6328 Evaluate side-chains 903 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 777 time to evaluate : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 221 ARG Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 254 GLU Chi-restraints excluded: chain E residue 256 GLN Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 305 CYS Chi-restraints excluded: chain E residue 336 LYS Chi-restraints excluded: chain E residue 413 MET Chi-restraints excluded: chain E residue 420 GLU Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain F residue 37 HIS Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 301 MET Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain F residue 430 SER Chi-restraints excluded: chain G residue 37 HIS Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 110 GLU Chi-restraints excluded: chain G residue 129 CYS Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 276 THR Chi-restraints excluded: chain G residue 324 SER Chi-restraints excluded: chain G residue 325 MET Chi-restraints excluded: chain G residue 330 GLU Chi-restraints excluded: chain G residue 356 CYS Chi-restraints excluded: chain G residue 430 SER Chi-restraints excluded: chain H residue 37 HIS Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 129 CYS Chi-restraints excluded: chain H residue 137 LEU Chi-restraints excluded: chain H residue 165 ILE Chi-restraints excluded: chain H residue 276 THR Chi-restraints excluded: chain H residue 324 SER Chi-restraints excluded: chain H residue 387 LEU Chi-restraints excluded: chain H residue 405 LEU Chi-restraints excluded: chain H residue 430 SER Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 129 CYS Chi-restraints excluded: chain I residue 149 MET Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 240 THR Chi-restraints excluded: chain I residue 248 LEU Chi-restraints excluded: chain I residue 293 GLN Chi-restraints excluded: chain I residue 313 LEU Chi-restraints excluded: chain I residue 324 SER Chi-restraints excluded: chain I residue 338 LYS Chi-restraints excluded: chain I residue 430 SER Chi-restraints excluded: chain J residue 4 CYS Chi-restraints excluded: chain J residue 36 MET Chi-restraints excluded: chain J residue 60 LYS Chi-restraints excluded: chain J residue 76 ASP Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain J residue 238 ILE Chi-restraints excluded: chain J residue 254 GLU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 287 SER Chi-restraints excluded: chain J residue 305 CYS Chi-restraints excluded: chain K residue 36 MET Chi-restraints excluded: chain K residue 76 ASP Chi-restraints excluded: chain K residue 145 THR Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 212 ILE Chi-restraints excluded: chain K residue 238 ILE Chi-restraints excluded: chain K residue 253 THR Chi-restraints excluded: chain K residue 254 GLU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 287 SER Chi-restraints excluded: chain K residue 378 LEU Chi-restraints excluded: chain L residue 36 MET Chi-restraints excluded: chain L residue 76 ASP Chi-restraints excluded: chain L residue 82 THR Chi-restraints excluded: chain L residue 145 THR Chi-restraints excluded: chain L residue 151 SER Chi-restraints excluded: chain L residue 158 SER Chi-restraints excluded: chain L residue 204 VAL Chi-restraints excluded: chain L residue 212 ILE Chi-restraints excluded: chain L residue 238 ILE Chi-restraints excluded: chain L residue 254 GLU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 287 SER Chi-restraints excluded: chain L residue 339 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 363 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 420 optimal weight: 10.0000 chunk 406 optimal weight: 6.9990 chunk 272 optimal weight: 7.9990 chunk 335 optimal weight: 9.9990 chunk 16 optimal weight: 0.0980 chunk 444 optimal weight: 0.8980 chunk 330 optimal weight: 2.9990 chunk 346 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN A 216 ASN A 309 HIS ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS ** B 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 HIS ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 282 GLN G 334 ASN H 6 HIS H 136 GLN ** I 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 331 GLN ** I 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 285 GLN K 216 ASN K 309 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.127469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.109338 restraints weight = 53692.434| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.26 r_work: 0.3263 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.4482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 41436 Z= 0.151 Angle : 0.551 7.334 56304 Z= 0.281 Chirality : 0.044 0.303 6156 Planarity : 0.005 0.057 7338 Dihedral : 11.342 178.379 5727 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.76 % Allowed : 21.05 % Favored : 75.20 % 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: 1.12 (0.12), residues: 5088 helix: 1.99 (0.11), residues: 2346 sheet: 0.86 (0.18), residues: 804 loop : -0.88 (0.14), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 390 TYR 0.018 0.001 TYR G 161 PHE 0.027 0.001 PHE E 49 TRP 0.023 0.002 TRP G 346 HIS 0.007 0.001 HIS B 37 Details of bonding type rmsd covalent geometry : bond 0.00344 (41436) covalent geometry : angle 0.55089 (56304) hydrogen bonds : bond 0.04652 ( 2058) hydrogen bonds : angle 4.44664 ( 5904) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 966 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 803 time to evaluate : 1.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.7890 (mp0) cc_final: 0.7393 (mp0) REVERT: A 35 GLN cc_start: 0.8444 (tt0) cc_final: 0.8203 (mt0) REVERT: A 76 ASP cc_start: 0.8388 (OUTLIER) cc_final: 0.7973 (m-30) REVERT: A 170 SER cc_start: 0.8848 (m) cc_final: 0.8539 (p) REVERT: A 203 MET cc_start: 0.8828 (OUTLIER) cc_final: 0.8151 (mtp) REVERT: A 221 ARG cc_start: 0.7977 (ptp-110) cc_final: 0.7611 (mtt90) REVERT: A 251 ASP cc_start: 0.8500 (p0) cc_final: 0.6845 (p0) REVERT: A 322 ASP cc_start: 0.8704 (t0) cc_final: 0.8293 (m-30) REVERT: A 393 HIS cc_start: 0.8137 (t70) cc_final: 0.7803 (t70) REVERT: B 113 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7953 (mm-30) REVERT: B 207 GLU cc_start: 0.8237 (tp30) cc_final: 0.7972 (mp0) REVERT: B 213 CYS cc_start: 0.8028 (m) cc_final: 0.7726 (m) REVERT: B 282 GLN cc_start: 0.8290 (mm110) cc_final: 0.7880 (mt0) REVERT: C 76 ASP cc_start: 0.7830 (OUTLIER) cc_final: 0.7326 (m-30) REVERT: C 77 GLU cc_start: 0.7989 (tp30) cc_final: 0.7615 (tp30) REVERT: C 149 PHE cc_start: 0.8901 (t80) cc_final: 0.8682 (t80) REVERT: C 285 GLN cc_start: 0.2329 (mm-40) cc_final: 0.1571 (mm-40) REVERT: C 322 ASP cc_start: 0.8474 (t0) cc_final: 0.8182 (m-30) REVERT: D 156 LYS cc_start: 0.8845 (mptt) cc_final: 0.8589 (mmtt) REVERT: E 76 ASP cc_start: 0.8128 (OUTLIER) cc_final: 0.7714 (m-30) REVERT: E 90 GLU cc_start: 0.8593 (mm-30) cc_final: 0.8124 (tp30) REVERT: E 172 TYR cc_start: 0.8786 (t80) cc_final: 0.7683 (t80) REVERT: E 251 ASP cc_start: 0.8388 (p0) cc_final: 0.6682 (p0) REVERT: E 254 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7155 (mp0) REVERT: E 259 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8761 (mp) REVERT: E 287 SER cc_start: 0.7911 (p) cc_final: 0.7647 (m) REVERT: E 322 ASP cc_start: 0.8674 (t0) cc_final: 0.8228 (m-30) REVERT: E 396 ASP cc_start: 0.7924 (m-30) cc_final: 0.7585 (m-30) REVERT: F 207 GLU cc_start: 0.8038 (tp30) cc_final: 0.7783 (mp0) REVERT: G 42 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8179 (mm) REVERT: G 88 ARG cc_start: 0.8333 (ttp-110) cc_final: 0.6712 (tpt170) REVERT: G 199 ASP cc_start: 0.8284 (m-30) cc_final: 0.7965 (m-30) REVERT: G 306 ASP cc_start: 0.8055 (t70) cc_final: 0.7678 (t0) REVERT: H 110 GLU cc_start: 0.7595 (mt-10) cc_final: 0.7318 (mt-10) REVERT: H 372 LYS cc_start: 0.8688 (ttmm) cc_final: 0.8200 (mmtt) REVERT: H 398 MET cc_start: 0.8209 (mtt) cc_final: 0.7995 (mtp) REVERT: H 405 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8890 (mp) REVERT: I 149 MET cc_start: 0.8293 (OUTLIER) cc_final: 0.7988 (tpt) REVERT: I 199 ASP cc_start: 0.8305 (m-30) cc_final: 0.7961 (m-30) REVERT: I 248 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8460 (tt) REVERT: I 306 ASP cc_start: 0.8074 (t70) cc_final: 0.7543 (t0) REVERT: I 312 TYR cc_start: 0.8924 (m-80) cc_final: 0.7955 (m-80) REVERT: I 398 MET cc_start: 0.8354 (mtt) cc_final: 0.8005 (mtp) REVERT: I 425 MET cc_start: 0.8342 (tpp) cc_final: 0.8071 (tpp) REVERT: J 71 GLU cc_start: 0.7912 (pt0) cc_final: 0.7612 (pt0) REVERT: J 154 MET cc_start: 0.8835 (mmt) cc_final: 0.8489 (mmt) REVERT: J 161 TYR cc_start: 0.8541 (m-80) cc_final: 0.8058 (m-80) REVERT: J 290 GLU cc_start: 0.7533 (tt0) cc_final: 0.7257 (tm-30) REVERT: J 301 GLN cc_start: 0.8228 (pt0) cc_final: 0.7980 (pt0) REVERT: J 424 ASP cc_start: 0.7891 (OUTLIER) cc_final: 0.7640 (m-30) REVERT: K 76 ASP cc_start: 0.8325 (OUTLIER) cc_final: 0.8065 (m-30) REVERT: K 83 TYR cc_start: 0.8585 (m-80) cc_final: 0.8329 (m-10) REVERT: K 212 ILE cc_start: 0.8799 (OUTLIER) cc_final: 0.8585 (mp) REVERT: K 301 GLN cc_start: 0.8214 (pt0) cc_final: 0.7934 (mt0) REVERT: K 302 MET cc_start: 0.8507 (mmt) cc_final: 0.8184 (mmt) REVERT: K 309 HIS cc_start: 0.8092 (m90) cc_final: 0.7682 (m90) REVERT: K 413 MET cc_start: 0.8287 (ttm) cc_final: 0.7946 (ttm) REVERT: L 76 ASP cc_start: 0.8289 (OUTLIER) cc_final: 0.7995 (m-30) REVERT: L 91 GLN cc_start: 0.8347 (mt0) cc_final: 0.8035 (mt0) REVERT: L 161 TYR cc_start: 0.8469 (m-80) cc_final: 0.8082 (m-80) REVERT: L 172 TYR cc_start: 0.8339 (t80) cc_final: 0.7656 (t80) REVERT: L 212 ILE cc_start: 0.8837 (OUTLIER) cc_final: 0.8425 (mp) REVERT: L 254 GLU cc_start: 0.7024 (OUTLIER) cc_final: 0.6658 (mm-30) REVERT: L 306 ASP cc_start: 0.8091 (t0) cc_final: 0.7675 (t0) REVERT: L 309 HIS cc_start: 0.8227 (m-70) cc_final: 0.7754 (m-70) REVERT: L 413 MET cc_start: 0.8255 (ttm) cc_final: 0.8050 (ttm) outliers start: 163 outliers final: 117 residues processed: 907 average time/residue: 0.2433 time to fit residues: 363.8059 Evaluate side-chains 906 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 773 time to evaluate : 1.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 221 ARG Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 430 SER Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 254 GLU Chi-restraints excluded: chain E residue 256 GLN Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 305 CYS Chi-restraints excluded: chain E residue 413 MET Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain F residue 37 HIS Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 301 MET Chi-restraints excluded: chain F residue 430 SER Chi-restraints excluded: chain G residue 37 HIS Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 129 CYS Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 276 THR Chi-restraints excluded: chain G residue 324 SER Chi-restraints excluded: chain G residue 325 MET Chi-restraints excluded: chain G residue 330 GLU Chi-restraints excluded: chain G residue 356 CYS Chi-restraints excluded: chain G residue 430 SER Chi-restraints excluded: chain H residue 37 HIS Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 129 CYS Chi-restraints excluded: chain H residue 137 LEU Chi-restraints excluded: chain H residue 165 ILE Chi-restraints excluded: chain H residue 276 THR Chi-restraints excluded: chain H residue 324 SER Chi-restraints excluded: chain H residue 387 LEU Chi-restraints excluded: chain H residue 405 LEU Chi-restraints excluded: chain H residue 430 SER Chi-restraints excluded: chain I residue 129 CYS Chi-restraints excluded: chain I residue 149 MET Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 240 THR Chi-restraints excluded: chain I residue 248 LEU Chi-restraints excluded: chain I residue 313 LEU Chi-restraints excluded: chain I residue 324 SER Chi-restraints excluded: chain I residue 338 LYS Chi-restraints excluded: chain I residue 430 SER Chi-restraints excluded: chain J residue 36 MET Chi-restraints excluded: chain J residue 76 ASP Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain J residue 238 ILE Chi-restraints excluded: chain J residue 254 GLU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 287 SER Chi-restraints excluded: chain J residue 305 CYS Chi-restraints excluded: chain J residue 424 ASP Chi-restraints excluded: chain K residue 36 MET Chi-restraints excluded: chain K residue 76 ASP Chi-restraints excluded: chain K residue 82 THR Chi-restraints excluded: chain K residue 145 THR Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 212 ILE Chi-restraints excluded: chain K residue 238 ILE Chi-restraints excluded: chain K residue 253 THR Chi-restraints excluded: chain K residue 254 GLU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 287 SER Chi-restraints excluded: chain K residue 371 VAL Chi-restraints excluded: chain K residue 378 LEU Chi-restraints excluded: chain K residue 381 THR Chi-restraints excluded: chain K residue 435 VAL Chi-restraints excluded: chain L residue 36 MET Chi-restraints excluded: chain L residue 76 ASP Chi-restraints excluded: chain L residue 82 THR Chi-restraints excluded: chain L residue 145 THR Chi-restraints excluded: chain L residue 151 SER Chi-restraints excluded: chain L residue 158 SER Chi-restraints excluded: chain L residue 204 VAL Chi-restraints excluded: chain L residue 212 ILE Chi-restraints excluded: chain L residue 238 ILE Chi-restraints excluded: chain L residue 254 GLU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 287 SER Chi-restraints excluded: chain L residue 339 ARG Chi-restraints excluded: chain L residue 371 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 216 optimal weight: 2.9990 chunk 322 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 298 optimal weight: 6.9990 chunk 168 optimal weight: 10.0000 chunk 269 optimal weight: 4.9990 chunk 189 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 210 optimal weight: 1.9990 chunk 256 optimal weight: 5.9990 chunk 250 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 HIS B 8 GLN ** B 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 ASN ** B 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 258 ASN F 258 ASN F 282 GLN ** F 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 206 ASN G 334 ASN H 6 HIS H 14 ASN H 136 GLN ** H 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 85 GLN J 101 ASN J 285 GLN K 50 ASN K 133 GLN K 216 ASN L 101 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.124018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.106129 restraints weight = 54313.785| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.24 r_work: 0.3263 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.4627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 41436 Z= 0.248 Angle : 0.622 7.603 56304 Z= 0.322 Chirality : 0.047 0.302 6156 Planarity : 0.005 0.054 7338 Dihedral : 11.441 178.936 5727 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.87 % Allowed : 21.18 % Favored : 74.94 % 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 (0.12), residues: 5088 helix: 1.90 (0.11), residues: 2310 sheet: 0.43 (0.18), residues: 798 loop : -0.97 (0.14), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 400 TYR 0.019 0.002 TYR G 161 PHE 0.021 0.002 PHE F 20 TRP 0.024 0.002 TRP G 346 HIS 0.018 0.001 HIS B 37 Details of bonding type rmsd covalent geometry : bond 0.00581 (41436) covalent geometry : angle 0.62243 (56304) hydrogen bonds : bond 0.05729 ( 2058) hydrogen bonds : angle 4.67831 ( 5904) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 968 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 800 time to evaluate : 1.598 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.8023 (mp0) cc_final: 0.7528 (mp0) REVERT: A 76 ASP cc_start: 0.8420 (OUTLIER) cc_final: 0.7966 (m-30) REVERT: A 170 SER cc_start: 0.8859 (m) cc_final: 0.8577 (p) REVERT: A 203 MET cc_start: 0.8890 (OUTLIER) cc_final: 0.8238 (mtp) REVERT: A 221 ARG cc_start: 0.8005 (ptp-110) cc_final: 0.7616 (mtt90) REVERT: A 393 HIS cc_start: 0.8215 (t70) cc_final: 0.7884 (t70) REVERT: B 71 GLU cc_start: 0.7171 (pt0) cc_final: 0.6911 (pt0) REVERT: B 207 GLU cc_start: 0.8153 (tp30) cc_final: 0.7868 (mp0) REVERT: B 213 CYS cc_start: 0.7862 (m) cc_final: 0.7566 (m) REVERT: B 282 GLN cc_start: 0.8274 (mm110) cc_final: 0.7849 (mt0) REVERT: C 76 ASP cc_start: 0.7976 (OUTLIER) cc_final: 0.7458 (m-30) REVERT: C 77 GLU cc_start: 0.8153 (tp30) cc_final: 0.7790 (tp30) REVERT: C 128 GLN cc_start: 0.8166 (mt0) cc_final: 0.7924 (mt0) REVERT: C 285 GLN cc_start: 0.2755 (mm-40) cc_final: 0.1799 (pt0) REVERT: C 377 MET cc_start: 0.8698 (tmm) cc_final: 0.8130 (tmm) REVERT: D 156 LYS cc_start: 0.8861 (mptt) cc_final: 0.8585 (mmtt) REVERT: E 76 ASP cc_start: 0.8202 (OUTLIER) cc_final: 0.7740 (m-30) REVERT: E 90 GLU cc_start: 0.8679 (mm-30) cc_final: 0.8213 (tp30) REVERT: E 163 LYS cc_start: 0.8934 (mtmt) cc_final: 0.8602 (pttm) REVERT: E 259 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8731 (mp) REVERT: E 287 SER cc_start: 0.8037 (p) cc_final: 0.7779 (m) REVERT: E 396 ASP cc_start: 0.8116 (m-30) cc_final: 0.7703 (m-30) REVERT: E 413 MET cc_start: 0.8517 (OUTLIER) cc_final: 0.8190 (ttm) REVERT: F 207 GLU cc_start: 0.8004 (tp30) cc_final: 0.7712 (mp0) REVERT: G 42 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8195 (mm) REVERT: G 88 ARG cc_start: 0.8363 (ttp-110) cc_final: 0.6765 (tpt170) REVERT: G 199 ASP cc_start: 0.8454 (m-30) cc_final: 0.8165 (m-30) REVERT: H 372 LYS cc_start: 0.8602 (ttmm) cc_final: 0.8149 (mmtt) REVERT: H 373 MET cc_start: 0.8589 (mtp) cc_final: 0.8303 (mtt) REVERT: H 398 MET cc_start: 0.8265 (mtt) cc_final: 0.8028 (mtp) REVERT: H 405 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8903 (mp) REVERT: I 90 ASP cc_start: 0.8309 (t0) cc_final: 0.7972 (m-30) REVERT: I 149 MET cc_start: 0.8186 (OUTLIER) cc_final: 0.7887 (tpp) REVERT: I 199 ASP cc_start: 0.8519 (m-30) cc_final: 0.8133 (m-30) REVERT: I 248 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8569 (tt) REVERT: I 259 MET cc_start: 0.8735 (mmm) cc_final: 0.8530 (mmm) REVERT: I 306 ASP cc_start: 0.8153 (t70) cc_final: 0.7676 (t0) REVERT: I 312 TYR cc_start: 0.8937 (m-80) cc_final: 0.7901 (m-80) REVERT: I 398 MET cc_start: 0.8430 (mtt) cc_final: 0.8075 (mtp) REVERT: I 425 MET cc_start: 0.8312 (tpp) cc_final: 0.8041 (tpp) REVERT: J 71 GLU cc_start: 0.7996 (pt0) cc_final: 0.7694 (pt0) REVERT: J 161 TYR cc_start: 0.8608 (m-80) cc_final: 0.8132 (m-80) REVERT: J 301 GLN cc_start: 0.8299 (pt0) cc_final: 0.7981 (pt0) REVERT: J 306 ASP cc_start: 0.8145 (t0) cc_final: 0.7756 (t70) REVERT: K 76 ASP cc_start: 0.8370 (OUTLIER) cc_final: 0.8062 (m-30) REVERT: K 83 TYR cc_start: 0.8656 (m-80) cc_final: 0.8412 (m-10) REVERT: K 212 ILE cc_start: 0.8830 (OUTLIER) cc_final: 0.8603 (mp) REVERT: K 290 GLU cc_start: 0.7655 (tm-30) cc_final: 0.7198 (tm-30) REVERT: K 301 GLN cc_start: 0.8194 (pt0) cc_final: 0.7914 (mt0) REVERT: K 413 MET cc_start: 0.8595 (ttm) cc_final: 0.8323 (ttm) REVERT: L 76 ASP cc_start: 0.8379 (OUTLIER) cc_final: 0.8051 (m-30) REVERT: L 91 GLN cc_start: 0.8454 (mt0) cc_final: 0.8218 (mt0) REVERT: L 161 TYR cc_start: 0.8526 (m-80) cc_final: 0.8057 (m-80) REVERT: L 172 TYR cc_start: 0.8531 (t80) cc_final: 0.7846 (t80) REVERT: L 212 ILE cc_start: 0.8835 (OUTLIER) cc_final: 0.8449 (mp) outliers start: 168 outliers final: 129 residues processed: 911 average time/residue: 0.2467 time to fit residues: 369.7035 Evaluate side-chains 916 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 773 time to evaluate : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 221 ARG Chi-restraints excluded: chain C residue 256 GLN Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 430 SER Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 254 GLU Chi-restraints excluded: chain E residue 256 GLN Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 305 CYS Chi-restraints excluded: chain E residue 336 LYS Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 413 MET Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 301 MET Chi-restraints excluded: chain F residue 430 SER Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 129 CYS Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 276 THR Chi-restraints excluded: chain G residue 324 SER Chi-restraints excluded: chain G residue 330 GLU Chi-restraints excluded: chain G residue 353 THR Chi-restraints excluded: chain G residue 356 CYS Chi-restraints excluded: chain G residue 430 SER Chi-restraints excluded: chain H residue 37 HIS Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 129 CYS Chi-restraints excluded: chain H residue 137 LEU Chi-restraints excluded: chain H residue 165 ILE Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain H residue 276 THR Chi-restraints excluded: chain H residue 324 SER Chi-restraints excluded: chain H residue 387 LEU Chi-restraints excluded: chain H residue 405 LEU Chi-restraints excluded: chain H residue 430 SER Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 129 CYS Chi-restraints excluded: chain I residue 149 MET Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 179 ASP Chi-restraints excluded: chain I residue 207 GLU Chi-restraints excluded: chain I residue 240 THR Chi-restraints excluded: chain I residue 248 LEU Chi-restraints excluded: chain I residue 313 LEU Chi-restraints excluded: chain I residue 324 SER Chi-restraints excluded: chain I residue 330 GLU Chi-restraints excluded: chain I residue 430 SER Chi-restraints excluded: chain J residue 36 MET Chi-restraints excluded: chain J residue 76 ASP Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain J residue 145 THR Chi-restraints excluded: chain J residue 238 ILE Chi-restraints excluded: chain J residue 241 SER Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 287 SER Chi-restraints excluded: chain J residue 424 ASP Chi-restraints excluded: chain K residue 76 ASP Chi-restraints excluded: chain K residue 82 THR Chi-restraints excluded: chain K residue 145 THR Chi-restraints excluded: chain K residue 158 SER Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 212 ILE Chi-restraints excluded: chain K residue 238 ILE Chi-restraints excluded: chain K residue 253 THR Chi-restraints excluded: chain K residue 254 GLU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 287 SER Chi-restraints excluded: chain K residue 371 VAL Chi-restraints excluded: chain K residue 378 LEU Chi-restraints excluded: chain K residue 381 THR Chi-restraints excluded: chain K residue 435 VAL Chi-restraints excluded: chain L residue 76 ASP Chi-restraints excluded: chain L residue 82 THR Chi-restraints excluded: chain L residue 145 THR Chi-restraints excluded: chain L residue 151 SER Chi-restraints excluded: chain L residue 158 SER Chi-restraints excluded: chain L residue 204 VAL Chi-restraints excluded: chain L residue 212 ILE Chi-restraints excluded: chain L residue 238 ILE Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 287 SER Chi-restraints excluded: chain L residue 335 ILE Chi-restraints excluded: chain L residue 339 ARG Chi-restraints excluded: chain L residue 371 VAL Chi-restraints excluded: chain L residue 435 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 357 optimal weight: 4.9990 chunk 212 optimal weight: 0.5980 chunk 497 optimal weight: 5.9990 chunk 272 optimal weight: 10.0000 chunk 162 optimal weight: 6.9990 chunk 59 optimal weight: 0.6980 chunk 475 optimal weight: 7.9990 chunk 318 optimal weight: 0.9980 chunk 135 optimal weight: 9.9990 chunk 348 optimal weight: 4.9990 chunk 244 optimal weight: 0.9980 overall best weight: 1.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 309 HIS B 436 GLN ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 206 ASN D 258 ASN E 197 HIS F 258 ASN F 282 GLN F 293 GLN ** F 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 HIS H 136 GLN H 334 ASN ** H 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 101 ASN J 285 GLN J 309 HIS K 50 ASN K 216 ASN L 101 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.127673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.109640 restraints weight = 53860.894| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.26 r_work: 0.3346 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.4750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 41436 Z= 0.140 Angle : 0.559 8.434 56304 Z= 0.286 Chirality : 0.043 0.319 6156 Planarity : 0.005 0.057 7338 Dihedral : 11.211 176.686 5727 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.30 % Allowed : 21.99 % Favored : 74.71 % 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 (0.12), residues: 5088 helix: 1.90 (0.11), residues: 2346 sheet: 0.62 (0.18), residues: 804 loop : -0.99 (0.14), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 390 TYR 0.017 0.001 TYR G 161 PHE 0.022 0.001 PHE J 49 TRP 0.026 0.002 TRP G 346 HIS 0.004 0.001 HIS J 309 Details of bonding type rmsd covalent geometry : bond 0.00312 (41436) covalent geometry : angle 0.55864 (56304) hydrogen bonds : bond 0.04593 ( 2058) hydrogen bonds : angle 4.48251 ( 5904) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 939 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 796 time to evaluate : 1.509 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.7946 (mp0) cc_final: 0.7446 (mp0) REVERT: A 76 ASP cc_start: 0.8333 (OUTLIER) cc_final: 0.7862 (m-30) REVERT: A 170 SER cc_start: 0.8799 (m) cc_final: 0.8591 (p) REVERT: A 203 MET cc_start: 0.8799 (OUTLIER) cc_final: 0.8233 (mtp) REVERT: A 221 ARG cc_start: 0.7984 (ptp-110) cc_final: 0.7605 (mtt90) REVERT: A 322 ASP cc_start: 0.8702 (t0) cc_final: 0.8313 (m-30) REVERT: A 393 HIS cc_start: 0.8266 (t70) cc_final: 0.7893 (t70) REVERT: B 71 GLU cc_start: 0.7177 (pt0) cc_final: 0.6935 (pt0) REVERT: B 207 GLU cc_start: 0.8071 (tp30) cc_final: 0.7812 (mp0) REVERT: B 213 CYS cc_start: 0.7847 (m) cc_final: 0.7517 (m) REVERT: B 282 GLN cc_start: 0.8251 (mm110) cc_final: 0.7842 (mt0) REVERT: C 76 ASP cc_start: 0.7898 (OUTLIER) cc_final: 0.7363 (m-30) REVERT: C 77 GLU cc_start: 0.8027 (tp30) cc_final: 0.7644 (tp30) REVERT: C 285 GLN cc_start: 0.2743 (mm-40) cc_final: 0.1943 (pt0) REVERT: C 290 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7340 (pt0) REVERT: C 322 ASP cc_start: 0.8471 (t0) cc_final: 0.8217 (m-30) REVERT: C 377 MET cc_start: 0.8641 (tmm) cc_final: 0.8096 (tmm) REVERT: D 156 LYS cc_start: 0.8860 (mptt) cc_final: 0.8593 (mmtt) REVERT: D 282 GLN cc_start: 0.8233 (mm110) cc_final: 0.7912 (mt0) REVERT: D 342 TYR cc_start: 0.8084 (m-10) cc_final: 0.7705 (m-10) REVERT: E 76 ASP cc_start: 0.8196 (OUTLIER) cc_final: 0.7757 (m-30) REVERT: E 90 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8243 (tp30) REVERT: E 251 ASP cc_start: 0.8525 (p0) cc_final: 0.6982 (p0) REVERT: E 254 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7497 (mp0) REVERT: E 259 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8751 (mp) REVERT: E 322 ASP cc_start: 0.8481 (t0) cc_final: 0.8032 (m-30) REVERT: E 396 ASP cc_start: 0.8007 (m-30) cc_final: 0.7645 (m-30) REVERT: E 413 MET cc_start: 0.8367 (OUTLIER) cc_final: 0.8014 (ttm) REVERT: F 88 ARG cc_start: 0.5474 (tpt170) cc_final: 0.4835 (tpt170) REVERT: F 207 GLU cc_start: 0.8013 (tp30) cc_final: 0.7748 (mp0) REVERT: G 88 ARG cc_start: 0.8361 (ttp-110) cc_final: 0.6786 (tpt170) REVERT: G 199 ASP cc_start: 0.8249 (m-30) cc_final: 0.7961 (m-30) REVERT: G 311 ARG cc_start: 0.7903 (mtt-85) cc_final: 0.7444 (mtt-85) REVERT: G 312 TYR cc_start: 0.8848 (m-80) cc_final: 0.8443 (m-80) REVERT: H 90 ASP cc_start: 0.8365 (t0) cc_final: 0.7934 (m-30) REVERT: H 248 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8579 (tt) REVERT: H 311 ARG cc_start: 0.8007 (mtt-85) cc_final: 0.7729 (mtt-85) REVERT: H 372 LYS cc_start: 0.8567 (ttmm) cc_final: 0.8113 (mmtt) REVERT: H 373 MET cc_start: 0.8520 (mtp) cc_final: 0.8261 (mtt) REVERT: H 398 MET cc_start: 0.8261 (mtt) cc_final: 0.8050 (mtp) REVERT: I 90 ASP cc_start: 0.8315 (t0) cc_final: 0.7970 (m-30) REVERT: I 149 MET cc_start: 0.8027 (OUTLIER) cc_final: 0.7758 (tpt) REVERT: I 199 ASP cc_start: 0.8324 (m-30) cc_final: 0.8007 (m-30) REVERT: I 248 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8517 (tt) REVERT: I 306 ASP cc_start: 0.8132 (t70) cc_final: 0.7687 (t0) REVERT: I 312 TYR cc_start: 0.8895 (m-80) cc_final: 0.7846 (m-80) REVERT: I 398 MET cc_start: 0.8440 (mtt) cc_final: 0.8107 (mtp) REVERT: I 425 MET cc_start: 0.8299 (tpp) cc_final: 0.8001 (tpp) REVERT: J 71 GLU cc_start: 0.7941 (pt0) cc_final: 0.7642 (pt0) REVERT: J 161 TYR cc_start: 0.8506 (m-80) cc_final: 0.8022 (m-80) REVERT: J 172 TYR cc_start: 0.8128 (t80) cc_final: 0.7623 (t80) REVERT: J 301 GLN cc_start: 0.8266 (pt0) cc_final: 0.7960 (pt0) REVERT: J 306 ASP cc_start: 0.8153 (t0) cc_final: 0.7711 (t70) REVERT: K 76 ASP cc_start: 0.8239 (OUTLIER) cc_final: 0.7925 (m-30) REVERT: K 83 TYR cc_start: 0.8639 (m-80) cc_final: 0.8379 (m-10) REVERT: K 212 ILE cc_start: 0.8805 (OUTLIER) cc_final: 0.8580 (mp) REVERT: K 309 HIS cc_start: 0.8032 (m90) cc_final: 0.7749 (m170) REVERT: K 413 MET cc_start: 0.8374 (ttm) cc_final: 0.8056 (ttm) REVERT: L 76 ASP cc_start: 0.8322 (OUTLIER) cc_final: 0.7977 (m-30) REVERT: L 91 GLN cc_start: 0.8469 (mt0) cc_final: 0.8239 (mt0) REVERT: L 161 TYR cc_start: 0.8482 (m-80) cc_final: 0.8024 (m-80) REVERT: L 172 TYR cc_start: 0.8499 (t80) cc_final: 0.7848 (t80) REVERT: L 212 ILE cc_start: 0.8832 (OUTLIER) cc_final: 0.8405 (mp) REVERT: L 309 HIS cc_start: 0.8318 (m-70) cc_final: 0.8086 (m-70) outliers start: 143 outliers final: 108 residues processed: 889 average time/residue: 0.2452 time to fit residues: 357.8436 Evaluate side-chains 883 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 760 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 221 ARG Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 430 SER Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 254 GLU Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 305 CYS Chi-restraints excluded: chain E residue 413 MET Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 301 MET Chi-restraints excluded: chain F residue 430 SER Chi-restraints excluded: chain G residue 37 HIS Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 129 CYS Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 190 SER Chi-restraints excluded: chain G residue 276 THR Chi-restraints excluded: chain G residue 324 SER Chi-restraints excluded: chain G residue 330 GLU Chi-restraints excluded: chain G residue 353 THR Chi-restraints excluded: chain G residue 356 CYS Chi-restraints excluded: chain G residue 430 SER Chi-restraints excluded: chain H residue 37 HIS Chi-restraints excluded: chain H residue 129 CYS Chi-restraints excluded: chain H residue 137 LEU Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 276 THR Chi-restraints excluded: chain H residue 324 SER Chi-restraints excluded: chain H residue 387 LEU Chi-restraints excluded: chain H residue 430 SER Chi-restraints excluded: chain I residue 129 CYS Chi-restraints excluded: chain I residue 149 MET Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 240 THR Chi-restraints excluded: chain I residue 248 LEU Chi-restraints excluded: chain I residue 313 LEU Chi-restraints excluded: chain I residue 324 SER Chi-restraints excluded: chain I residue 430 SER Chi-restraints excluded: chain J residue 4 CYS Chi-restraints excluded: chain J residue 36 MET Chi-restraints excluded: chain J residue 76 ASP Chi-restraints excluded: chain J residue 145 THR Chi-restraints excluded: chain J residue 238 ILE Chi-restraints excluded: chain J residue 241 SER Chi-restraints excluded: chain J residue 254 GLU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 287 SER Chi-restraints excluded: chain J residue 379 SER Chi-restraints excluded: chain K residue 76 ASP Chi-restraints excluded: chain K residue 82 THR Chi-restraints excluded: chain K residue 145 THR Chi-restraints excluded: chain K residue 158 SER Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 212 ILE Chi-restraints excluded: chain K residue 238 ILE Chi-restraints excluded: chain K residue 253 THR Chi-restraints excluded: chain K residue 254 GLU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 287 SER Chi-restraints excluded: chain K residue 378 LEU Chi-restraints excluded: chain K residue 381 THR Chi-restraints excluded: chain K residue 435 VAL Chi-restraints excluded: chain L residue 76 ASP Chi-restraints excluded: chain L residue 82 THR Chi-restraints excluded: chain L residue 145 THR Chi-restraints excluded: chain L residue 151 SER Chi-restraints excluded: chain L residue 158 SER Chi-restraints excluded: chain L residue 204 VAL Chi-restraints excluded: chain L residue 212 ILE Chi-restraints excluded: chain L residue 230 LEU Chi-restraints excluded: chain L residue 238 ILE Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 287 SER Chi-restraints excluded: chain L residue 339 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 31 optimal weight: 0.8980 chunk 156 optimal weight: 0.9990 chunk 397 optimal weight: 3.9990 chunk 374 optimal weight: 2.9990 chunk 135 optimal weight: 5.9990 chunk 67 optimal weight: 0.6980 chunk 146 optimal weight: 5.9990 chunk 474 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 chunk 10 optimal weight: 0.1980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 309 HIS ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 258 ASN F 282 GLN ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 206 ASN H 334 ASN ** H 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 285 GLN K 50 ASN K 266 HIS L 101 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.129364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.111266 restraints weight = 53147.439| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.26 r_work: 0.3356 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.4864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 41436 Z= 0.124 Angle : 0.553 9.317 56304 Z= 0.282 Chirality : 0.043 0.322 6156 Planarity : 0.005 0.057 7338 Dihedral : 10.997 173.215 5727 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.97 % Allowed : 22.29 % Favored : 74.73 % 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 (0.12), residues: 5088 helix: 1.92 (0.11), residues: 2358 sheet: 0.68 (0.18), residues: 804 loop : -0.95 (0.14), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 390 TYR 0.016 0.001 TYR G 161 PHE 0.021 0.001 PHE J 49 TRP 0.029 0.002 TRP G 346 HIS 0.007 0.001 HIS K 309 Details of bonding type rmsd covalent geometry : bond 0.00273 (41436) covalent geometry : angle 0.55307 (56304) hydrogen bonds : bond 0.04257 ( 2058) hydrogen bonds : angle 4.38697 ( 5904) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 916 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 787 time to evaluate : 1.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.7888 (mp0) cc_final: 0.7382 (mp0) REVERT: A 76 ASP cc_start: 0.8308 (OUTLIER) cc_final: 0.7854 (m-30) REVERT: A 96 LYS cc_start: 0.8092 (mtmm) cc_final: 0.7644 (mtpp) REVERT: A 161 TYR cc_start: 0.8351 (m-80) cc_final: 0.8094 (m-80) REVERT: A 221 ARG cc_start: 0.7995 (ptp-110) cc_final: 0.7662 (mtt90) REVERT: A 322 ASP cc_start: 0.8704 (t0) cc_final: 0.8342 (m-30) REVERT: B 207 GLU cc_start: 0.8058 (tp30) cc_final: 0.7819 (mp0) REVERT: B 213 CYS cc_start: 0.7904 (m) cc_final: 0.7569 (m) REVERT: B 215 ARG cc_start: 0.8423 (mtp180) cc_final: 0.8206 (mtp180) REVERT: B 282 GLN cc_start: 0.8222 (mm110) cc_final: 0.7925 (mt0) REVERT: B 299 LYS cc_start: 0.8492 (ttmm) cc_final: 0.8212 (tttm) REVERT: C 60 LYS cc_start: 0.8049 (OUTLIER) cc_final: 0.7704 (tttm) REVERT: C 76 ASP cc_start: 0.7750 (OUTLIER) cc_final: 0.7216 (m-30) REVERT: C 77 GLU cc_start: 0.8030 (tp30) cc_final: 0.7664 (tp30) REVERT: C 128 GLN cc_start: 0.7971 (mt0) cc_final: 0.7667 (mt0) REVERT: C 285 GLN cc_start: 0.2694 (mm-40) cc_final: 0.2034 (pt0) REVERT: C 322 ASP cc_start: 0.8571 (t0) cc_final: 0.8259 (m-30) REVERT: C 377 MET cc_start: 0.8605 (tmm) cc_final: 0.8023 (tmm) REVERT: D 156 LYS cc_start: 0.8797 (mptt) cc_final: 0.8536 (mmtt) REVERT: D 259 MET cc_start: 0.8562 (mmm) cc_final: 0.8086 (mmm) REVERT: D 342 TYR cc_start: 0.8077 (m-10) cc_final: 0.7747 (m-10) REVERT: E 76 ASP cc_start: 0.8172 (OUTLIER) cc_final: 0.7736 (m-30) REVERT: E 90 GLU cc_start: 0.8645 (mm-30) cc_final: 0.8186 (tp30) REVERT: E 172 TYR cc_start: 0.8842 (t80) cc_final: 0.7815 (t80) REVERT: E 251 ASP cc_start: 0.8458 (p0) cc_final: 0.6936 (p0) REVERT: E 254 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7448 (mp0) REVERT: E 259 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8783 (mp) REVERT: E 322 ASP cc_start: 0.8461 (t0) cc_final: 0.8027 (m-30) REVERT: E 396 ASP cc_start: 0.8002 (m-30) cc_final: 0.7617 (m-30) REVERT: E 413 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.8014 (ttm) REVERT: F 88 ARG cc_start: 0.5041 (tpt170) cc_final: 0.4335 (tpt170) REVERT: F 207 GLU cc_start: 0.8018 (tp30) cc_final: 0.7766 (mp0) REVERT: G 88 ARG cc_start: 0.8275 (ttp-110) cc_final: 0.6669 (tpt170) REVERT: G 199 ASP cc_start: 0.8124 (m-30) cc_final: 0.7839 (m-30) REVERT: G 311 ARG cc_start: 0.7919 (mtt-85) cc_final: 0.7464 (mtt-85) REVERT: G 312 TYR cc_start: 0.8836 (m-80) cc_final: 0.8339 (m-80) REVERT: H 248 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8596 (tt) REVERT: H 311 ARG cc_start: 0.8041 (mtt-85) cc_final: 0.7747 (mtt-85) REVERT: H 372 LYS cc_start: 0.8536 (ttmm) cc_final: 0.8094 (mmtt) REVERT: I 50 ASN cc_start: 0.9078 (p0) cc_final: 0.8824 (p0) REVERT: I 90 ASP cc_start: 0.8294 (t0) cc_final: 0.7955 (m-30) REVERT: I 149 MET cc_start: 0.8013 (OUTLIER) cc_final: 0.7806 (tpt) REVERT: I 199 ASP cc_start: 0.8264 (m-30) cc_final: 0.8010 (m-30) REVERT: I 248 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8506 (tt) REVERT: I 259 MET cc_start: 0.8609 (mmm) cc_final: 0.8346 (mmp) REVERT: I 306 ASP cc_start: 0.8150 (t70) cc_final: 0.7513 (t0) REVERT: I 311 ARG cc_start: 0.8235 (mtt-85) cc_final: 0.7972 (mtt-85) REVERT: I 312 TYR cc_start: 0.8758 (m-80) cc_final: 0.7731 (m-80) REVERT: I 398 MET cc_start: 0.8432 (mtt) cc_final: 0.8111 (mtp) REVERT: I 400 ARG cc_start: 0.8133 (ttm-80) cc_final: 0.7928 (ttm-80) REVERT: I 425 MET cc_start: 0.8280 (tpp) cc_final: 0.7969 (tpp) REVERT: J 71 GLU cc_start: 0.7849 (pt0) cc_final: 0.7598 (pt0) REVERT: J 161 TYR cc_start: 0.8480 (m-80) cc_final: 0.8000 (m-80) REVERT: J 172 TYR cc_start: 0.7988 (t80) cc_final: 0.7565 (t80) REVERT: J 254 GLU cc_start: 0.6739 (OUTLIER) cc_final: 0.6499 (mm-30) REVERT: J 279 GLU cc_start: 0.8338 (mp0) cc_final: 0.7992 (mp0) REVERT: J 285 GLN cc_start: 0.7727 (tt0) cc_final: 0.7233 (tt0) REVERT: J 306 ASP cc_start: 0.8104 (t0) cc_final: 0.7757 (t70) REVERT: J 425 MET cc_start: 0.8263 (tpp) cc_final: 0.7884 (tpp) REVERT: K 83 TYR cc_start: 0.8641 (m-80) cc_final: 0.8392 (m-10) REVERT: K 212 ILE cc_start: 0.8771 (OUTLIER) cc_final: 0.8531 (mp) REVERT: K 254 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.6836 (mm-30) REVERT: K 413 MET cc_start: 0.8247 (ttm) cc_final: 0.7919 (ttm) REVERT: K 425 MET cc_start: 0.8387 (tpp) cc_final: 0.8073 (tpp) REVERT: L 76 ASP cc_start: 0.8262 (OUTLIER) cc_final: 0.7924 (m-30) REVERT: L 91 GLN cc_start: 0.8421 (mt0) cc_final: 0.8176 (mt0) REVERT: L 97 GLU cc_start: 0.7360 (tt0) cc_final: 0.7004 (tt0) REVERT: L 161 TYR cc_start: 0.8505 (m-80) cc_final: 0.8071 (m-80) REVERT: L 172 TYR cc_start: 0.8498 (t80) cc_final: 0.7839 (t80) REVERT: L 212 ILE cc_start: 0.8789 (OUTLIER) cc_final: 0.8336 (mp) REVERT: L 254 GLU cc_start: 0.6904 (OUTLIER) cc_final: 0.6621 (mm-30) REVERT: L 306 ASP cc_start: 0.8158 (t0) cc_final: 0.7936 (t0) REVERT: L 313 MET cc_start: 0.8805 (mtm) cc_final: 0.8605 (mtp) REVERT: L 425 MET cc_start: 0.8247 (tpp) cc_final: 0.7958 (tpp) outliers start: 129 outliers final: 104 residues processed: 865 average time/residue: 0.2430 time to fit residues: 345.7064 Evaluate side-chains 890 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 770 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 221 ARG Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 430 SER Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 254 GLU Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 305 CYS Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 413 MET Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 301 MET Chi-restraints excluded: chain G residue 37 HIS Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 129 CYS Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 190 SER Chi-restraints excluded: chain G residue 276 THR Chi-restraints excluded: chain G residue 324 SER Chi-restraints excluded: chain G residue 330 GLU Chi-restraints excluded: chain G residue 353 THR Chi-restraints excluded: chain G residue 356 CYS Chi-restraints excluded: chain G residue 430 SER Chi-restraints excluded: chain H residue 37 HIS Chi-restraints excluded: chain H residue 129 CYS Chi-restraints excluded: chain H residue 137 LEU Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 276 THR Chi-restraints excluded: chain H residue 324 SER Chi-restraints excluded: chain H residue 387 LEU Chi-restraints excluded: chain H residue 430 SER Chi-restraints excluded: chain I residue 129 CYS Chi-restraints excluded: chain I residue 149 MET Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 190 SER Chi-restraints excluded: chain I residue 240 THR Chi-restraints excluded: chain I residue 248 LEU Chi-restraints excluded: chain I residue 324 SER Chi-restraints excluded: chain I residue 430 SER Chi-restraints excluded: chain J residue 4 CYS Chi-restraints excluded: chain J residue 36 MET Chi-restraints excluded: chain J residue 76 ASP Chi-restraints excluded: chain J residue 145 THR Chi-restraints excluded: chain J residue 238 ILE Chi-restraints excluded: chain J residue 241 SER Chi-restraints excluded: chain J residue 254 GLU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 287 SER Chi-restraints excluded: chain J residue 379 SER Chi-restraints excluded: chain K residue 36 MET Chi-restraints excluded: chain K residue 76 ASP Chi-restraints excluded: chain K residue 82 THR Chi-restraints excluded: chain K residue 145 THR Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 212 ILE Chi-restraints excluded: chain K residue 238 ILE Chi-restraints excluded: chain K residue 253 THR Chi-restraints excluded: chain K residue 254 GLU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 287 SER Chi-restraints excluded: chain K residue 378 LEU Chi-restraints excluded: chain K residue 381 THR Chi-restraints excluded: chain L residue 76 ASP Chi-restraints excluded: chain L residue 82 THR Chi-restraints excluded: chain L residue 151 SER Chi-restraints excluded: chain L residue 158 SER Chi-restraints excluded: chain L residue 212 ILE Chi-restraints excluded: chain L residue 230 LEU Chi-restraints excluded: chain L residue 238 ILE Chi-restraints excluded: chain L residue 254 GLU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 287 SER Chi-restraints excluded: chain L residue 339 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 331 optimal weight: 0.0170 chunk 254 optimal weight: 4.9990 chunk 397 optimal weight: 7.9990 chunk 340 optimal weight: 0.0670 chunk 337 optimal weight: 5.9990 chunk 320 optimal weight: 5.9990 chunk 324 optimal weight: 9.9990 chunk 266 optimal weight: 9.9990 chunk 419 optimal weight: 2.9990 chunk 201 optimal weight: 0.8980 chunk 430 optimal weight: 0.9990 overall best weight: 0.9960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 309 HIS ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 GLN B 406 HIS ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 258 ASN D 282 GLN F 282 GLN H 334 ASN ** H 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 50 ASN L 101 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.129860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.111905 restraints weight = 53575.403| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.23 r_work: 0.3399 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.4938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 41436 Z= 0.117 Angle : 0.541 8.869 56304 Z= 0.276 Chirality : 0.043 0.324 6156 Planarity : 0.005 0.056 7338 Dihedral : 10.821 171.050 5727 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.77 % Allowed : 22.54 % Favored : 74.69 % 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: 1.06 (0.12), residues: 5088 helix: 1.96 (0.11), residues: 2352 sheet: 0.72 (0.18), residues: 804 loop : -0.90 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 390 TYR 0.016 0.001 TYR G 161 PHE 0.020 0.001 PHE J 49 TRP 0.027 0.002 TRP G 346 HIS 0.003 0.001 HIS K 309 Details of bonding type rmsd covalent geometry : bond 0.00255 (41436) covalent geometry : angle 0.54102 (56304) hydrogen bonds : bond 0.04071 ( 2058) hydrogen bonds : angle 4.33057 ( 5904) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11364.51 seconds wall clock time: 195 minutes 18.15 seconds (11718.15 seconds total)