Starting phenix.real_space_refine on Thu Nov 20 22:47:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6evz_3964/11_2025/6evz_3964.cif Found real_map, /net/cci-nas-00/data/ceres_data/6evz_3964/11_2025/6evz_3964.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6evz_3964/11_2025/6evz_3964.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6evz_3964/11_2025/6evz_3964.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6evz_3964/11_2025/6evz_3964.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6evz_3964/11_2025/6evz_3964.map" } resolution = 3.8 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= 0.010 sd= 0.061 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 25674 2.51 5 N 6978 2.21 5 O 7902 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.04s 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: 40866 Number of models: 1 Model: "" Number of chains: 24 Chain: "F" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3368 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "G" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3368 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "D" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3368 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "I" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3368 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "A" Number of atoms: 3382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3382 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3368 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "H" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3368 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "E" Number of atoms: 3382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3382 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 3382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3382 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 3382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3382 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 3382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3382 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "K" Number of atoms: 3382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3382 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 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: "D" 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: "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: "H" 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: "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: "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: "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} 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} Time building chain proxies: 9.86, per 1000 atoms: 0.24 Number of scatterers: 40866 At special positions: 0 Unit cell: (119.54, 172.36, 212.67, 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 7902 8.00 N 6978 7.00 C 25674 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: 3.42 Conformation dependent library (CDL) restraints added in 1.9 seconds 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9576 Finding SS restraints... Secondary structure from input PDB file: 198 helices and 30 sheets defined 45.1% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'F' and resid 10 through 29 removed outlier: 3.987A pdb=" N LYS F 19 " --> pdb=" O GLN F 15 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLU F 22 " --> pdb=" O ALA F 18 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP F 26 " --> pdb=" O GLU F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 49 removed outlier: 3.694A pdb=" N VAL F 49 " --> pdb=" O ARG F 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 46 through 49' Processing helix chain 'F' and resid 70 through 77 removed outlier: 3.755A pdb=" N SER F 75 " --> pdb=" O GLY F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 106 Processing helix chain 'F' and resid 112 through 125 removed outlier: 4.119A pdb=" N ASP F 118 " --> pdb=" O ASP F 114 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N VAL F 119 " --> pdb=" O SER F 115 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS F 122 " --> pdb=" O ASP F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 159 removed outlier: 3.848A pdb=" N ILE F 152 " --> pdb=" O GLY F 148 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLU F 157 " --> pdb=" O SER F 153 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU F 158 " --> pdb=" O LYS F 154 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 193 removed outlier: 4.039A pdb=" N SER F 188 " --> pdb=" O ASN F 184 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N HIS F 190 " --> pdb=" O THR F 186 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N GLN F 191 " --> pdb=" O LEU F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 214 removed outlier: 3.716A pdb=" N ILE F 210 " --> pdb=" O ALA F 206 " (cutoff:3.500A) Processing helix chain 'F' and resid 221 through 237 removed outlier: 3.721A pdb=" N HIS F 227 " --> pdb=" O GLY F 223 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU F 228 " --> pdb=" O ASP F 224 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL F 229 " --> pdb=" O LEU F 225 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N THR F 237 " --> pdb=" O MET F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 238 through 240 No H-bonds generated for 'chain 'F' and resid 238 through 240' Processing helix chain 'F' and resid 251 through 256 Processing helix chain 'F' and resid 285 through 294 removed outlier: 3.560A pdb=" N LEU F 289 " --> pdb=" O THR F 285 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR F 290 " --> pdb=" O VAL F 286 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE F 294 " --> pdb=" O THR F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 336 removed outlier: 3.606A pdb=" N VAL F 326 " --> pdb=" O SER F 322 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLN F 334 " --> pdb=" O MET F 330 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 390 removed outlier: 3.591A pdb=" N ILE F 381 " --> pdb=" O LEU F 377 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU F 383 " --> pdb=" O LYS F 379 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG F 390 " --> pdb=" O THR F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 400 Processing helix chain 'F' and resid 404 through 427 removed outlier: 3.851A pdb=" N PHE F 408 " --> pdb=" O ASP F 404 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA F 411 " --> pdb=" O GLU F 407 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU F 421 " --> pdb=" O ASP F 417 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN F 424 " --> pdb=" O SER F 420 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP F 427 " --> pdb=" O GLN F 423 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 29 removed outlier: 3.987A pdb=" N LYS G 19 " --> pdb=" O GLN G 15 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLU G 22 " --> pdb=" O ALA G 18 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP G 26 " --> pdb=" O GLU G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 49 removed outlier: 3.695A pdb=" N VAL G 49 " --> pdb=" O ARG G 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 46 through 49' Processing helix chain 'G' and resid 70 through 77 removed outlier: 3.755A pdb=" N SER G 75 " --> pdb=" O GLY G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 106 Processing helix chain 'G' and resid 112 through 125 removed outlier: 4.120A pdb=" N ASP G 118 " --> pdb=" O ASP G 114 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N VAL G 119 " --> pdb=" O SER G 115 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS G 122 " --> pdb=" O ASP G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 159 removed outlier: 3.848A pdb=" N ILE G 152 " --> pdb=" O GLY G 148 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLU G 157 " --> pdb=" O SER G 153 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU G 158 " --> pdb=" O LYS G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 193 removed outlier: 4.039A pdb=" N SER G 188 " --> pdb=" O ASN G 184 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N HIS G 190 " --> pdb=" O THR G 186 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N GLN G 191 " --> pdb=" O LEU G 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 214 removed outlier: 3.717A pdb=" N ILE G 210 " --> pdb=" O ALA G 206 " (cutoff:3.500A) Processing helix chain 'G' and resid 221 through 237 removed outlier: 3.721A pdb=" N HIS G 227 " --> pdb=" O GLY G 223 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU G 228 " --> pdb=" O ASP G 224 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL G 229 " --> pdb=" O LEU G 225 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N THR G 237 " --> pdb=" O MET G 233 " (cutoff:3.500A) Processing helix chain 'G' and resid 238 through 240 No H-bonds generated for 'chain 'G' and resid 238 through 240' Processing helix chain 'G' and resid 251 through 256 Processing helix chain 'G' and resid 285 through 294 removed outlier: 3.561A pdb=" N LEU G 289 " --> pdb=" O THR G 285 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR G 290 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE G 294 " --> pdb=" O THR G 290 " (cutoff:3.500A) Processing helix chain 'G' and resid 322 through 336 removed outlier: 3.605A pdb=" N VAL G 326 " --> pdb=" O SER G 322 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLN G 334 " --> pdb=" O MET G 330 " (cutoff:3.500A) Processing helix chain 'G' and resid 374 through 390 removed outlier: 3.590A pdb=" N ILE G 381 " --> pdb=" O LEU G 377 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU G 383 " --> pdb=" O LYS G 379 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG G 390 " --> pdb=" O THR G 386 " (cutoff:3.500A) Processing helix chain 'G' and resid 395 through 400 Processing helix chain 'G' and resid 404 through 427 removed outlier: 3.852A pdb=" N PHE G 408 " --> pdb=" O ASP G 404 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA G 411 " --> pdb=" O GLU G 407 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU G 421 " --> pdb=" O ASP G 417 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN G 424 " --> pdb=" O SER G 420 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP G 427 " --> pdb=" O GLN G 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 29 removed outlier: 3.987A pdb=" N LYS D 19 " --> pdb=" O GLN D 15 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLU D 22 " --> pdb=" O ALA D 18 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP D 26 " --> pdb=" O GLU D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 49 removed outlier: 3.695A pdb=" N VAL D 49 " --> pdb=" O ARG D 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 46 through 49' Processing helix chain 'D' and resid 70 through 77 removed outlier: 3.755A pdb=" N SER D 75 " --> pdb=" O GLY D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 106 Processing helix chain 'D' and resid 112 through 125 removed outlier: 4.119A pdb=" N ASP D 118 " --> pdb=" O ASP D 114 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N VAL D 119 " --> pdb=" O SER D 115 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS D 122 " --> pdb=" O ASP D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 159 removed outlier: 3.848A pdb=" N ILE D 152 " --> pdb=" O GLY D 148 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLU D 157 " --> pdb=" O SER D 153 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU D 158 " --> pdb=" O LYS D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 193 removed outlier: 4.039A pdb=" N SER D 188 " --> pdb=" O ASN D 184 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N HIS D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N GLN D 191 " --> pdb=" O LEU D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 214 removed outlier: 3.716A pdb=" N ILE D 210 " --> pdb=" O ALA D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 237 removed outlier: 3.722A pdb=" N HIS D 227 " --> pdb=" O GLY D 223 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU D 228 " --> pdb=" O ASP D 224 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL D 229 " --> pdb=" O LEU D 225 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N THR D 237 " --> pdb=" O MET D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 240 No H-bonds generated for 'chain 'D' and resid 238 through 240' Processing helix chain 'D' and resid 251 through 256 Processing helix chain 'D' and resid 285 through 294 removed outlier: 3.561A pdb=" N LEU D 289 " --> pdb=" O THR D 285 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR D 290 " --> pdb=" O VAL D 286 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE D 294 " --> pdb=" O THR D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 336 removed outlier: 3.606A pdb=" N VAL D 326 " --> pdb=" O SER D 322 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLN D 334 " --> pdb=" O MET D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 390 removed outlier: 3.590A pdb=" N ILE D 381 " --> pdb=" O LEU D 377 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU D 383 " --> pdb=" O LYS D 379 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG D 390 " --> pdb=" O THR D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 400 Processing helix chain 'D' and resid 404 through 427 removed outlier: 3.851A pdb=" N PHE D 408 " --> pdb=" O ASP D 404 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA D 411 " --> pdb=" O GLU D 407 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU D 421 " --> pdb=" O ASP D 417 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN D 424 " --> pdb=" O SER D 420 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASP D 427 " --> pdb=" O GLN D 423 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 29 removed outlier: 3.987A pdb=" N LYS I 19 " --> pdb=" O GLN I 15 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLU I 22 " --> pdb=" O ALA I 18 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP I 26 " --> pdb=" O GLU I 22 " (cutoff:3.500A) Processing helix chain 'I' and resid 46 through 49 removed outlier: 3.695A pdb=" N VAL I 49 " --> pdb=" O ARG I 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 46 through 49' Processing helix chain 'I' and resid 70 through 77 removed outlier: 3.756A pdb=" N SER I 75 " --> pdb=" O GLY I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 101 through 106 Processing helix chain 'I' and resid 112 through 125 removed outlier: 4.119A pdb=" N ASP I 118 " --> pdb=" O ASP I 114 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N VAL I 119 " --> pdb=" O SER I 115 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS I 122 " --> pdb=" O ASP I 118 " (cutoff:3.500A) Processing helix chain 'I' and resid 145 through 159 removed outlier: 3.848A pdb=" N ILE I 152 " --> pdb=" O GLY I 148 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLU I 157 " --> pdb=" O SER I 153 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU I 158 " --> pdb=" O LYS I 154 " (cutoff:3.500A) Processing helix chain 'I' and resid 180 through 193 removed outlier: 4.039A pdb=" N SER I 188 " --> pdb=" O ASN I 184 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N HIS I 190 " --> pdb=" O THR I 186 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N GLN I 191 " --> pdb=" O LEU I 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 204 through 214 removed outlier: 3.716A pdb=" N ILE I 210 " --> pdb=" O ALA I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 221 through 237 removed outlier: 3.721A pdb=" N HIS I 227 " --> pdb=" O GLY I 223 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU I 228 " --> pdb=" O ASP I 224 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL I 229 " --> pdb=" O LEU I 225 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N THR I 237 " --> pdb=" O MET I 233 " (cutoff:3.500A) Processing helix chain 'I' and resid 238 through 240 No H-bonds generated for 'chain 'I' and resid 238 through 240' Processing helix chain 'I' and resid 251 through 256 Processing helix chain 'I' and resid 285 through 294 removed outlier: 3.561A pdb=" N LEU I 289 " --> pdb=" O THR I 285 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR I 290 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE I 294 " --> pdb=" O THR I 290 " (cutoff:3.500A) Processing helix chain 'I' and resid 322 through 336 removed outlier: 3.606A pdb=" N VAL I 326 " --> pdb=" O SER I 322 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN I 334 " --> pdb=" O MET I 330 " (cutoff:3.500A) Processing helix chain 'I' and resid 374 through 390 removed outlier: 3.591A pdb=" N ILE I 381 " --> pdb=" O LEU I 377 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU I 383 " --> pdb=" O LYS I 379 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG I 390 " --> pdb=" O THR I 386 " (cutoff:3.500A) Processing helix chain 'I' and resid 395 through 400 Processing helix chain 'I' and resid 404 through 427 removed outlier: 3.851A pdb=" N PHE I 408 " --> pdb=" O ASP I 404 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA I 411 " --> pdb=" O GLU I 407 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU I 421 " --> pdb=" O ASP I 417 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN I 424 " --> pdb=" O SER I 420 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP I 427 " --> pdb=" O GLN I 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 28 removed outlier: 3.573A pdb=" N ILE A 16 " --> pdb=" O ALA A 12 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA A 19 " --> pdb=" O GLN A 15 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU A 22 " --> pdb=" O ASN A 18 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU A 23 " --> pdb=" O ALA A 19 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N CYS A 25 " --> pdb=" O TRP A 21 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 26 " --> pdb=" O GLU A 22 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N HIS A 28 " --> pdb=" O TYR A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 51 removed outlier: 3.643A pdb=" N ASN A 50 " --> pdb=" O ASP A 47 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N THR A 51 " --> pdb=" O SER A 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 47 through 51' Processing helix chain 'A' and resid 74 through 81 removed outlier: 4.028A pdb=" N VAL A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 114 through 127 removed outlier: 3.553A pdb=" N ASP A 120 " --> pdb=" O ASP A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 161 removed outlier: 4.500A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU A 155 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER A 158 " --> pdb=" O MET A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 195 removed outlier: 3.720A pdb=" N ILE A 188 " --> pdb=" O PRO A 184 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 216 Processing helix chain 'A' and resid 223 through 239 removed outlier: 3.821A pdb=" N LEU A 230 " --> pdb=" O ASN A 226 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE A 234 " --> pdb=" O LEU A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 244 removed outlier: 3.782A pdb=" N ARG A 243 " --> pdb=" O THR A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 259 removed outlier: 3.695A pdb=" N ASN A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 292 Processing helix chain 'A' and resid 292 through 297 removed outlier: 3.681A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 336 removed outlier: 3.668A pdb=" N ASN A 329 " --> pdb=" O PRO A 325 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR A 334 " --> pdb=" O ALA A 330 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE A 335 " --> pdb=" O ALA A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 401 removed outlier: 3.924A pdb=" N LYS A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 4.110A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY A 410 " --> pdb=" O HIS A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 437 removed outlier: 3.569A pdb=" N GLU A 423 " --> pdb=" O SER A 419 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR A 432 " --> pdb=" O LEU A 428 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLU A 433 " --> pdb=" O GLU A 429 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 29 removed outlier: 3.986A pdb=" N LYS B 19 " --> pdb=" O GLN B 15 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLU B 22 " --> pdb=" O ALA B 18 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP B 26 " --> pdb=" O GLU B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 49 removed outlier: 3.694A pdb=" N VAL B 49 " --> pdb=" O ARG B 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 46 through 49' Processing helix chain 'B' and resid 70 through 77 removed outlier: 3.755A pdb=" N SER B 75 " --> pdb=" O GLY B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 106 Processing helix chain 'B' and resid 112 through 125 removed outlier: 4.119A pdb=" N ASP B 118 " --> pdb=" O ASP B 114 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N VAL B 119 " --> pdb=" O SER B 115 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS B 122 " --> pdb=" O ASP B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 159 removed outlier: 3.849A pdb=" N ILE B 152 " --> pdb=" O GLY B 148 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLU B 157 " --> pdb=" O SER B 153 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU B 158 " --> pdb=" O LYS B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 193 removed outlier: 4.039A pdb=" N SER B 188 " --> pdb=" O ASN B 184 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N HIS B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N GLN B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 214 removed outlier: 3.717A pdb=" N ILE B 210 " --> pdb=" O ALA B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.722A pdb=" N HIS B 227 " --> pdb=" O GLY B 223 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU B 228 " --> pdb=" O ASP B 224 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N THR B 237 " --> pdb=" O MET B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 240 No H-bonds generated for 'chain 'B' and resid 238 through 240' Processing helix chain 'B' and resid 251 through 256 Processing helix chain 'B' and resid 285 through 294 removed outlier: 3.561A pdb=" N LEU B 289 " --> pdb=" O THR B 285 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR B 290 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE B 294 " --> pdb=" O THR B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 336 removed outlier: 3.607A pdb=" N VAL B 326 " --> pdb=" O SER B 322 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN B 334 " --> pdb=" O MET B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 390 removed outlier: 3.590A pdb=" N ILE B 381 " --> pdb=" O LEU B 377 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU B 383 " --> pdb=" O LYS B 379 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG B 390 " --> pdb=" O THR B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 400 Processing helix chain 'B' and resid 404 through 427 removed outlier: 3.851A pdb=" N PHE B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA B 411 " --> pdb=" O GLU B 407 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU B 421 " --> pdb=" O ASP B 417 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN B 424 " --> pdb=" O SER B 420 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP B 427 " --> pdb=" O GLN B 423 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 29 removed outlier: 3.986A pdb=" N LYS H 19 " --> pdb=" O GLN H 15 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLU H 22 " --> pdb=" O ALA H 18 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP H 26 " --> pdb=" O GLU H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 49 removed outlier: 3.695A pdb=" N VAL H 49 " --> pdb=" O ARG H 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 46 through 49' Processing helix chain 'H' and resid 70 through 77 removed outlier: 3.755A pdb=" N SER H 75 " --> pdb=" O GLY H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 106 Processing helix chain 'H' and resid 112 through 125 removed outlier: 4.119A pdb=" N ASP H 118 " --> pdb=" O ASP H 114 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N VAL H 119 " --> pdb=" O SER H 115 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS H 122 " --> pdb=" O ASP H 118 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 159 removed outlier: 3.849A pdb=" N ILE H 152 " --> pdb=" O GLY H 148 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLU H 157 " --> pdb=" O SER H 153 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU H 158 " --> pdb=" O LYS H 154 " (cutoff:3.500A) Processing helix chain 'H' and resid 180 through 193 removed outlier: 4.039A pdb=" N SER H 188 " --> pdb=" O ASN H 184 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N HIS H 190 " --> pdb=" O THR H 186 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N GLN H 191 " --> pdb=" O LEU H 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 214 removed outlier: 3.717A pdb=" N ILE H 210 " --> pdb=" O ALA H 206 " (cutoff:3.500A) Processing helix chain 'H' and resid 221 through 237 removed outlier: 3.722A pdb=" N HIS H 227 " --> pdb=" O GLY H 223 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU H 228 " --> pdb=" O ASP H 224 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL H 229 " --> pdb=" O LEU H 225 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N THR H 237 " --> pdb=" O MET H 233 " (cutoff:3.500A) Processing helix chain 'H' and resid 238 through 240 No H-bonds generated for 'chain 'H' and resid 238 through 240' Processing helix chain 'H' and resid 251 through 256 Processing helix chain 'H' and resid 285 through 294 removed outlier: 3.560A pdb=" N LEU H 289 " --> pdb=" O THR H 285 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR H 290 " --> pdb=" O VAL H 286 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE H 294 " --> pdb=" O THR H 290 " (cutoff:3.500A) Processing helix chain 'H' and resid 322 through 336 removed outlier: 3.606A pdb=" N VAL H 326 " --> pdb=" O SER H 322 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLN H 334 " --> pdb=" O MET H 330 " (cutoff:3.500A) Processing helix chain 'H' and resid 374 through 390 removed outlier: 3.591A pdb=" N ILE H 381 " --> pdb=" O LEU H 377 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU H 383 " --> pdb=" O LYS H 379 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG H 390 " --> pdb=" O THR H 386 " (cutoff:3.500A) Processing helix chain 'H' and resid 395 through 400 Processing helix chain 'H' and resid 404 through 427 removed outlier: 3.850A pdb=" N PHE H 408 " --> pdb=" O ASP H 404 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA H 411 " --> pdb=" O GLU H 407 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLU H 421 " --> pdb=" O ASP H 417 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN H 424 " --> pdb=" O SER H 420 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASP H 427 " --> pdb=" O GLN H 423 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 28 removed outlier: 3.573A pdb=" N ILE E 16 " --> pdb=" O ALA E 12 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA E 19 " --> pdb=" O GLN E 15 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU E 22 " --> pdb=" O ASN E 18 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU E 23 " --> pdb=" O ALA E 19 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N CYS E 25 " --> pdb=" O TRP E 21 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU E 26 " --> pdb=" O GLU E 22 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N HIS E 28 " --> pdb=" O TYR E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 51 removed outlier: 3.643A pdb=" N ASN E 50 " --> pdb=" O ASP E 47 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N THR E 51 " --> pdb=" O SER E 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 47 through 51' Processing helix chain 'E' and resid 74 through 81 removed outlier: 4.028A pdb=" N VAL E 78 " --> pdb=" O VAL E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 108 Processing helix chain 'E' and resid 114 through 127 removed outlier: 3.553A pdb=" N ASP E 120 " --> pdb=" O ASP E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 161 removed outlier: 4.500A pdb=" N THR E 150 " --> pdb=" O GLY E 146 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU E 155 " --> pdb=" O SER E 151 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER E 158 " --> pdb=" O MET E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 195 removed outlier: 3.721A pdb=" N ILE E 188 " --> pdb=" O PRO E 184 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR E 193 " --> pdb=" O LEU E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 216 Processing helix chain 'E' and resid 223 through 239 removed outlier: 3.821A pdb=" N LEU E 230 " --> pdb=" O ASN E 226 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE E 234 " --> pdb=" O LEU E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 239 through 244 removed outlier: 3.782A pdb=" N ARG E 243 " --> pdb=" O THR E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 259 removed outlier: 3.696A pdb=" N ASN E 258 " --> pdb=" O GLU E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 292 Processing helix chain 'E' and resid 292 through 297 removed outlier: 3.680A pdb=" N PHE E 296 " --> pdb=" O THR E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 336 removed outlier: 3.667A pdb=" N ASN E 329 " --> pdb=" O PRO E 325 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR E 334 " --> pdb=" O ALA E 330 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE E 335 " --> pdb=" O ALA E 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 384 through 401 removed outlier: 3.925A pdb=" N LYS E 401 " --> pdb=" O LEU E 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 410 removed outlier: 4.110A pdb=" N TYR E 408 " --> pdb=" O PHE E 404 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY E 410 " --> pdb=" O HIS E 406 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 437 removed outlier: 3.569A pdb=" N GLU E 423 " --> pdb=" O SER E 419 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N TYR E 432 " --> pdb=" O LEU E 428 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLU E 433 " --> pdb=" O GLU E 429 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL E 437 " --> pdb=" O GLU E 433 " (cutoff:3.500A) Processing helix chain 'J' and resid 10 through 28 removed outlier: 3.572A pdb=" N ILE J 16 " --> pdb=" O ALA J 12 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA J 19 " --> pdb=" O GLN J 15 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU J 22 " --> pdb=" O ASN J 18 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU J 23 " --> pdb=" O ALA J 19 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N CYS J 25 " --> pdb=" O TRP J 21 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU J 26 " --> pdb=" O GLU J 22 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N HIS J 28 " --> pdb=" O TYR J 24 " (cutoff:3.500A) Processing helix chain 'J' and resid 47 through 51 removed outlier: 3.644A pdb=" N ASN J 50 " --> pdb=" O ASP J 47 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N THR J 51 " --> pdb=" O SER J 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 47 through 51' Processing helix chain 'J' and resid 74 through 81 removed outlier: 4.028A pdb=" N VAL J 78 " --> pdb=" O VAL J 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 102 through 108 Processing helix chain 'J' and resid 114 through 127 removed outlier: 3.554A pdb=" N ASP J 120 " --> pdb=" O ASP J 116 " (cutoff:3.500A) Processing helix chain 'J' and resid 143 through 161 removed outlier: 4.499A pdb=" N THR J 150 " --> pdb=" O GLY J 146 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU J 155 " --> pdb=" O SER J 151 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER J 158 " --> pdb=" O MET J 154 " (cutoff:3.500A) Processing helix chain 'J' and resid 182 through 195 removed outlier: 3.720A pdb=" N ILE J 188 " --> pdb=" O PRO J 184 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR J 193 " --> pdb=" O LEU J 189 " (cutoff:3.500A) Processing helix chain 'J' and resid 206 through 216 Processing helix chain 'J' and resid 223 through 239 removed outlier: 3.821A pdb=" N LEU J 230 " --> pdb=" O ASN J 226 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE J 234 " --> pdb=" O LEU J 230 " (cutoff:3.500A) Processing helix chain 'J' and resid 239 through 244 removed outlier: 3.782A pdb=" N ARG J 243 " --> pdb=" O THR J 239 " (cutoff:3.500A) Processing helix chain 'J' and resid 254 through 259 removed outlier: 3.695A pdb=" N ASN J 258 " --> pdb=" O GLU J 254 " (cutoff:3.500A) Processing helix chain 'J' and resid 287 through 292 Processing helix chain 'J' and resid 292 through 297 removed outlier: 3.682A pdb=" N PHE J 296 " --> pdb=" O THR J 292 " (cutoff:3.500A) Processing helix chain 'J' and resid 324 through 336 removed outlier: 3.667A pdb=" N ASN J 329 " --> pdb=" O PRO J 325 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR J 334 " --> pdb=" O ALA J 330 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE J 335 " --> pdb=" O ALA J 331 " (cutoff:3.500A) Processing helix chain 'J' and resid 384 through 401 removed outlier: 3.924A pdb=" N LYS J 401 " --> pdb=" O LEU J 397 " (cutoff:3.500A) Processing helix chain 'J' and resid 404 through 410 removed outlier: 4.110A pdb=" N TYR J 408 " --> pdb=" O PHE J 404 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY J 410 " --> pdb=" O HIS J 406 " (cutoff:3.500A) Processing helix chain 'J' and resid 416 through 437 removed outlier: 3.569A pdb=" N GLU J 423 " --> pdb=" O SER J 419 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N TYR J 432 " --> pdb=" O LEU J 428 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLU J 433 " --> pdb=" O GLU J 429 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL J 437 " --> pdb=" O GLU J 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 28 removed outlier: 3.572A pdb=" N ILE C 16 " --> pdb=" O ALA C 12 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA C 19 " --> pdb=" O GLN C 15 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU C 22 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU C 23 " --> pdb=" O ALA C 19 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N CYS C 25 " --> pdb=" O TRP C 21 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU C 26 " --> pdb=" O GLU C 22 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N HIS C 28 " --> pdb=" O TYR C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 51 removed outlier: 3.644A pdb=" N ASN C 50 " --> pdb=" O ASP C 47 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N THR C 51 " --> pdb=" O SER C 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 47 through 51' Processing helix chain 'C' and resid 74 through 81 removed outlier: 4.027A pdb=" N VAL C 78 " --> pdb=" O VAL C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 108 Processing helix chain 'C' and resid 114 through 127 removed outlier: 3.553A pdb=" N ASP C 120 " --> pdb=" O ASP C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 161 removed outlier: 4.500A pdb=" N THR C 150 " --> pdb=" O GLY C 146 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU C 155 " --> pdb=" O SER C 151 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER C 158 " --> pdb=" O MET C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 195 removed outlier: 3.721A pdb=" N ILE C 188 " --> pdb=" O PRO C 184 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THR C 193 " --> pdb=" O LEU C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 216 Processing helix chain 'C' and resid 223 through 239 removed outlier: 3.821A pdb=" N LEU C 230 " --> pdb=" O ASN C 226 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE C 234 " --> pdb=" O LEU C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 244 removed outlier: 3.782A pdb=" N ARG C 243 " --> pdb=" O THR C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 259 removed outlier: 3.695A pdb=" N ASN C 258 " --> pdb=" O GLU C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 292 Processing helix chain 'C' and resid 292 through 297 removed outlier: 3.681A pdb=" N PHE C 296 " --> pdb=" O THR C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 336 removed outlier: 3.667A pdb=" N ASN C 329 " --> pdb=" O PRO C 325 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR C 334 " --> pdb=" O ALA C 330 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE C 335 " --> pdb=" O ALA C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 401 removed outlier: 3.924A pdb=" N LYS C 401 " --> pdb=" O LEU C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 removed outlier: 4.110A pdb=" N TYR C 408 " --> pdb=" O PHE C 404 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY C 410 " --> pdb=" O HIS C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 437 removed outlier: 3.570A pdb=" N GLU C 423 " --> pdb=" O SER C 419 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N TYR C 432 " --> pdb=" O LEU C 428 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLU C 433 " --> pdb=" O GLU C 429 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL C 437 " --> pdb=" O GLU C 433 " (cutoff:3.500A) Processing helix chain 'L' and resid 10 through 28 removed outlier: 3.573A pdb=" N ILE L 16 " --> pdb=" O ALA L 12 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA L 19 " --> pdb=" O GLN L 15 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU L 22 " --> pdb=" O ASN L 18 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU L 23 " --> pdb=" O ALA L 19 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N CYS L 25 " --> pdb=" O TRP L 21 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU L 26 " --> pdb=" O GLU L 22 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N HIS L 28 " --> pdb=" O TYR L 24 " (cutoff:3.500A) Processing helix chain 'L' and resid 47 through 51 removed outlier: 3.644A pdb=" N ASN L 50 " --> pdb=" O ASP L 47 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N THR L 51 " --> pdb=" O SER L 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 47 through 51' Processing helix chain 'L' and resid 74 through 81 removed outlier: 4.028A pdb=" N VAL L 78 " --> pdb=" O VAL L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 102 through 108 Processing helix chain 'L' and resid 114 through 127 removed outlier: 3.554A pdb=" N ASP L 120 " --> pdb=" O ASP L 116 " (cutoff:3.500A) Processing helix chain 'L' and resid 143 through 161 removed outlier: 4.501A pdb=" N THR L 150 " --> pdb=" O GLY L 146 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU L 155 " --> pdb=" O SER L 151 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER L 158 " --> pdb=" O MET L 154 " (cutoff:3.500A) Processing helix chain 'L' and resid 182 through 195 removed outlier: 3.721A pdb=" N ILE L 188 " --> pdb=" O PRO L 184 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR L 193 " --> pdb=" O LEU L 189 " (cutoff:3.500A) Processing helix chain 'L' and resid 206 through 216 Processing helix chain 'L' and resid 223 through 239 removed outlier: 3.822A pdb=" N LEU L 230 " --> pdb=" O ASN L 226 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE L 234 " --> pdb=" O LEU L 230 " (cutoff:3.500A) Processing helix chain 'L' and resid 239 through 244 removed outlier: 3.782A pdb=" N ARG L 243 " --> pdb=" O THR L 239 " (cutoff:3.500A) Processing helix chain 'L' and resid 254 through 259 removed outlier: 3.695A pdb=" N ASN L 258 " --> pdb=" O GLU L 254 " (cutoff:3.500A) Processing helix chain 'L' and resid 287 through 292 Processing helix chain 'L' and resid 292 through 297 removed outlier: 3.680A pdb=" N PHE L 296 " --> pdb=" O THR L 292 " (cutoff:3.500A) Processing helix chain 'L' and resid 324 through 336 removed outlier: 3.668A pdb=" N ASN L 329 " --> pdb=" O PRO L 325 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR L 334 " --> pdb=" O ALA L 330 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE L 335 " --> pdb=" O ALA L 331 " (cutoff:3.500A) Processing helix chain 'L' and resid 384 through 401 removed outlier: 3.925A pdb=" N LYS L 401 " --> pdb=" O LEU L 397 " (cutoff:3.500A) Processing helix chain 'L' and resid 404 through 410 removed outlier: 4.110A pdb=" N TYR L 408 " --> pdb=" O PHE L 404 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY L 410 " --> pdb=" O HIS L 406 " (cutoff:3.500A) Processing helix chain 'L' and resid 416 through 437 removed outlier: 3.569A pdb=" N GLU L 423 " --> pdb=" O SER L 419 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR L 432 " --> pdb=" O LEU L 428 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLU L 433 " --> pdb=" O GLU L 429 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL L 437 " --> pdb=" O GLU L 433 " (cutoff:3.500A) Processing helix chain 'K' and resid 10 through 28 removed outlier: 3.572A pdb=" N ILE K 16 " --> pdb=" O ALA K 12 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA K 19 " --> pdb=" O GLN K 15 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU K 22 " --> pdb=" O ASN K 18 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU K 23 " --> pdb=" O ALA K 19 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N CYS K 25 " --> pdb=" O TRP K 21 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU K 26 " --> pdb=" O GLU K 22 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N HIS K 28 " --> pdb=" O TYR K 24 " (cutoff:3.500A) Processing helix chain 'K' and resid 47 through 51 removed outlier: 3.643A pdb=" N ASN K 50 " --> pdb=" O ASP K 47 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N THR K 51 " --> pdb=" O SER K 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 47 through 51' Processing helix chain 'K' and resid 74 through 81 removed outlier: 4.028A pdb=" N VAL K 78 " --> pdb=" O VAL K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 102 through 108 Processing helix chain 'K' and resid 114 through 127 removed outlier: 3.553A pdb=" N ASP K 120 " --> pdb=" O ASP K 116 " (cutoff:3.500A) Processing helix chain 'K' and resid 143 through 161 removed outlier: 4.499A pdb=" N THR K 150 " --> pdb=" O GLY K 146 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU K 155 " --> pdb=" O SER K 151 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER K 158 " --> pdb=" O MET K 154 " (cutoff:3.500A) Processing helix chain 'K' and resid 182 through 195 removed outlier: 3.721A pdb=" N ILE K 188 " --> pdb=" O PRO K 184 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR K 193 " --> pdb=" O LEU K 189 " (cutoff:3.500A) Processing helix chain 'K' and resid 206 through 216 Processing helix chain 'K' and resid 223 through 239 removed outlier: 3.821A pdb=" N LEU K 230 " --> pdb=" O ASN K 226 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE K 234 " --> pdb=" O LEU K 230 " (cutoff:3.500A) Processing helix chain 'K' and resid 239 through 244 removed outlier: 3.782A pdb=" N ARG K 243 " --> pdb=" O THR K 239 " (cutoff:3.500A) Processing helix chain 'K' and resid 254 through 259 removed outlier: 3.695A pdb=" N ASN K 258 " --> pdb=" O GLU K 254 " (cutoff:3.500A) Processing helix chain 'K' and resid 287 through 292 Processing helix chain 'K' and resid 292 through 297 removed outlier: 3.680A pdb=" N PHE K 296 " --> pdb=" O THR K 292 " (cutoff:3.500A) Processing helix chain 'K' and resid 324 through 336 removed outlier: 3.667A pdb=" N ASN K 329 " --> pdb=" O PRO K 325 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR K 334 " --> pdb=" O ALA K 330 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE K 335 " --> pdb=" O ALA K 331 " (cutoff:3.500A) Processing helix chain 'K' and resid 384 through 401 removed outlier: 3.925A pdb=" N LYS K 401 " --> pdb=" O LEU K 397 " (cutoff:3.500A) Processing helix chain 'K' and resid 404 through 410 removed outlier: 4.110A pdb=" N TYR K 408 " --> pdb=" O PHE K 404 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY K 410 " --> pdb=" O HIS K 406 " (cutoff:3.500A) Processing helix chain 'K' and resid 416 through 437 removed outlier: 3.569A pdb=" N GLU K 423 " --> pdb=" O SER K 419 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N TYR K 432 " --> pdb=" O LEU K 428 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLU K 433 " --> pdb=" O GLU K 429 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL K 437 " --> pdb=" O GLU K 433 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 90 through 92 removed outlier: 8.104A pdb=" N VAL F 91 " --> pdb=" O ALA F 63 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N LEU F 65 " --> pdb=" O VAL F 91 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLU F 3 " --> pdb=" O GLN F 131 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N PHE F 133 " --> pdb=" O GLU F 3 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N VAL F 5 " --> pdb=" O PHE F 133 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N LEU F 135 " --> pdb=" O VAL F 5 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE F 7 " --> pdb=" O LEU F 135 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N GLN F 131 " --> pdb=" O ILE F 163 " (cutoff:3.500A) removed outlier: 8.938A pdb=" N ASN F 165 " --> pdb=" O GLN F 131 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N PHE F 133 " --> pdb=" O ASN F 165 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N PHE F 167 " --> pdb=" O PHE F 133 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N LEU F 135 " --> pdb=" O PHE F 167 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N VAL F 169 " --> pdb=" O LEU F 135 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N MET F 164 " --> pdb=" O GLU F 198 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N TYR F 200 " --> pdb=" O MET F 164 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N THR F 166 " --> pdb=" O TYR F 200 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N ILE F 202 " --> pdb=" O THR F 166 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N SER F 168 " --> pdb=" O ILE F 202 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N THR F 199 " --> pdb=" O PHE F 266 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N CYS F 201 " --> pdb=" O PRO F 268 " (cutoff:3.500A) removed outlier: 10.690A pdb=" N PHE F 270 " --> pdb=" O CYS F 201 " (cutoff:3.500A) removed outlier: 13.851A pdb=" N ASP F 203 " --> pdb=" O PHE F 270 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA F 271 " --> pdb=" O ALA F 365 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL F 313 " --> pdb=" O LYS F 350 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N ALA F 352 " --> pdb=" O VAL F 313 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ALA F 315 " --> pdb=" O ALA F 352 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 51 through 53 Processing sheet with id=AA3, first strand: chain 'G' and resid 90 through 92 removed outlier: 8.104A pdb=" N VAL G 91 " --> pdb=" O ALA G 63 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N LEU G 65 " --> pdb=" O VAL G 91 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLU G 3 " --> pdb=" O GLN G 131 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N PHE G 133 " --> pdb=" O GLU G 3 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N VAL G 5 " --> pdb=" O PHE G 133 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N LEU G 135 " --> pdb=" O VAL G 5 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE G 7 " --> pdb=" O LEU G 135 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N GLN G 131 " --> pdb=" O ILE G 163 " (cutoff:3.500A) removed outlier: 8.937A pdb=" N ASN G 165 " --> pdb=" O GLN G 131 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N PHE G 133 " --> pdb=" O ASN G 165 " (cutoff:3.500A) removed outlier: 8.659A pdb=" N PHE G 167 " --> pdb=" O PHE G 133 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N LEU G 135 " --> pdb=" O PHE G 167 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N VAL G 169 " --> pdb=" O LEU G 135 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N MET G 164 " --> pdb=" O GLU G 198 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N TYR G 200 " --> pdb=" O MET G 164 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N THR G 166 " --> pdb=" O TYR G 200 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N ILE G 202 " --> pdb=" O THR G 166 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N SER G 168 " --> pdb=" O ILE G 202 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N THR G 199 " --> pdb=" O PHE G 266 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N CYS G 201 " --> pdb=" O PRO G 268 " (cutoff:3.500A) removed outlier: 10.689A pdb=" N PHE G 270 " --> pdb=" O CYS G 201 " (cutoff:3.500A) removed outlier: 13.851A pdb=" N ASP G 203 " --> pdb=" O PHE G 270 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA G 271 " --> pdb=" O ALA G 365 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL G 313 " --> pdb=" O LYS G 350 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N ALA G 352 " --> pdb=" O VAL G 313 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ALA G 315 " --> pdb=" O ALA G 352 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 51 through 53 Processing sheet with id=AA5, first strand: chain 'D' and resid 90 through 92 removed outlier: 8.104A pdb=" N VAL D 91 " --> pdb=" O ALA D 63 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LEU D 65 " --> pdb=" O VAL D 91 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLU D 3 " --> pdb=" O GLN D 131 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N PHE D 133 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N VAL D 5 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N LEU D 135 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE D 7 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N GLN D 131 " --> pdb=" O ILE D 163 " (cutoff:3.500A) removed outlier: 8.938A pdb=" N ASN D 165 " --> pdb=" O GLN D 131 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N PHE D 133 " --> pdb=" O ASN D 165 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N PHE D 167 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N LEU D 135 " --> pdb=" O PHE D 167 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N VAL D 169 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N MET D 164 " --> pdb=" O GLU D 198 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N TYR D 200 " --> pdb=" O MET D 164 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N THR D 166 " --> pdb=" O TYR D 200 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N ILE D 202 " --> pdb=" O THR D 166 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N SER D 168 " --> pdb=" O ILE D 202 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N THR D 199 " --> pdb=" O PHE D 266 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N CYS D 201 " --> pdb=" O PRO D 268 " (cutoff:3.500A) removed outlier: 10.689A pdb=" N PHE D 270 " --> pdb=" O CYS D 201 " (cutoff:3.500A) removed outlier: 13.852A pdb=" N ASP D 203 " --> pdb=" O PHE D 270 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA D 271 " --> pdb=" O ALA D 365 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL D 313 " --> pdb=" O LYS D 350 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N ALA D 352 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ALA D 315 " --> pdb=" O ALA D 352 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 51 through 53 Processing sheet with id=AA7, first strand: chain 'I' and resid 90 through 92 removed outlier: 8.104A pdb=" N VAL I 91 " --> pdb=" O ALA I 63 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N LEU I 65 " --> pdb=" O VAL I 91 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N GLU I 3 " --> pdb=" O GLN I 131 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N PHE I 133 " --> pdb=" O GLU I 3 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N VAL I 5 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N LEU I 135 " --> pdb=" O VAL I 5 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE I 7 " --> pdb=" O LEU I 135 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N GLN I 131 " --> pdb=" O ILE I 163 " (cutoff:3.500A) removed outlier: 8.938A pdb=" N ASN I 165 " --> pdb=" O GLN I 131 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N PHE I 133 " --> pdb=" O ASN I 165 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N PHE I 167 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N LEU I 135 " --> pdb=" O PHE I 167 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N VAL I 169 " --> pdb=" O LEU I 135 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N MET I 164 " --> pdb=" O GLU I 198 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N TYR I 200 " --> pdb=" O MET I 164 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N THR I 166 " --> pdb=" O TYR I 200 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N ILE I 202 " --> pdb=" O THR I 166 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N SER I 168 " --> pdb=" O ILE I 202 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N THR I 199 " --> pdb=" O PHE I 266 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N CYS I 201 " --> pdb=" O PRO I 268 " (cutoff:3.500A) removed outlier: 10.690A pdb=" N PHE I 270 " --> pdb=" O CYS I 201 " (cutoff:3.500A) removed outlier: 13.851A pdb=" N ASP I 203 " --> pdb=" O PHE I 270 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA I 271 " --> pdb=" O ALA I 365 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL I 313 " --> pdb=" O LYS I 350 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N ALA I 352 " --> pdb=" O VAL I 313 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ALA I 315 " --> pdb=" O ALA I 352 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 51 through 53 Processing sheet with id=AA9, first strand: chain 'A' and resid 65 through 68 removed outlier: 7.054A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LYS A 166 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N PHE A 202 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N GLU A 168 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N VAL A 204 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N SER A 170 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 53 through 55 removed outlier: 3.796A pdb=" N VAL A 62 " --> pdb=" O SER A 54 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 246 through 248 Processing sheet with id=AB3, first strand: chain 'B' and resid 90 through 92 removed outlier: 8.104A pdb=" N VAL B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N LEU B 65 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLU B 3 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N PHE B 133 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N VAL B 5 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N LEU B 135 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE B 7 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N GLN B 131 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 8.939A pdb=" N ASN B 165 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N PHE B 133 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 8.659A pdb=" N PHE B 167 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N LEU B 135 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N VAL B 169 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N MET B 164 " --> pdb=" O GLU B 198 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N TYR B 200 " --> pdb=" O MET B 164 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N THR B 166 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N ILE B 202 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N SER B 168 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N THR B 199 " --> pdb=" O PHE B 266 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N CYS B 201 " --> pdb=" O PRO B 268 " (cutoff:3.500A) removed outlier: 10.689A pdb=" N PHE B 270 " --> pdb=" O CYS B 201 " (cutoff:3.500A) removed outlier: 13.851A pdb=" N ASP B 203 " --> pdb=" O PHE B 270 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA B 271 " --> pdb=" O ALA B 365 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL B 313 " --> pdb=" O LYS B 350 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N ALA B 352 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ALA B 315 " --> pdb=" O ALA B 352 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 51 through 53 Processing sheet with id=AB5, first strand: chain 'H' and resid 90 through 92 removed outlier: 8.103A pdb=" N VAL H 91 " --> pdb=" O ALA H 63 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N LEU H 65 " --> pdb=" O VAL H 91 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLU H 3 " --> pdb=" O GLN H 131 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N PHE H 133 " --> pdb=" O GLU H 3 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N VAL H 5 " --> pdb=" O PHE H 133 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N LEU H 135 " --> pdb=" O VAL H 5 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE H 7 " --> pdb=" O LEU H 135 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N GLN H 131 " --> pdb=" O ILE H 163 " (cutoff:3.500A) removed outlier: 8.938A pdb=" N ASN H 165 " --> pdb=" O GLN H 131 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N PHE H 133 " --> pdb=" O ASN H 165 " (cutoff:3.500A) removed outlier: 8.659A pdb=" N PHE H 167 " --> pdb=" O PHE H 133 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N LEU H 135 " --> pdb=" O PHE H 167 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N VAL H 169 " --> pdb=" O LEU H 135 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N MET H 164 " --> pdb=" O GLU H 198 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N TYR H 200 " --> pdb=" O MET H 164 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N THR H 166 " --> pdb=" O TYR H 200 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N ILE H 202 " --> pdb=" O THR H 166 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N SER H 168 " --> pdb=" O ILE H 202 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N THR H 199 " --> pdb=" O PHE H 266 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N CYS H 201 " --> pdb=" O PRO H 268 " (cutoff:3.500A) removed outlier: 10.690A pdb=" N PHE H 270 " --> pdb=" O CYS H 201 " (cutoff:3.500A) removed outlier: 13.851A pdb=" N ASP H 203 " --> pdb=" O PHE H 270 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA H 271 " --> pdb=" O ALA H 365 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL H 313 " --> pdb=" O LYS H 350 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N ALA H 352 " --> pdb=" O VAL H 313 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ALA H 315 " --> pdb=" O ALA H 352 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 51 through 53 Processing sheet with id=AB7, first strand: chain 'E' and resid 65 through 68 removed outlier: 7.054A pdb=" N SER E 6 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N VAL E 68 " --> pdb=" O SER E 6 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N HIS E 8 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LYS E 166 " --> pdb=" O CYS E 200 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N PHE E 202 " --> pdb=" O LYS E 166 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N GLU E 168 " --> pdb=" O PHE E 202 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N VAL E 204 " --> pdb=" O GLU E 168 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N SER E 170 " --> pdb=" O VAL E 204 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 53 through 55 removed outlier: 3.797A pdb=" N VAL E 62 " --> pdb=" O SER E 54 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 246 through 248 Processing sheet with id=AC1, first strand: chain 'J' and resid 65 through 68 removed outlier: 7.053A pdb=" N SER J 6 " --> pdb=" O VAL J 66 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N VAL J 68 " --> pdb=" O SER J 6 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N HIS J 8 " --> pdb=" O VAL J 68 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LYS J 166 " --> pdb=" O CYS J 200 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N PHE J 202 " --> pdb=" O LYS J 166 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N GLU J 168 " --> pdb=" O PHE J 202 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N VAL J 204 " --> pdb=" O GLU J 168 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N SER J 170 " --> pdb=" O VAL J 204 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 53 through 55 removed outlier: 3.797A pdb=" N VAL J 62 " --> pdb=" O SER J 54 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 246 through 248 Processing sheet with id=AC4, first strand: chain 'C' and resid 65 through 68 removed outlier: 7.054A pdb=" N SER C 6 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N VAL C 68 " --> pdb=" O SER C 6 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N HIS C 8 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LYS C 166 " --> pdb=" O CYS C 200 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N PHE C 202 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N GLU C 168 " --> pdb=" O PHE C 202 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N VAL C 204 " --> pdb=" O GLU C 168 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N SER C 170 " --> pdb=" O VAL C 204 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 53 through 55 removed outlier: 3.796A pdb=" N VAL C 62 " --> pdb=" O SER C 54 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 246 through 248 Processing sheet with id=AC7, first strand: chain 'L' and resid 65 through 68 removed outlier: 7.054A pdb=" N SER L 6 " --> pdb=" O VAL L 66 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N VAL L 68 " --> pdb=" O SER L 6 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N HIS L 8 " --> pdb=" O VAL L 68 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LYS L 166 " --> pdb=" O CYS L 200 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N PHE L 202 " --> pdb=" O LYS L 166 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N GLU L 168 " --> pdb=" O PHE L 202 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N VAL L 204 " --> pdb=" O GLU L 168 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N SER L 170 " --> pdb=" O VAL L 204 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 53 through 55 removed outlier: 3.796A pdb=" N VAL L 62 " --> pdb=" O SER L 54 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 246 through 248 Processing sheet with id=AD1, first strand: chain 'K' and resid 65 through 68 removed outlier: 7.053A pdb=" N SER K 6 " --> pdb=" O VAL K 66 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N VAL K 68 " --> pdb=" O SER K 6 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N HIS K 8 " --> pdb=" O VAL K 68 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LYS K 166 " --> pdb=" O CYS K 200 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N PHE K 202 " --> pdb=" O LYS K 166 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N GLU K 168 " --> pdb=" O PHE K 202 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N VAL K 204 " --> pdb=" O GLU K 168 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N SER K 170 " --> pdb=" O VAL K 204 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 53 through 55 removed outlier: 3.796A pdb=" N VAL K 62 " --> pdb=" O SER K 54 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 246 through 248 1440 hydrogen bonds defined for protein. 4284 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: 9.05 Time building geometry restraints manager: 4.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 13505 1.34 - 1.46: 6233 1.46 - 1.57: 21578 1.57 - 1.69: 48 1.69 - 1.80: 432 Bond restraints: 41796 Sorted by residual: bond pdb=" C5 GDP B 501 " pdb=" C4 GDP B 501 " ideal model delta sigma weight residual 1.490 1.375 0.115 2.00e-02 2.50e+03 3.30e+01 bond pdb=" C5 GDP F 501 " pdb=" C4 GDP F 501 " ideal model delta sigma weight residual 1.490 1.375 0.115 2.00e-02 2.50e+03 3.29e+01 bond pdb=" C5 GDP G 501 " pdb=" C4 GDP G 501 " ideal model delta sigma weight residual 1.490 1.376 0.114 2.00e-02 2.50e+03 3.27e+01 bond pdb=" C5 GDP H 501 " pdb=" C4 GDP H 501 " ideal model delta sigma weight residual 1.490 1.376 0.114 2.00e-02 2.50e+03 3.25e+01 bond pdb=" C5 GDP I 501 " pdb=" C4 GDP I 501 " ideal model delta sigma weight residual 1.490 1.376 0.114 2.00e-02 2.50e+03 3.24e+01 ... (remaining 41791 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 55442 2.32 - 4.64: 1112 4.64 - 6.96: 122 6.96 - 9.28: 87 9.28 - 11.61: 21 Bond angle restraints: 56784 Sorted by residual: angle pdb=" N ILE H 84 " pdb=" CA ILE H 84 " pdb=" C ILE H 84 " ideal model delta sigma weight residual 113.42 108.69 4.73 1.17e+00 7.31e-01 1.63e+01 angle pdb=" N ILE D 84 " pdb=" CA ILE D 84 " pdb=" C ILE D 84 " ideal model delta sigma weight residual 113.42 108.70 4.72 1.17e+00 7.31e-01 1.63e+01 angle pdb=" N ILE I 84 " pdb=" CA ILE I 84 " pdb=" C ILE I 84 " ideal model delta sigma weight residual 113.42 108.71 4.71 1.17e+00 7.31e-01 1.62e+01 angle pdb=" N ILE F 84 " pdb=" CA ILE F 84 " pdb=" C ILE F 84 " ideal model delta sigma weight residual 113.42 108.74 4.68 1.17e+00 7.31e-01 1.60e+01 angle pdb=" N ILE B 84 " pdb=" CA ILE B 84 " pdb=" C ILE B 84 " ideal model delta sigma weight residual 113.42 108.74 4.68 1.17e+00 7.31e-01 1.60e+01 ... (remaining 56779 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.55: 24574 32.55 - 65.09: 219 65.09 - 97.64: 25 97.64 - 130.18: 17 130.18 - 162.73: 17 Dihedral angle restraints: 24852 sinusoidal: 9924 harmonic: 14928 Sorted by residual: dihedral pdb=" C8 GTP E 501 " pdb=" C1' GTP E 501 " pdb=" N9 GTP E 501 " pdb=" O4' GTP E 501 " ideal model delta sinusoidal sigma weight residual 104.59 -58.14 162.73 1 2.00e+01 2.50e-03 4.69e+01 dihedral pdb=" C8 GTP J 501 " pdb=" C1' GTP J 501 " pdb=" N9 GTP J 501 " pdb=" O4' GTP J 501 " ideal model delta sinusoidal sigma weight residual 104.59 -57.05 161.65 1 2.00e+01 2.50e-03 4.68e+01 dihedral pdb=" C8 GTP L 501 " pdb=" C1' GTP L 501 " pdb=" N9 GTP L 501 " pdb=" O4' GTP L 501 " ideal model delta sinusoidal sigma weight residual 104.59 -56.30 160.89 1 2.00e+01 2.50e-03 4.67e+01 ... (remaining 24849 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 4235 0.045 - 0.089: 1441 0.089 - 0.134: 462 0.134 - 0.178: 48 0.178 - 0.223: 30 Chirality restraints: 6216 Sorted by residual: chirality pdb=" C2' GTP K 501 " pdb=" C1' GTP K 501 " pdb=" C3' GTP K 501 " pdb=" O2' GTP K 501 " both_signs ideal model delta sigma weight residual False -2.47 -2.69 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" C2' GTP A 501 " pdb=" C1' GTP A 501 " pdb=" C3' GTP A 501 " pdb=" O2' GTP A 501 " both_signs ideal model delta sigma weight residual False -2.47 -2.69 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" C2' GTP C 501 " pdb=" C1' GTP C 501 " pdb=" C3' GTP C 501 " pdb=" O2' GTP C 501 " both_signs ideal model delta sigma weight residual False -2.47 -2.69 0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 6213 not shown) Planarity restraints: 7398 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' GDP H 501 " 0.060 2.00e-02 2.50e+03 2.51e-02 1.90e+01 pdb=" N9 GDP H 501 " -0.011 2.00e-02 2.50e+03 pdb=" C8 GDP H 501 " -0.007 2.00e-02 2.50e+03 pdb=" N7 GDP H 501 " -0.015 2.00e-02 2.50e+03 pdb=" C5 GDP H 501 " -0.021 2.00e-02 2.50e+03 pdb=" C6 GDP H 501 " 0.009 2.00e-02 2.50e+03 pdb=" O6 GDP H 501 " 0.028 2.00e-02 2.50e+03 pdb=" N1 GDP H 501 " 0.021 2.00e-02 2.50e+03 pdb=" C2 GDP H 501 " -0.000 2.00e-02 2.50e+03 pdb=" N2 GDP H 501 " -0.004 2.00e-02 2.50e+03 pdb=" N3 GDP H 501 " -0.028 2.00e-02 2.50e+03 pdb=" C4 GDP H 501 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GDP I 501 " -0.054 2.00e-02 2.50e+03 2.29e-02 1.57e+01 pdb=" N9 GDP I 501 " 0.009 2.00e-02 2.50e+03 pdb=" C8 GDP I 501 " 0.009 2.00e-02 2.50e+03 pdb=" N7 GDP I 501 " 0.015 2.00e-02 2.50e+03 pdb=" C5 GDP I 501 " 0.019 2.00e-02 2.50e+03 pdb=" C6 GDP I 501 " -0.010 2.00e-02 2.50e+03 pdb=" O6 GDP I 501 " -0.023 2.00e-02 2.50e+03 pdb=" N1 GDP I 501 " -0.024 2.00e-02 2.50e+03 pdb=" C2 GDP I 501 " -0.002 2.00e-02 2.50e+03 pdb=" N2 GDP I 501 " 0.010 2.00e-02 2.50e+03 pdb=" N3 GDP I 501 " 0.023 2.00e-02 2.50e+03 pdb=" C4 GDP I 501 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GDP B 501 " 0.053 2.00e-02 2.50e+03 2.20e-02 1.45e+01 pdb=" N9 GDP B 501 " -0.010 2.00e-02 2.50e+03 pdb=" C8 GDP B 501 " -0.011 2.00e-02 2.50e+03 pdb=" N7 GDP B 501 " -0.015 2.00e-02 2.50e+03 pdb=" C5 GDP B 501 " -0.017 2.00e-02 2.50e+03 pdb=" C6 GDP B 501 " 0.010 2.00e-02 2.50e+03 pdb=" O6 GDP B 501 " 0.025 2.00e-02 2.50e+03 pdb=" N1 GDP B 501 " 0.020 2.00e-02 2.50e+03 pdb=" C2 GDP B 501 " 0.001 2.00e-02 2.50e+03 pdb=" N2 GDP B 501 " -0.009 2.00e-02 2.50e+03 pdb=" N3 GDP B 501 " -0.021 2.00e-02 2.50e+03 pdb=" C4 GDP B 501 " -0.025 2.00e-02 2.50e+03 ... (remaining 7395 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 420 2.65 - 3.21: 35314 3.21 - 3.78: 59256 3.78 - 4.34: 86796 4.34 - 4.90: 142232 Nonbonded interactions: 324018 Sorted by model distance: nonbonded pdb=" O2G GTP C 501 " pdb="MG MG C 502 " model vdw 2.091 2.170 nonbonded pdb=" O2G GTP L 501 " pdb="MG MG L 502 " model vdw 2.094 2.170 nonbonded pdb=" O2G GTP E 501 " pdb="MG MG E 502 " model vdw 2.097 2.170 nonbonded pdb=" O2G GTP J 501 " pdb="MG MG J 502 " model vdw 2.100 2.170 nonbonded pdb=" O2G GTP A 501 " pdb="MG MG A 502 " model vdw 2.101 2.170 ... (remaining 324013 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: 0.14 Found NCS groups: ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'D' selection = chain 'I' selection = chain 'B' selection = chain 'H' } ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'J' selection = chain 'C' selection = chain 'L' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.570 Check model and map are aligned: 0.140 Set scattering table: 0.120 Process input model: 38.660 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 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 : 0.006 0.115 41796 Z= 0.256 Angle : 0.919 11.606 56784 Z= 0.512 Chirality : 0.050 0.223 6216 Planarity : 0.007 0.055 7398 Dihedral : 11.513 162.731 15276 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % 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: -5.24 (0.09), residues: 5130 helix: -4.67 (0.04), residues: 2208 sheet: -1.45 (0.18), residues: 846 loop : -2.72 (0.11), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 390 TYR 0.026 0.002 TYR C 210 PHE 0.018 0.002 PHE J 138 TRP 0.017 0.003 TRP F 101 HIS 0.013 0.002 HIS E 28 Details of bonding type rmsd covalent geometry : bond 0.00556 (41796) covalent geometry : angle 0.91911 (56784) hydrogen bonds : bond 0.32719 ( 1440) hydrogen bonds : angle 10.41760 ( 4284) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1339 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1339 time to evaluate : 1.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 3 GLU cc_start: 0.7652 (mp0) cc_final: 0.7439 (mp0) REVERT: F 74 ASP cc_start: 0.7659 (t70) cc_final: 0.7077 (t0) REVERT: F 86 ARG cc_start: 0.7915 (mtp180) cc_final: 0.6826 (mmp-170) REVERT: F 129 CYS cc_start: 0.8275 (t) cc_final: 0.7607 (t) REVERT: F 225 LEU cc_start: 0.8775 (mp) cc_final: 0.8356 (mp) REVERT: F 253 LEU cc_start: 0.8667 (mt) cc_final: 0.8395 (mt) REVERT: F 351 THR cc_start: 0.9264 (m) cc_final: 0.8916 (p) REVERT: G 74 ASP cc_start: 0.7736 (t70) cc_final: 0.7142 (t0) REVERT: G 86 ARG cc_start: 0.7949 (mtp180) cc_final: 0.6943 (mmp-170) REVERT: G 213 ARG cc_start: 0.7451 (ttm110) cc_final: 0.7190 (ttm170) REVERT: G 224 ASP cc_start: 0.8059 (m-30) cc_final: 0.7812 (m-30) REVERT: G 225 LEU cc_start: 0.8648 (mp) cc_final: 0.8258 (mp) REVERT: G 253 LEU cc_start: 0.8725 (mt) cc_final: 0.8481 (mt) REVERT: G 404 ASP cc_start: 0.7709 (p0) cc_final: 0.7507 (p0) REVERT: D 74 ASP cc_start: 0.7720 (t70) cc_final: 0.7237 (t0) REVERT: D 103 LYS cc_start: 0.8794 (mttt) cc_final: 0.8510 (mtmt) REVERT: D 167 PHE cc_start: 0.8792 (m-80) cc_final: 0.8220 (m-10) REVERT: D 178 THR cc_start: 0.8845 (m) cc_final: 0.8589 (m) REVERT: D 407 GLU cc_start: 0.8482 (tp30) cc_final: 0.8217 (mm-30) REVERT: I 74 ASP cc_start: 0.7785 (t70) cc_final: 0.7319 (t0) REVERT: I 103 LYS cc_start: 0.8968 (mttt) cc_final: 0.8710 (mtmt) REVERT: I 125 GLU cc_start: 0.7481 (mm-30) cc_final: 0.7092 (mm-30) REVERT: I 164 MET cc_start: 0.8127 (tpt) cc_final: 0.7691 (tpt) REVERT: A 24 TYR cc_start: 0.8984 (m-80) cc_final: 0.8735 (m-10) REVERT: A 193 THR cc_start: 0.9172 (m) cc_final: 0.8847 (p) REVERT: A 235 VAL cc_start: 0.9284 (t) cc_final: 0.9042 (t) REVERT: A 302 MET cc_start: 0.7882 (mtt) cc_final: 0.7623 (mtt) REVERT: A 319 TYR cc_start: 0.9186 (m-80) cc_final: 0.8909 (m-80) REVERT: A 327 ASP cc_start: 0.8161 (m-30) cc_final: 0.7925 (m-30) REVERT: A 351 PHE cc_start: 0.8873 (m-80) cc_final: 0.8657 (m-80) REVERT: A 370 LYS cc_start: 0.8984 (tttp) cc_final: 0.8624 (tptt) REVERT: A 393 HIS cc_start: 0.8071 (t70) cc_final: 0.7693 (t70) REVERT: B 3 GLU cc_start: 0.7634 (mp0) cc_final: 0.7236 (mp0) REVERT: B 74 ASP cc_start: 0.7433 (t70) cc_final: 0.7194 (t0) REVERT: B 129 CYS cc_start: 0.8645 (t) cc_final: 0.8206 (t) REVERT: B 178 THR cc_start: 0.9121 (m) cc_final: 0.8802 (m) REVERT: B 246 LEU cc_start: 0.9019 (tp) cc_final: 0.8792 (tt) REVERT: B 274 THR cc_start: 0.9278 (p) cc_final: 0.9057 (p) REVERT: B 332 ASN cc_start: 0.8340 (t0) cc_final: 0.7617 (t0) REVERT: B 340 TYR cc_start: 0.7823 (m-80) cc_final: 0.7609 (m-10) REVERT: B 379 LYS cc_start: 0.8527 (mtpt) cc_final: 0.8125 (tttm) REVERT: H 3 GLU cc_start: 0.8076 (mp0) cc_final: 0.7561 (mp0) REVERT: H 7 ILE cc_start: 0.9089 (mt) cc_final: 0.8631 (tt) REVERT: H 37 HIS cc_start: 0.6926 (m90) cc_final: 0.6714 (m170) REVERT: H 74 ASP cc_start: 0.7602 (t70) cc_final: 0.7222 (t0) REVERT: H 213 ARG cc_start: 0.7695 (ttm110) cc_final: 0.7241 (mtp-110) REVERT: H 379 LYS cc_start: 0.8406 (mtpt) cc_final: 0.7999 (tttm) REVERT: E 24 TYR cc_start: 0.8822 (m-80) cc_final: 0.8476 (m-10) REVERT: E 93 ILE cc_start: 0.9225 (mt) cc_final: 0.8991 (mm) REVERT: E 154 MET cc_start: 0.8430 (mmm) cc_final: 0.8209 (mmt) REVERT: E 156 ARG cc_start: 0.7931 (mmt90) cc_final: 0.7360 (mmt180) REVERT: E 170 SER cc_start: 0.9232 (m) cc_final: 0.8940 (p) REVERT: E 221 ARG cc_start: 0.7444 (mtt90) cc_final: 0.7158 (mtm-85) REVERT: E 271 THR cc_start: 0.9041 (m) cc_final: 0.8835 (p) REVERT: E 319 TYR cc_start: 0.8973 (m-80) cc_final: 0.8369 (m-10) REVERT: E 377 MET cc_start: 0.8524 (ttp) cc_final: 0.8201 (ttt) REVERT: E 420 GLU cc_start: 0.7900 (tt0) cc_final: 0.7473 (tp30) REVERT: J 24 TYR cc_start: 0.8771 (m-80) cc_final: 0.8339 (m-10) REVERT: J 170 SER cc_start: 0.9262 (m) cc_final: 0.8980 (p) REVERT: J 254 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7203 (mm-30) REVERT: J 271 THR cc_start: 0.8816 (m) cc_final: 0.8535 (p) REVERT: J 297 GLU cc_start: 0.8709 (tt0) cc_final: 0.8489 (tt0) REVERT: J 393 HIS cc_start: 0.8495 (t70) cc_final: 0.8263 (t-90) REVERT: C 2 ARG cc_start: 0.7718 (mpp80) cc_final: 0.7515 (mtm180) REVERT: C 91 GLN cc_start: 0.8371 (mt0) cc_final: 0.7898 (mt0) REVERT: C 117 LEU cc_start: 0.8973 (tp) cc_final: 0.8751 (tt) REVERT: C 203 MET cc_start: 0.8670 (mmp) cc_final: 0.8454 (mmm) REVERT: C 230 LEU cc_start: 0.9003 (mp) cc_final: 0.8513 (tt) REVERT: C 327 ASP cc_start: 0.8269 (m-30) cc_final: 0.8042 (m-30) REVERT: C 415 GLU cc_start: 0.7486 (tm-30) cc_final: 0.7198 (tp30) REVERT: C 425 MET cc_start: 0.8481 (tpp) cc_final: 0.8210 (tpp) REVERT: L 91 GLN cc_start: 0.8310 (mt0) cc_final: 0.7901 (mt0) REVERT: L 103 TYR cc_start: 0.8727 (t80) cc_final: 0.8281 (t80) REVERT: L 161 TYR cc_start: 0.8112 (m-80) cc_final: 0.7803 (m-80) REVERT: L 172 TYR cc_start: 0.8020 (t80) cc_final: 0.7488 (t80) REVERT: L 203 MET cc_start: 0.8570 (mmp) cc_final: 0.7827 (mmt) REVERT: L 254 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7534 (mm-30) REVERT: L 271 THR cc_start: 0.8764 (m) cc_final: 0.7810 (m) REVERT: L 304 LYS cc_start: 0.8567 (tppt) cc_final: 0.8333 (tppp) REVERT: L 393 HIS cc_start: 0.8310 (t70) cc_final: 0.7804 (t70) REVERT: K 103 TYR cc_start: 0.8369 (t80) cc_final: 0.8135 (t80) REVERT: K 216 ASN cc_start: 0.8846 (m110) cc_final: 0.8639 (t0) outliers start: 0 outliers final: 0 residues processed: 1339 average time/residue: 0.2596 time to fit residues: 554.9064 Evaluate side-chains 727 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 727 time to evaluate : 1.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 432 optimal weight: 9.9990 chunk 197 optimal weight: 7.9990 chunk 388 optimal weight: 10.0000 chunk 455 optimal weight: 9.9990 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 10.0000 chunk 494 optimal weight: 9.9990 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 0.0870 chunk 207 optimal weight: 9.9990 overall best weight: 5.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 8 GLN F 137 HIS F 190 HIS F 204 ASN F 226 ASN F 335 ASN F 396 HIS G 8 GLN G 37 HIS G 137 HIS ** G 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 335 ASN G 396 HIS G 423 GLN D 8 GLN D 11 GLN D 137 HIS ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 ASN D 307 HIS D 396 HIS I 8 GLN I 137 HIS ** I 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 226 ASN I 307 HIS I 396 HIS A 28 HIS A 61 HIS A 88 HIS A 107 HIS ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 ASN A 192 HIS A 266 HIS A 283 HIS B 8 GLN ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 HIS B 190 HIS B 226 ASN ** B 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 GLN B 396 HIS B 423 GLN ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 HIS H 190 HIS H 204 ASN H 226 ASN ** H 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 307 HIS H 396 HIS H 423 GLN E 28 HIS E 61 HIS E 88 HIS E 107 HIS E 139 HIS E 192 HIS E 197 HIS E 206 ASN E 258 ASN E 266 HIS E 283 HIS J 28 HIS J 61 HIS J 88 HIS J 107 HIS J 139 HIS J 192 HIS J 197 HIS J 206 ASN J 258 ASN J 266 HIS J 283 HIS C 28 HIS C 61 HIS C 88 HIS C 133 GLN ** C 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 ASN C 192 HIS C 206 ASN C 266 HIS L 28 HIS L 50 ASN L 61 HIS L 88 HIS L 107 HIS L 133 GLN L 139 HIS L 192 HIS L 206 ASN L 258 ASN L 266 HIS L 301 GLN K 28 HIS K 61 HIS K 88 HIS K 107 HIS ** K 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 186 ASN K 192 HIS K 206 ASN K 258 ASN K 283 HIS Total number of N/Q/H flips: 97 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.098422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.086356 restraints weight = 65145.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.089051 restraints weight = 35299.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.090943 restraints weight = 22424.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.092261 restraints weight = 15713.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.093252 restraints weight = 11818.846| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 41796 Z= 0.186 Angle : 0.614 8.130 56784 Z= 0.321 Chirality : 0.046 0.161 6216 Planarity : 0.005 0.075 7398 Dihedral : 11.712 151.678 5760 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.87 % Allowed : 9.68 % Favored : 88.46 % 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: -3.38 (0.10), residues: 5130 helix: -2.61 (0.08), residues: 2160 sheet: -1.18 (0.18), residues: 846 loop : -2.10 (0.12), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 282 TYR 0.022 0.002 TYR L 24 PHE 0.014 0.001 PHE A 296 TRP 0.014 0.002 TRP D 21 HIS 0.008 0.001 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00427 (41796) covalent geometry : angle 0.61447 (56784) hydrogen bonds : bond 0.05007 ( 1440) hydrogen bonds : angle 5.34677 ( 4284) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 896 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 814 time to evaluate : 1.600 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 74 ASP cc_start: 0.7532 (t70) cc_final: 0.7016 (t0) REVERT: F 150 LEU cc_start: 0.9203 (tp) cc_final: 0.8894 (tp) REVERT: F 203 ASP cc_start: 0.7118 (m-30) cc_final: 0.6601 (m-30) REVERT: F 323 MET cc_start: 0.8255 (tpp) cc_final: 0.8049 (mmm) REVERT: G 74 ASP cc_start: 0.7655 (t70) cc_final: 0.7096 (t0) REVERT: G 224 ASP cc_start: 0.8024 (m-30) cc_final: 0.7818 (m-30) REVERT: D 74 ASP cc_start: 0.7401 (t70) cc_final: 0.6970 (t0) REVERT: D 103 LYS cc_start: 0.8946 (mttt) cc_final: 0.8605 (mtmt) REVERT: D 167 PHE cc_start: 0.8768 (m-80) cc_final: 0.7992 (m-80) REVERT: I 69 GLU cc_start: 0.7658 (pm20) cc_final: 0.7362 (pm20) REVERT: I 74 ASP cc_start: 0.7682 (t70) cc_final: 0.7298 (t0) REVERT: I 103 LYS cc_start: 0.9086 (mttt) cc_final: 0.8800 (mtmt) REVERT: I 125 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7564 (mm-30) REVERT: I 150 LEU cc_start: 0.9217 (tp) cc_final: 0.8925 (tt) REVERT: I 178 THR cc_start: 0.8713 (m) cc_final: 0.8510 (p) REVERT: I 257 MET cc_start: 0.8766 (mmm) cc_final: 0.8426 (mmm) REVERT: A 154 MET cc_start: 0.8220 (mmt) cc_final: 0.7878 (mmt) REVERT: A 279 GLU cc_start: 0.8479 (tp30) cc_final: 0.8141 (tp30) REVERT: A 351 PHE cc_start: 0.9092 (m-80) cc_final: 0.8813 (m-80) REVERT: B 69 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7352 (pt0) REVERT: B 213 ARG cc_start: 0.7952 (mtp-110) cc_final: 0.7665 (mtm110) REVERT: B 274 THR cc_start: 0.9073 (p) cc_final: 0.8854 (p) REVERT: B 332 ASN cc_start: 0.8255 (t0) cc_final: 0.7850 (t0) REVERT: B 379 LYS cc_start: 0.8509 (mtpt) cc_final: 0.8189 (tttm) REVERT: H 74 ASP cc_start: 0.7465 (t70) cc_final: 0.7093 (t0) REVERT: H 330 MET cc_start: 0.7908 (mmm) cc_final: 0.7664 (mmm) REVERT: H 379 LYS cc_start: 0.8544 (mtpt) cc_final: 0.8068 (tttm) REVERT: H 407 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7744 (mt-10) REVERT: E 24 TYR cc_start: 0.8783 (m-80) cc_final: 0.8381 (m-10) REVERT: E 79 ARG cc_start: 0.9046 (OUTLIER) cc_final: 0.8759 (mtt180) REVERT: E 124 LYS cc_start: 0.8767 (ttmm) cc_final: 0.8275 (ttmt) REVERT: E 170 SER cc_start: 0.9383 (m) cc_final: 0.9068 (p) REVERT: E 269 LEU cc_start: 0.8796 (pp) cc_final: 0.8221 (pp) REVERT: E 271 THR cc_start: 0.9033 (m) cc_final: 0.8215 (p) REVERT: E 319 TYR cc_start: 0.9094 (m-80) cc_final: 0.8400 (m-80) REVERT: E 422 ARG cc_start: 0.8118 (tpt90) cc_final: 0.7830 (tpt-90) REVERT: J 254 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7294 (mm-30) REVERT: J 271 THR cc_start: 0.8996 (m) cc_final: 0.8304 (p) REVERT: J 422 ARG cc_start: 0.8282 (tpt90) cc_final: 0.7944 (tpt-90) REVERT: C 91 GLN cc_start: 0.8407 (mt0) cc_final: 0.7891 (mt0) REVERT: C 123 ARG cc_start: 0.8104 (tpp80) cc_final: 0.7855 (tpp80) REVERT: C 127 ASP cc_start: 0.8195 (m-30) cc_final: 0.7823 (m-30) REVERT: C 319 TYR cc_start: 0.9054 (m-80) cc_final: 0.8804 (m-80) REVERT: C 433 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7668 (tp30) REVERT: L 91 GLN cc_start: 0.8475 (mt0) cc_final: 0.8071 (mt0) REVERT: L 154 MET cc_start: 0.8480 (mmm) cc_final: 0.8178 (mmm) REVERT: L 172 TYR cc_start: 0.7957 (t80) cc_final: 0.7495 (t80) REVERT: L 203 MET cc_start: 0.8759 (mmp) cc_final: 0.7990 (mmt) REVERT: L 254 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7583 (tp30) REVERT: L 319 TYR cc_start: 0.8962 (m-80) cc_final: 0.8705 (m-10) REVERT: L 429 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8302 (tt0) REVERT: K 194 THR cc_start: 0.8631 (p) cc_final: 0.8394 (m) REVERT: K 254 GLU cc_start: 0.5999 (tp30) cc_final: 0.5730 (mm-30) outliers start: 82 outliers final: 47 residues processed: 867 average time/residue: 0.2408 time to fit residues: 342.5414 Evaluate side-chains 690 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 640 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain F residue 381 ILE Chi-restraints excluded: chain G residue 157 GLU Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain I residue 225 LEU Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain H residue 374 ILE Chi-restraints excluded: chain H residue 419 VAL Chi-restraints excluded: chain E residue 4 CYS Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 79 ARG Chi-restraints excluded: chain E residue 151 SER Chi-restraints excluded: chain E residue 284 GLU Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain J residue 36 MET Chi-restraints excluded: chain J residue 207 GLU Chi-restraints excluded: chain J residue 284 GLU Chi-restraints excluded: chain J residue 285 GLN Chi-restraints excluded: chain J residue 288 VAL Chi-restraints excluded: chain J residue 324 VAL Chi-restraints excluded: chain J residue 362 VAL Chi-restraints excluded: chain J residue 367 ASP Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 133 GLN Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain L residue 5 ILE Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 133 GLN Chi-restraints excluded: chain L residue 288 VAL Chi-restraints excluded: chain L residue 324 VAL Chi-restraints excluded: chain L residue 362 VAL Chi-restraints excluded: chain L residue 381 THR Chi-restraints excluded: chain L residue 429 GLU Chi-restraints excluded: chain K residue 4 CYS Chi-restraints excluded: chain K residue 195 LEU Chi-restraints excluded: chain K residue 284 GLU Chi-restraints excluded: chain K residue 324 VAL Chi-restraints excluded: chain K residue 345 ASP Chi-restraints excluded: chain K residue 419 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 79 optimal weight: 9.9990 chunk 463 optimal weight: 10.0000 chunk 273 optimal weight: 5.9990 chunk 69 optimal weight: 10.0000 chunk 476 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 419 optimal weight: 4.9990 chunk 396 optimal weight: 7.9990 chunk 345 optimal weight: 2.9990 chunk 103 optimal weight: 20.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 37 HIS F 190 HIS F 334 GLN ** G 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 226 ASN G 375 GLN D 99 ASN ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 347 ASN D 423 GLN ** I 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 423 GLN ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 ASN ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 307 HIS ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 HIS C 107 HIS C 133 GLN ** C 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.100476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.086550 restraints weight = 65524.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.089588 restraints weight = 35674.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.091702 restraints weight = 23005.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.093179 restraints weight = 16437.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.094256 restraints weight = 12631.402| |-----------------------------------------------------------------------------| r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 41796 Z= 0.145 Angle : 0.549 7.469 56784 Z= 0.281 Chirality : 0.045 0.151 6216 Planarity : 0.004 0.070 7398 Dihedral : 11.107 147.269 5760 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.25 % Allowed : 11.79 % Favored : 85.95 % 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: -2.21 (0.11), residues: 5130 helix: -1.26 (0.10), residues: 2172 sheet: -0.91 (0.18), residues: 846 loop : -1.77 (0.12), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 123 TYR 0.026 0.001 TYR J 24 PHE 0.022 0.001 PHE F 167 TRP 0.012 0.001 TRP H 21 HIS 0.009 0.001 HIS F 190 Details of bonding type rmsd covalent geometry : bond 0.00336 (41796) covalent geometry : angle 0.54940 (56784) hydrogen bonds : bond 0.03948 ( 1440) hydrogen bonds : angle 4.72841 ( 4284) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 819 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 720 time to evaluate : 1.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 150 LEU cc_start: 0.9054 (tp) cc_final: 0.8701 (tp) REVERT: F 203 ASP cc_start: 0.6823 (m-30) cc_final: 0.6512 (m-30) REVERT: F 230 SER cc_start: 0.9280 (p) cc_final: 0.8975 (t) REVERT: F 292 GLN cc_start: 0.8654 (tt0) cc_final: 0.8202 (tt0) REVERT: G 74 ASP cc_start: 0.7803 (t70) cc_final: 0.7257 (t0) REVERT: G 292 GLN cc_start: 0.8066 (tt0) cc_final: 0.7627 (tt0) REVERT: G 332 ASN cc_start: 0.7828 (t0) cc_final: 0.7487 (t0) REVERT: G 375 GLN cc_start: 0.7769 (OUTLIER) cc_final: 0.7523 (tt0) REVERT: G 379 LYS cc_start: 0.8642 (mtmt) cc_final: 0.8364 (mtpt) REVERT: D 74 ASP cc_start: 0.7432 (t70) cc_final: 0.7072 (t0) REVERT: D 103 LYS cc_start: 0.9010 (mttt) cc_final: 0.8634 (mtmt) REVERT: D 257 MET cc_start: 0.8857 (mmm) cc_final: 0.8220 (mmm) REVERT: I 69 GLU cc_start: 0.7705 (pm20) cc_final: 0.7219 (pm20) REVERT: I 74 ASP cc_start: 0.7682 (t70) cc_final: 0.7267 (t0) REVERT: I 103 LYS cc_start: 0.9106 (mttt) cc_final: 0.8746 (mtmt) REVERT: I 125 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7564 (mm-30) REVERT: I 257 MET cc_start: 0.8821 (mmm) cc_final: 0.8343 (mmm) REVERT: I 330 MET cc_start: 0.8628 (mmp) cc_final: 0.8235 (mmm) REVERT: I 336 LYS cc_start: 0.8312 (mttt) cc_final: 0.8091 (mttt) REVERT: A 154 MET cc_start: 0.8261 (mmt) cc_final: 0.7963 (mmt) REVERT: A 279 GLU cc_start: 0.8570 (tp30) cc_final: 0.8198 (tp30) REVERT: A 351 PHE cc_start: 0.9122 (m-80) cc_final: 0.8765 (m-80) REVERT: B 233 MET cc_start: 0.7906 (mtm) cc_final: 0.7633 (ttp) REVERT: B 322 SER cc_start: 0.9229 (p) cc_final: 0.8889 (t) REVERT: B 332 ASN cc_start: 0.8314 (t0) cc_final: 0.7855 (t0) REVERT: B 364 SER cc_start: 0.9414 (t) cc_final: 0.9064 (m) REVERT: B 379 LYS cc_start: 0.8608 (mtpt) cc_final: 0.8147 (tttm) REVERT: H 74 ASP cc_start: 0.7457 (t70) cc_final: 0.7175 (t0) REVERT: H 300 MET cc_start: 0.8552 (mtt) cc_final: 0.8340 (mtt) REVERT: H 332 ASN cc_start: 0.8023 (t0) cc_final: 0.7674 (t0) REVERT: H 407 GLU cc_start: 0.8276 (mm-30) cc_final: 0.7609 (mt-10) REVERT: E 24 TYR cc_start: 0.8768 (m-80) cc_final: 0.8356 (m-10) REVERT: E 154 MET cc_start: 0.8520 (mmm) cc_final: 0.8073 (mmt) REVERT: E 170 SER cc_start: 0.9376 (m) cc_final: 0.9055 (p) REVERT: E 319 TYR cc_start: 0.9148 (m-80) cc_final: 0.8420 (m-80) REVERT: E 377 MET cc_start: 0.8369 (ttt) cc_final: 0.8108 (tmm) REVERT: E 422 ARG cc_start: 0.8196 (tpt90) cc_final: 0.7867 (tpt-90) REVERT: E 430 LYS cc_start: 0.8826 (mmtp) cc_final: 0.8408 (tttt) REVERT: J 254 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7270 (mm-30) REVERT: J 319 TYR cc_start: 0.9014 (m-80) cc_final: 0.8761 (m-10) REVERT: J 327 ASP cc_start: 0.8374 (m-30) cc_final: 0.7977 (m-30) REVERT: J 422 ARG cc_start: 0.8234 (tpt90) cc_final: 0.7896 (tpt170) REVERT: C 80 THR cc_start: 0.8967 (m) cc_final: 0.8648 (t) REVERT: C 91 GLN cc_start: 0.8585 (mt0) cc_final: 0.8163 (mt0) REVERT: C 245 ASP cc_start: 0.7862 (p0) cc_final: 0.7566 (p0) REVERT: C 433 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7792 (tp30) REVERT: L 91 GLN cc_start: 0.8494 (mt0) cc_final: 0.8113 (mt0) REVERT: L 154 MET cc_start: 0.8603 (mmm) cc_final: 0.8247 (mmm) REVERT: L 172 TYR cc_start: 0.8117 (t80) cc_final: 0.7561 (t80) REVERT: L 203 MET cc_start: 0.8743 (mmp) cc_final: 0.7992 (mmt) REVERT: L 207 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7095 (tm-30) REVERT: L 254 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7746 (tp30) REVERT: L 429 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8280 (tt0) REVERT: L 430 LYS cc_start: 0.8785 (mmtp) cc_final: 0.8575 (ttpt) outliers start: 99 outliers final: 67 residues processed: 788 average time/residue: 0.2359 time to fit residues: 306.1978 Evaluate side-chains 700 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 630 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain G residue 157 GLU Chi-restraints excluded: chain G residue 375 GLN Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain I residue 198 GLU Chi-restraints excluded: chain I residue 225 LEU Chi-restraints excluded: chain I residue 239 CYS Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 368 ILE Chi-restraints excluded: chain I residue 374 ILE Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 239 CYS Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain H residue 219 THR Chi-restraints excluded: chain H residue 239 CYS Chi-restraints excluded: chain H residue 374 ILE Chi-restraints excluded: chain H residue 375 GLN Chi-restraints excluded: chain H residue 419 VAL Chi-restraints excluded: chain E residue 4 CYS Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 85 GLN Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain J residue 36 MET Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 194 THR Chi-restraints excluded: chain J residue 207 GLU Chi-restraints excluded: chain J residue 284 GLU Chi-restraints excluded: chain J residue 285 GLN Chi-restraints excluded: chain J residue 288 VAL Chi-restraints excluded: chain J residue 324 VAL Chi-restraints excluded: chain J residue 367 ASP Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain L residue 5 ILE Chi-restraints excluded: chain L residue 207 GLU Chi-restraints excluded: chain L residue 288 VAL Chi-restraints excluded: chain L residue 324 VAL Chi-restraints excluded: chain L residue 362 VAL Chi-restraints excluded: chain L residue 381 THR Chi-restraints excluded: chain L residue 429 GLU Chi-restraints excluded: chain K residue 4 CYS Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 133 GLN Chi-restraints excluded: chain K residue 160 ASP Chi-restraints excluded: chain K residue 163 LYS Chi-restraints excluded: chain K residue 218 ASP Chi-restraints excluded: chain K residue 324 VAL Chi-restraints excluded: chain K residue 345 ASP Chi-restraints excluded: chain K residue 419 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 177 optimal weight: 20.0000 chunk 273 optimal weight: 6.9990 chunk 39 optimal weight: 9.9990 chunk 355 optimal weight: 7.9990 chunk 226 optimal weight: 6.9990 chunk 165 optimal weight: 9.9990 chunk 229 optimal weight: 6.9990 chunk 497 optimal weight: 5.9990 chunk 360 optimal weight: 10.0000 chunk 368 optimal weight: 9.9990 chunk 452 optimal weight: 3.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 57 ASN G 83 GLN ** G 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 204 ASN ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 ASN I 190 HIS ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 301 GLN B 37 HIS ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 HIS ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 ASN J 186 ASN J 301 GLN C 31 GLN C 139 HIS C 301 GLN L 186 ASN ** K 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 266 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.092796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.080836 restraints weight = 66701.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.083338 restraints weight = 37405.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.085071 restraints weight = 24475.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.086413 restraints weight = 17686.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.087328 restraints weight = 13545.168| |-----------------------------------------------------------------------------| r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.3890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 41796 Z= 0.209 Angle : 0.588 7.224 56784 Z= 0.301 Chirality : 0.047 0.166 6216 Planarity : 0.004 0.065 7398 Dihedral : 10.933 147.475 5760 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.78 % Allowed : 12.50 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.11), residues: 5130 helix: -0.75 (0.11), residues: 2208 sheet: -0.83 (0.18), residues: 846 loop : -1.59 (0.13), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 282 TYR 0.021 0.002 TYR L 24 PHE 0.023 0.002 PHE F 167 TRP 0.012 0.002 TRP D 21 HIS 0.005 0.001 HIS H 28 Details of bonding type rmsd covalent geometry : bond 0.00492 (41796) covalent geometry : angle 0.58758 (56784) hydrogen bonds : bond 0.04045 ( 1440) hydrogen bonds : angle 4.69511 ( 4284) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 790 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 668 time to evaluate : 1.636 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 150 LEU cc_start: 0.9290 (tp) cc_final: 0.8985 (tp) REVERT: F 178 THR cc_start: 0.9223 (m) cc_final: 0.8798 (p) REVERT: F 203 ASP cc_start: 0.6746 (m-30) cc_final: 0.6424 (m-30) REVERT: F 292 GLN cc_start: 0.8659 (tt0) cc_final: 0.8312 (tt0) REVERT: F 332 ASN cc_start: 0.7827 (t0) cc_final: 0.7626 (t0) REVERT: G 26 ASP cc_start: 0.8141 (t0) cc_final: 0.7893 (t0) REVERT: G 74 ASP cc_start: 0.7574 (t70) cc_final: 0.7078 (t0) REVERT: G 147 MET cc_start: 0.8190 (ttm) cc_final: 0.7824 (ttm) REVERT: G 178 THR cc_start: 0.9224 (m) cc_final: 0.8953 (p) REVERT: G 292 GLN cc_start: 0.8105 (tt0) cc_final: 0.7736 (tt0) REVERT: G 379 LYS cc_start: 0.8682 (mtmt) cc_final: 0.8466 (mtmm) REVERT: D 74 ASP cc_start: 0.7231 (t70) cc_final: 0.6906 (t0) REVERT: D 103 LYS cc_start: 0.9066 (mttt) cc_final: 0.8778 (mtmt) REVERT: I 69 GLU cc_start: 0.7863 (pm20) cc_final: 0.7335 (pm20) REVERT: I 74 ASP cc_start: 0.7379 (t70) cc_final: 0.7036 (t0) REVERT: I 103 LYS cc_start: 0.9078 (mttt) cc_final: 0.8830 (mtmt) REVERT: I 257 MET cc_start: 0.8700 (mmm) cc_final: 0.8150 (mmm) REVERT: I 336 LYS cc_start: 0.8379 (mttt) cc_final: 0.8143 (mtmt) REVERT: A 124 LYS cc_start: 0.9008 (ttmm) cc_final: 0.8624 (ttpt) REVERT: A 207 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7512 (tm-30) REVERT: A 279 GLU cc_start: 0.8566 (tp30) cc_final: 0.8152 (tp30) REVERT: A 351 PHE cc_start: 0.8967 (m-80) cc_final: 0.8565 (m-80) REVERT: B 69 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7526 (pt0) REVERT: B 233 MET cc_start: 0.7986 (mtm) cc_final: 0.7690 (ttp) REVERT: B 332 ASN cc_start: 0.8425 (t0) cc_final: 0.8032 (t0) REVERT: B 379 LYS cc_start: 0.8735 (mtpt) cc_final: 0.8320 (tttm) REVERT: H 74 ASP cc_start: 0.7315 (t70) cc_final: 0.7068 (t0) REVERT: H 379 LYS cc_start: 0.8606 (mtpt) cc_final: 0.8132 (tttm) REVERT: E 24 TYR cc_start: 0.8834 (m-80) cc_final: 0.8441 (m-10) REVERT: E 79 ARG cc_start: 0.9116 (OUTLIER) cc_final: 0.8825 (mtt180) REVERT: E 154 MET cc_start: 0.8478 (mmm) cc_final: 0.7804 (mmt) REVERT: E 170 SER cc_start: 0.9369 (m) cc_final: 0.8943 (p) REVERT: E 207 GLU cc_start: 0.7609 (tm-30) cc_final: 0.7366 (tm-30) REVERT: E 319 TYR cc_start: 0.9085 (m-80) cc_final: 0.8316 (m-80) REVERT: E 422 ARG cc_start: 0.8401 (tpt90) cc_final: 0.8185 (tpt-90) REVERT: E 429 GLU cc_start: 0.8725 (tp30) cc_final: 0.8418 (tt0) REVERT: J 154 MET cc_start: 0.8562 (mmt) cc_final: 0.8315 (mmt) REVERT: J 254 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7606 (tp30) REVERT: J 271 THR cc_start: 0.9044 (m) cc_final: 0.8763 (p) REVERT: J 319 TYR cc_start: 0.9048 (m-80) cc_final: 0.8799 (m-10) REVERT: J 327 ASP cc_start: 0.8272 (m-30) cc_final: 0.7846 (m-30) REVERT: C 80 THR cc_start: 0.8917 (m) cc_final: 0.8646 (t) REVERT: C 91 GLN cc_start: 0.8478 (mt0) cc_final: 0.8076 (mt0) REVERT: C 433 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7570 (tp30) REVERT: L 80 THR cc_start: 0.9018 (m) cc_final: 0.8679 (t) REVERT: L 91 GLN cc_start: 0.8420 (mt0) cc_final: 0.8028 (mt0) REVERT: L 154 MET cc_start: 0.8639 (mmm) cc_final: 0.8287 (mmm) REVERT: L 172 TYR cc_start: 0.8131 (t80) cc_final: 0.7448 (t80) REVERT: L 203 MET cc_start: 0.8890 (mmp) cc_final: 0.7921 (mmt) REVERT: L 207 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7069 (tm-30) REVERT: L 254 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7692 (tp30) REVERT: L 353 VAL cc_start: 0.9439 (t) cc_final: 0.9190 (m) REVERT: L 430 LYS cc_start: 0.8866 (mmtp) cc_final: 0.8663 (ttpt) REVERT: L 433 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7781 (mm-30) REVERT: K 296 PHE cc_start: 0.8860 (m-80) cc_final: 0.8596 (m-10) REVERT: K 433 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7604 (tp30) outliers start: 122 outliers final: 86 residues processed: 751 average time/residue: 0.2369 time to fit residues: 294.0641 Evaluate side-chains 710 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 620 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain F residue 381 ILE Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 164 MET Chi-restraints excluded: chain G residue 326 VAL Chi-restraints excluded: chain D residue 239 CYS Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain I residue 26 ASP Chi-restraints excluded: chain I residue 127 CYS Chi-restraints excluded: chain I residue 198 GLU Chi-restraints excluded: chain I residue 205 GLU Chi-restraints excluded: chain I residue 225 LEU Chi-restraints excluded: chain I residue 239 CYS Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 368 ILE Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 239 CYS Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain H residue 219 THR Chi-restraints excluded: chain H residue 239 CYS Chi-restraints excluded: chain H residue 326 VAL Chi-restraints excluded: chain H residue 374 ILE Chi-restraints excluded: chain H residue 375 GLN Chi-restraints excluded: chain H residue 419 VAL Chi-restraints excluded: chain E residue 4 CYS Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 79 ARG Chi-restraints excluded: chain E residue 85 GLN Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain J residue 36 MET Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 194 THR Chi-restraints excluded: chain J residue 207 GLU Chi-restraints excluded: chain J residue 284 GLU Chi-restraints excluded: chain J residue 285 GLN Chi-restraints excluded: chain J residue 288 VAL Chi-restraints excluded: chain J residue 324 VAL Chi-restraints excluded: chain J residue 362 VAL Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain L residue 5 ILE Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 151 SER Chi-restraints excluded: chain L residue 207 GLU Chi-restraints excluded: chain L residue 288 VAL Chi-restraints excluded: chain L residue 324 VAL Chi-restraints excluded: chain L residue 362 VAL Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 381 THR Chi-restraints excluded: chain K residue 4 CYS Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 151 SER Chi-restraints excluded: chain K residue 160 ASP Chi-restraints excluded: chain K residue 218 ASP Chi-restraints excluded: chain K residue 324 VAL Chi-restraints excluded: chain K residue 345 ASP Chi-restraints excluded: chain K residue 353 VAL Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 419 SER Chi-restraints excluded: chain K residue 428 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 445 optimal weight: 6.9990 chunk 477 optimal weight: 5.9990 chunk 318 optimal weight: 2.9990 chunk 432 optimal weight: 10.0000 chunk 383 optimal weight: 6.9990 chunk 14 optimal weight: 20.0000 chunk 476 optimal weight: 10.0000 chunk 290 optimal weight: 6.9990 chunk 400 optimal weight: 6.9990 chunk 466 optimal weight: 0.9990 chunk 152 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 335 ASN D 57 ASN ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.094369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.083192 restraints weight = 65578.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.085620 restraints weight = 36985.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.087328 restraints weight = 24165.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.088546 restraints weight = 17322.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.089445 restraints weight = 13198.778| |-----------------------------------------------------------------------------| r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.4140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 41796 Z= 0.157 Angle : 0.540 7.592 56784 Z= 0.274 Chirality : 0.045 0.142 6216 Planarity : 0.004 0.060 7398 Dihedral : 10.682 146.452 5760 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.87 % Allowed : 13.16 % Favored : 83.97 % 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: -1.41 (0.11), residues: 5130 helix: -0.40 (0.11), residues: 2220 sheet: -0.70 (0.18), residues: 846 loop : -1.51 (0.13), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 282 TYR 0.018 0.001 TYR L 24 PHE 0.020 0.001 PHE F 167 TRP 0.010 0.001 TRP C 21 HIS 0.004 0.001 HIS G 37 Details of bonding type rmsd covalent geometry : bond 0.00366 (41796) covalent geometry : angle 0.53973 (56784) hydrogen bonds : bond 0.03498 ( 1440) hydrogen bonds : angle 4.47210 ( 4284) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 795 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 669 time to evaluate : 1.507 Fit side-chains revert: symmetry clash REVERT: F 46 ARG cc_start: 0.8784 (mmt-90) cc_final: 0.8523 (mmp80) REVERT: F 150 LEU cc_start: 0.9211 (tp) cc_final: 0.8920 (tp) REVERT: F 292 GLN cc_start: 0.8607 (tt0) cc_final: 0.8027 (tt0) REVERT: F 335 ASN cc_start: 0.8418 (m-40) cc_final: 0.8068 (m-40) REVERT: G 26 ASP cc_start: 0.8224 (t0) cc_final: 0.7965 (t0) REVERT: G 74 ASP cc_start: 0.7510 (t70) cc_final: 0.7037 (t0) REVERT: G 147 MET cc_start: 0.8154 (ttm) cc_final: 0.7784 (ttm) REVERT: G 178 THR cc_start: 0.9214 (m) cc_final: 0.8916 (p) REVERT: G 292 GLN cc_start: 0.7867 (tt0) cc_final: 0.7666 (tt0) REVERT: G 332 ASN cc_start: 0.8000 (t0) cc_final: 0.7692 (t0) REVERT: G 335 ASN cc_start: 0.8351 (m-40) cc_final: 0.8060 (m-40) REVERT: D 74 ASP cc_start: 0.7154 (t70) cc_final: 0.6837 (t0) REVERT: D 103 LYS cc_start: 0.9032 (mttt) cc_final: 0.8751 (mtmt) REVERT: D 167 PHE cc_start: 0.8735 (m-80) cc_final: 0.7907 (m-80) REVERT: D 257 MET cc_start: 0.8636 (mmm) cc_final: 0.7978 (mmm) REVERT: D 374 ILE cc_start: 0.8819 (OUTLIER) cc_final: 0.8619 (pp) REVERT: I 69 GLU cc_start: 0.8005 (pm20) cc_final: 0.7508 (pm20) REVERT: I 74 ASP cc_start: 0.7303 (t70) cc_final: 0.6951 (t0) REVERT: I 103 LYS cc_start: 0.9056 (mttt) cc_final: 0.8813 (mtmt) REVERT: I 257 MET cc_start: 0.8680 (mmm) cc_final: 0.8204 (mmm) REVERT: A 80 THR cc_start: 0.8685 (m) cc_final: 0.8469 (t) REVERT: A 154 MET cc_start: 0.8371 (mmt) cc_final: 0.7945 (mmt) REVERT: A 279 GLU cc_start: 0.8580 (tp30) cc_final: 0.8132 (tp30) REVERT: A 351 PHE cc_start: 0.8911 (m-80) cc_final: 0.8517 (m-80) REVERT: A 431 ASP cc_start: 0.7312 (m-30) cc_final: 0.7040 (m-30) REVERT: B 164 MET cc_start: 0.8118 (tpp) cc_final: 0.7770 (ttm) REVERT: B 233 MET cc_start: 0.7922 (mtm) cc_final: 0.7612 (ttp) REVERT: B 332 ASN cc_start: 0.8425 (t0) cc_final: 0.8042 (t0) REVERT: H 323 MET cc_start: 0.8376 (mmm) cc_final: 0.8079 (mmm) REVERT: H 330 MET cc_start: 0.8674 (mmm) cc_final: 0.7888 (mmm) REVERT: E 154 MET cc_start: 0.8536 (mmm) cc_final: 0.7788 (mmt) REVERT: E 170 SER cc_start: 0.9313 (m) cc_final: 0.9079 (t) REVERT: E 319 TYR cc_start: 0.9062 (m-80) cc_final: 0.8359 (m-80) REVERT: E 429 GLU cc_start: 0.8652 (tp30) cc_final: 0.8389 (tt0) REVERT: E 430 LYS cc_start: 0.8764 (mmtp) cc_final: 0.8409 (tttt) REVERT: J 154 MET cc_start: 0.8564 (mmt) cc_final: 0.8218 (mmt) REVERT: J 254 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7679 (tp30) REVERT: J 271 THR cc_start: 0.8982 (m) cc_final: 0.8779 (p) REVERT: J 319 TYR cc_start: 0.8993 (m-80) cc_final: 0.8704 (m-10) REVERT: J 327 ASP cc_start: 0.8265 (m-30) cc_final: 0.7858 (m-30) REVERT: J 430 LYS cc_start: 0.8872 (mmtp) cc_final: 0.8412 (tttt) REVERT: C 80 THR cc_start: 0.8904 (m) cc_final: 0.8640 (t) REVERT: C 91 GLN cc_start: 0.8442 (mt0) cc_final: 0.8047 (mt0) REVERT: C 245 ASP cc_start: 0.7743 (p0) cc_final: 0.7510 (p0) REVERT: C 254 GLU cc_start: 0.7901 (mp0) cc_final: 0.7013 (mp0) REVERT: C 433 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7547 (tp30) REVERT: L 80 THR cc_start: 0.9012 (m) cc_final: 0.8677 (t) REVERT: L 91 GLN cc_start: 0.8447 (mt0) cc_final: 0.8029 (mt0) REVERT: L 120 ASP cc_start: 0.7924 (t70) cc_final: 0.7666 (t0) REVERT: L 154 MET cc_start: 0.8602 (mmm) cc_final: 0.8258 (mmm) REVERT: L 172 TYR cc_start: 0.8130 (t80) cc_final: 0.7423 (t80) REVERT: L 203 MET cc_start: 0.8842 (mmp) cc_final: 0.7893 (mmt) REVERT: L 207 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7118 (tm-30) REVERT: L 248 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8071 (tt) REVERT: L 254 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7690 (tp30) REVERT: L 353 VAL cc_start: 0.9434 (t) cc_final: 0.8783 (m) REVERT: L 433 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7581 (tp30) REVERT: K 296 PHE cc_start: 0.8789 (m-80) cc_final: 0.8562 (m-10) REVERT: K 433 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7669 (tp30) outliers start: 126 outliers final: 94 residues processed: 751 average time/residue: 0.2387 time to fit residues: 296.8376 Evaluate side-chains 724 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 627 time to evaluate : 1.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 326 VAL Chi-restraints excluded: chain G residue 415 MET Chi-restraints excluded: chain D residue 127 CYS Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 239 CYS Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 368 ILE Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain I residue 26 ASP Chi-restraints excluded: chain I residue 127 CYS Chi-restraints excluded: chain I residue 181 GLU Chi-restraints excluded: chain I residue 205 GLU Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 225 LEU Chi-restraints excluded: chain I residue 239 CYS Chi-restraints excluded: chain I residue 368 ILE Chi-restraints excluded: chain I residue 374 ILE Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain H residue 163 ILE Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain H residue 203 ASP Chi-restraints excluded: chain H residue 219 THR Chi-restraints excluded: chain H residue 326 VAL Chi-restraints excluded: chain H residue 374 ILE Chi-restraints excluded: chain H residue 419 VAL Chi-restraints excluded: chain E residue 4 CYS Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain J residue 36 MET Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 194 THR Chi-restraints excluded: chain J residue 207 GLU Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 285 GLN Chi-restraints excluded: chain J residue 288 VAL Chi-restraints excluded: chain J residue 324 VAL Chi-restraints excluded: chain J residue 341 ILE Chi-restraints excluded: chain J residue 362 VAL Chi-restraints excluded: chain J residue 398 MET Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain L residue 5 ILE Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 151 SER Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 207 GLU Chi-restraints excluded: chain L residue 248 LEU Chi-restraints excluded: chain L residue 288 VAL Chi-restraints excluded: chain L residue 324 VAL Chi-restraints excluded: chain L residue 362 VAL Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 381 THR Chi-restraints excluded: chain K residue 4 CYS Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 133 GLN Chi-restraints excluded: chain K residue 160 ASP Chi-restraints excluded: chain K residue 218 ASP Chi-restraints excluded: chain K residue 324 VAL Chi-restraints excluded: chain K residue 353 VAL Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 419 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 461 optimal weight: 9.9990 chunk 174 optimal weight: 7.9990 chunk 288 optimal weight: 10.0000 chunk 110 optimal weight: 4.9990 chunk 321 optimal weight: 5.9990 chunk 420 optimal weight: 7.9990 chunk 484 optimal weight: 10.0000 chunk 106 optimal weight: 8.9990 chunk 277 optimal weight: 0.2980 chunk 460 optimal weight: 7.9990 chunk 262 optimal weight: 9.9990 overall best weight: 5.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 57 ASN ** G 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 190 HIS B 37 HIS ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 8 GLN ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.110365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.097743 restraints weight = 60611.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.100863 restraints weight = 31684.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.102996 restraints weight = 19706.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.104469 restraints weight = 13631.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.105526 restraints weight = 10124.596| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.4342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 41796 Z= 0.185 Angle : 0.566 8.479 56784 Z= 0.288 Chirality : 0.046 0.155 6216 Planarity : 0.004 0.060 7398 Dihedral : 10.629 148.480 5760 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.16 % Allowed : 13.27 % Favored : 83.56 % 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: -1.23 (0.12), residues: 5130 helix: -0.19 (0.11), residues: 2220 sheet: -0.56 (0.19), residues: 798 loop : -1.50 (0.13), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 339 TYR 0.018 0.001 TYR C 24 PHE 0.021 0.001 PHE H 212 TRP 0.015 0.001 TRP A 21 HIS 0.004 0.001 HIS E 28 Details of bonding type rmsd covalent geometry : bond 0.00436 (41796) covalent geometry : angle 0.56560 (56784) hydrogen bonds : bond 0.03673 ( 1440) hydrogen bonds : angle 4.50457 ( 4284) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 793 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 654 time to evaluate : 1.657 Fit side-chains REVERT: F 74 ASP cc_start: 0.7552 (t70) cc_final: 0.7168 (t0) REVERT: F 150 LEU cc_start: 0.9134 (tp) cc_final: 0.8831 (tp) REVERT: F 205 GLU cc_start: 0.7759 (tt0) cc_final: 0.7493 (tt0) REVERT: F 230 SER cc_start: 0.9273 (p) cc_final: 0.9032 (t) REVERT: F 292 GLN cc_start: 0.8656 (tt0) cc_final: 0.8189 (tt0) REVERT: G 26 ASP cc_start: 0.8318 (t0) cc_final: 0.8026 (t0) REVERT: G 74 ASP cc_start: 0.7681 (t70) cc_final: 0.7184 (t0) REVERT: G 147 MET cc_start: 0.8268 (ttm) cc_final: 0.7877 (ttm) REVERT: G 332 ASN cc_start: 0.8116 (t0) cc_final: 0.7786 (t0) REVERT: D 74 ASP cc_start: 0.7275 (t70) cc_final: 0.6900 (t0) REVERT: D 103 LYS cc_start: 0.9117 (mttt) cc_final: 0.8804 (mtmt) REVERT: D 297 LYS cc_start: 0.8154 (ptpt) cc_final: 0.7904 (tmmt) REVERT: D 336 LYS cc_start: 0.8600 (mttt) cc_final: 0.8380 (mtmt) REVERT: I 69 GLU cc_start: 0.7949 (pm20) cc_final: 0.7417 (pm20) REVERT: I 74 ASP cc_start: 0.7381 (t70) cc_final: 0.7013 (t0) REVERT: I 103 LYS cc_start: 0.9101 (mttt) cc_final: 0.8849 (mtmt) REVERT: I 257 MET cc_start: 0.8756 (mmm) cc_final: 0.8289 (mtm) REVERT: I 297 LYS cc_start: 0.8269 (ptpt) cc_final: 0.8055 (tmmt) REVERT: A 80 THR cc_start: 0.8763 (m) cc_final: 0.8505 (t) REVERT: A 124 LYS cc_start: 0.8930 (ttmm) cc_final: 0.8415 (ttpp) REVERT: A 154 MET cc_start: 0.8436 (mmt) cc_final: 0.8052 (mmt) REVERT: A 221 ARG cc_start: 0.7704 (mtt-85) cc_final: 0.7486 (mtm-85) REVERT: A 279 GLU cc_start: 0.8654 (tp30) cc_final: 0.8197 (tp30) REVERT: A 351 PHE cc_start: 0.9013 (m-80) cc_final: 0.8647 (m-80) REVERT: B 332 ASN cc_start: 0.8409 (t0) cc_final: 0.7984 (t0) REVERT: H 323 MET cc_start: 0.8428 (mmm) cc_final: 0.8148 (mmm) REVERT: H 379 LYS cc_start: 0.8549 (mtpt) cc_final: 0.8111 (tttm) REVERT: E 79 ARG cc_start: 0.9085 (OUTLIER) cc_final: 0.8822 (mtt180) REVERT: E 154 MET cc_start: 0.8761 (mmm) cc_final: 0.8103 (mmt) REVERT: E 170 SER cc_start: 0.9325 (m) cc_final: 0.9038 (t) REVERT: E 319 TYR cc_start: 0.9168 (m-80) cc_final: 0.8636 (m-80) REVERT: E 429 GLU cc_start: 0.8689 (tp30) cc_final: 0.8384 (tt0) REVERT: E 430 LYS cc_start: 0.8739 (mmtp) cc_final: 0.8346 (tttt) REVERT: J 154 MET cc_start: 0.8646 (mmt) cc_final: 0.8284 (mmt) REVERT: J 254 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7655 (tp30) REVERT: J 319 TYR cc_start: 0.9111 (m-80) cc_final: 0.8765 (m-10) REVERT: J 327 ASP cc_start: 0.8472 (m-30) cc_final: 0.8094 (m-30) REVERT: C 80 THR cc_start: 0.8930 (m) cc_final: 0.8655 (t) REVERT: C 91 GLN cc_start: 0.8419 (mt0) cc_final: 0.7999 (mt0) REVERT: C 254 GLU cc_start: 0.7941 (mp0) cc_final: 0.6881 (mp0) REVERT: C 433 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7671 (tp30) REVERT: L 80 THR cc_start: 0.9068 (m) cc_final: 0.8724 (t) REVERT: L 91 GLN cc_start: 0.8461 (mt0) cc_final: 0.8057 (mt0) REVERT: L 120 ASP cc_start: 0.8067 (t70) cc_final: 0.7635 (t0) REVERT: L 154 MET cc_start: 0.8646 (mmm) cc_final: 0.8251 (mmm) REVERT: L 172 TYR cc_start: 0.8244 (t80) cc_final: 0.7456 (t80) REVERT: L 203 MET cc_start: 0.8876 (mmp) cc_final: 0.7887 (mmt) REVERT: L 207 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7052 (tm-30) REVERT: L 248 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7928 (tt) REVERT: L 254 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7820 (tp30) REVERT: L 339 ARG cc_start: 0.7594 (ptt90) cc_final: 0.7153 (ttp-110) REVERT: L 353 VAL cc_start: 0.9448 (t) cc_final: 0.8806 (m) REVERT: L 433 GLU cc_start: 0.8262 (mm-30) cc_final: 0.7940 (tp30) REVERT: K 124 LYS cc_start: 0.8945 (ttmm) cc_final: 0.8583 (ttpp) REVERT: K 296 PHE cc_start: 0.8828 (m-80) cc_final: 0.8576 (m-10) REVERT: K 433 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7809 (tp30) outliers start: 139 outliers final: 113 residues processed: 744 average time/residue: 0.2432 time to fit residues: 299.0872 Evaluate side-chains 726 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 610 time to evaluate : 2.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 326 VAL Chi-restraints excluded: chain D residue 127 CYS Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 239 CYS Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 368 ILE Chi-restraints excluded: chain I residue 26 ASP Chi-restraints excluded: chain I residue 84 ILE Chi-restraints excluded: chain I residue 127 CYS Chi-restraints excluded: chain I residue 181 GLU Chi-restraints excluded: chain I residue 198 GLU Chi-restraints excluded: chain I residue 205 GLU Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 225 LEU Chi-restraints excluded: chain I residue 239 CYS Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 368 ILE Chi-restraints excluded: chain I residue 374 ILE Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 239 CYS Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain H residue 163 ILE Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain H residue 203 ASP Chi-restraints excluded: chain H residue 219 THR Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain H residue 326 VAL Chi-restraints excluded: chain H residue 374 ILE Chi-restraints excluded: chain H residue 375 GLN Chi-restraints excluded: chain H residue 419 VAL Chi-restraints excluded: chain E residue 4 CYS Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 79 ARG Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain J residue 36 MET Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 194 THR Chi-restraints excluded: chain J residue 207 GLU Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 285 GLN Chi-restraints excluded: chain J residue 288 VAL Chi-restraints excluded: chain J residue 324 VAL Chi-restraints excluded: chain J residue 335 ILE Chi-restraints excluded: chain J residue 362 VAL Chi-restraints excluded: chain J residue 367 ASP Chi-restraints excluded: chain J residue 398 MET Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain L residue 5 ILE Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 36 MET Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 119 LEU Chi-restraints excluded: chain L residue 151 SER Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 207 GLU Chi-restraints excluded: chain L residue 248 LEU Chi-restraints excluded: chain L residue 252 LEU Chi-restraints excluded: chain L residue 288 VAL Chi-restraints excluded: chain L residue 324 VAL Chi-restraints excluded: chain L residue 362 VAL Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 381 THR Chi-restraints excluded: chain L residue 397 LEU Chi-restraints excluded: chain K residue 4 CYS Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 133 GLN Chi-restraints excluded: chain K residue 151 SER Chi-restraints excluded: chain K residue 160 ASP Chi-restraints excluded: chain K residue 194 THR Chi-restraints excluded: chain K residue 218 ASP Chi-restraints excluded: chain K residue 253 THR Chi-restraints excluded: chain K residue 324 VAL Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 419 SER Chi-restraints excluded: chain K residue 428 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 377 optimal weight: 10.0000 chunk 218 optimal weight: 6.9990 chunk 415 optimal weight: 10.0000 chunk 393 optimal weight: 10.0000 chunk 14 optimal weight: 20.0000 chunk 63 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 382 optimal weight: 2.9990 chunk 252 optimal weight: 5.9990 chunk 313 optimal weight: 6.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 335 ASN ** G 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 335 ASN ** D 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.111300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.098640 restraints weight = 60446.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.101778 restraints weight = 31737.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.103908 restraints weight = 19783.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.105368 restraints weight = 13722.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.106444 restraints weight = 10212.712| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.4462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 41796 Z= 0.146 Angle : 0.537 8.335 56784 Z= 0.271 Chirality : 0.045 0.160 6216 Planarity : 0.003 0.058 7398 Dihedral : 10.484 148.001 5760 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.76 % Allowed : 14.23 % Favored : 83.01 % 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: 5130 helix: 0.02 (0.11), residues: 2220 sheet: -0.44 (0.19), residues: 798 loop : -1.40 (0.13), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 339 TYR 0.016 0.001 TYR C 24 PHE 0.023 0.001 PHE H 212 TRP 0.011 0.001 TRP A 21 HIS 0.005 0.001 HIS G 37 Details of bonding type rmsd covalent geometry : bond 0.00342 (41796) covalent geometry : angle 0.53722 (56784) hydrogen bonds : bond 0.03347 ( 1440) hydrogen bonds : angle 4.35602 ( 4284) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 759 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 638 time to evaluate : 1.624 Fit side-chains REVERT: F 26 ASP cc_start: 0.8342 (t0) cc_final: 0.8089 (t0) REVERT: F 65 LEU cc_start: 0.8929 (mp) cc_final: 0.8621 (mt) REVERT: F 150 LEU cc_start: 0.9160 (tp) cc_final: 0.8891 (tp) REVERT: F 292 GLN cc_start: 0.8513 (tt0) cc_final: 0.7969 (tt0) REVERT: G 26 ASP cc_start: 0.8194 (t0) cc_final: 0.7913 (t0) REVERT: G 74 ASP cc_start: 0.7522 (t70) cc_final: 0.7052 (t0) REVERT: G 147 MET cc_start: 0.8150 (ttm) cc_final: 0.7913 (ttm) REVERT: G 332 ASN cc_start: 0.8070 (t0) cc_final: 0.7798 (t0) REVERT: D 74 ASP cc_start: 0.7106 (t70) cc_final: 0.6759 (t0) REVERT: D 103 LYS cc_start: 0.9044 (mttt) cc_final: 0.8786 (mtmt) REVERT: D 257 MET cc_start: 0.8656 (mmm) cc_final: 0.8432 (mmm) REVERT: I 69 GLU cc_start: 0.8051 (pm20) cc_final: 0.7573 (pm20) REVERT: I 74 ASP cc_start: 0.7217 (t70) cc_final: 0.6899 (t0) REVERT: I 103 LYS cc_start: 0.9072 (mttt) cc_final: 0.8859 (mtmt) REVERT: I 291 GLN cc_start: 0.8421 (tt0) cc_final: 0.8068 (tp-100) REVERT: I 330 MET cc_start: 0.8359 (mmm) cc_final: 0.7940 (mtp) REVERT: I 332 ASN cc_start: 0.8599 (t0) cc_final: 0.8350 (t0) REVERT: A 80 THR cc_start: 0.8729 (m) cc_final: 0.8476 (t) REVERT: A 124 LYS cc_start: 0.8923 (ttmm) cc_final: 0.8429 (ttpp) REVERT: A 154 MET cc_start: 0.8390 (mmt) cc_final: 0.8002 (mmt) REVERT: A 279 GLU cc_start: 0.8601 (tp30) cc_final: 0.8144 (tp30) REVERT: A 319 TYR cc_start: 0.8734 (m-80) cc_final: 0.8523 (m-80) REVERT: A 351 PHE cc_start: 0.8954 (m-80) cc_final: 0.8605 (m-80) REVERT: B 167 PHE cc_start: 0.8934 (m-80) cc_final: 0.8433 (m-80) REVERT: B 332 ASN cc_start: 0.8375 (t0) cc_final: 0.7956 (t0) REVERT: H 323 MET cc_start: 0.8357 (mmm) cc_final: 0.8098 (mmm) REVERT: H 379 LYS cc_start: 0.8535 (mtpt) cc_final: 0.8185 (tttm) REVERT: E 79 ARG cc_start: 0.9125 (OUTLIER) cc_final: 0.8850 (mtt180) REVERT: E 154 MET cc_start: 0.8710 (mmm) cc_final: 0.8068 (mmt) REVERT: E 170 SER cc_start: 0.9317 (m) cc_final: 0.9082 (t) REVERT: E 319 TYR cc_start: 0.9142 (m-80) cc_final: 0.8580 (m-80) REVERT: E 430 LYS cc_start: 0.8747 (mmtp) cc_final: 0.8378 (tttt) REVERT: J 154 MET cc_start: 0.8585 (mmt) cc_final: 0.8269 (mmt) REVERT: J 254 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7656 (tp30) REVERT: J 319 TYR cc_start: 0.9096 (m-80) cc_final: 0.8756 (m-10) REVERT: J 327 ASP cc_start: 0.8413 (m-30) cc_final: 0.8046 (m-30) REVERT: J 425 MET cc_start: 0.8555 (tpt) cc_final: 0.8349 (mmm) REVERT: J 430 LYS cc_start: 0.8695 (mmtp) cc_final: 0.8318 (tttt) REVERT: C 80 THR cc_start: 0.8908 (m) cc_final: 0.8630 (t) REVERT: C 91 GLN cc_start: 0.8412 (mt0) cc_final: 0.8000 (mt0) REVERT: C 254 GLU cc_start: 0.7898 (mp0) cc_final: 0.7021 (mp0) REVERT: C 279 GLU cc_start: 0.8598 (tp30) cc_final: 0.7994 (tt0) REVERT: C 433 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7552 (tp30) REVERT: L 80 THR cc_start: 0.9021 (m) cc_final: 0.8684 (t) REVERT: L 91 GLN cc_start: 0.8359 (mt0) cc_final: 0.7953 (mt0) REVERT: L 120 ASP cc_start: 0.7777 (t70) cc_final: 0.7513 (t0) REVERT: L 154 MET cc_start: 0.8613 (mmm) cc_final: 0.8220 (mmm) REVERT: L 172 TYR cc_start: 0.8193 (t80) cc_final: 0.7464 (t80) REVERT: L 203 MET cc_start: 0.8846 (mmp) cc_final: 0.7844 (mmt) REVERT: L 207 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7098 (tm-30) REVERT: L 248 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8039 (tt) REVERT: L 254 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7736 (tp30) REVERT: L 339 ARG cc_start: 0.7536 (ptt90) cc_final: 0.7133 (ttp-110) REVERT: L 353 VAL cc_start: 0.9429 (t) cc_final: 0.8782 (m) REVERT: L 377 MET cc_start: 0.8762 (ttp) cc_final: 0.8305 (tmm) REVERT: L 433 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7660 (tp30) REVERT: K 124 LYS cc_start: 0.8932 (ttmm) cc_final: 0.8552 (ttpp) REVERT: K 433 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7650 (tp30) outliers start: 121 outliers final: 99 residues processed: 719 average time/residue: 0.2432 time to fit residues: 289.1243 Evaluate side-chains 708 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 606 time to evaluate : 1.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 224 ASP Chi-restraints excluded: chain G residue 326 VAL Chi-restraints excluded: chain D residue 127 CYS Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 239 CYS Chi-restraints excluded: chain D residue 368 ILE Chi-restraints excluded: chain I residue 84 ILE Chi-restraints excluded: chain I residue 127 CYS Chi-restraints excluded: chain I residue 181 GLU Chi-restraints excluded: chain I residue 198 GLU Chi-restraints excluded: chain I residue 205 GLU Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 225 LEU Chi-restraints excluded: chain I residue 239 CYS Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 368 ILE Chi-restraints excluded: chain I residue 374 ILE Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain H residue 203 ASP Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 219 THR Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain H residue 326 VAL Chi-restraints excluded: chain H residue 375 GLN Chi-restraints excluded: chain H residue 419 VAL Chi-restraints excluded: chain E residue 4 CYS Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 79 ARG Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain J residue 36 MET Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 194 THR Chi-restraints excluded: chain J residue 207 GLU Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 285 GLN Chi-restraints excluded: chain J residue 288 VAL Chi-restraints excluded: chain J residue 324 VAL Chi-restraints excluded: chain J residue 335 ILE Chi-restraints excluded: chain J residue 353 VAL Chi-restraints excluded: chain J residue 362 VAL Chi-restraints excluded: chain J residue 367 ASP Chi-restraints excluded: chain J residue 398 MET Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 36 MET Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 151 SER Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 207 GLU Chi-restraints excluded: chain L residue 248 LEU Chi-restraints excluded: chain L residue 252 LEU Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain L residue 288 VAL Chi-restraints excluded: chain L residue 303 VAL Chi-restraints excluded: chain L residue 324 VAL Chi-restraints excluded: chain L residue 362 VAL Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 381 THR Chi-restraints excluded: chain K residue 4 CYS Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 133 GLN Chi-restraints excluded: chain K residue 151 SER Chi-restraints excluded: chain K residue 160 ASP Chi-restraints excluded: chain K residue 218 ASP Chi-restraints excluded: chain K residue 253 THR Chi-restraints excluded: chain K residue 324 VAL Chi-restraints excluded: chain K residue 353 VAL Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 379 SER Chi-restraints excluded: chain K residue 419 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 337 optimal weight: 7.9990 chunk 377 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 319 optimal weight: 7.9990 chunk 184 optimal weight: 3.9990 chunk 317 optimal weight: 6.9990 chunk 403 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 451 optimal weight: 7.9990 chunk 477 optimal weight: 4.9990 chunk 216 optimal weight: 0.9980 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 57 ASN F 335 ASN G 37 HIS ** G 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 197 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.095342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.083671 restraints weight = 64832.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.086301 restraints weight = 35369.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.088137 restraints weight = 22534.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.089415 restraints weight = 15858.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.090348 restraints weight = 11980.799| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.4574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 41796 Z= 0.127 Angle : 0.528 9.186 56784 Z= 0.265 Chirality : 0.044 0.158 6216 Planarity : 0.003 0.057 7398 Dihedral : 10.293 146.752 5760 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.73 % Allowed : 14.39 % Favored : 82.88 % 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: -0.82 (0.12), residues: 5130 helix: 0.20 (0.11), residues: 2226 sheet: -0.53 (0.19), residues: 840 loop : -1.28 (0.13), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 339 TYR 0.016 0.001 TYR K 103 PHE 0.025 0.001 PHE H 212 TRP 0.011 0.001 TRP A 21 HIS 0.004 0.001 HIS G 37 Details of bonding type rmsd covalent geometry : bond 0.00297 (41796) covalent geometry : angle 0.52758 (56784) hydrogen bonds : bond 0.03160 ( 1440) hydrogen bonds : angle 4.26311 ( 4284) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 769 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 649 time to evaluate : 1.648 Fit side-chains revert: symmetry clash REVERT: F 26 ASP cc_start: 0.8279 (t0) cc_final: 0.8057 (t0) REVERT: F 65 LEU cc_start: 0.8911 (mp) cc_final: 0.8609 (mt) REVERT: F 150 LEU cc_start: 0.9178 (tp) cc_final: 0.8955 (tp) REVERT: F 292 GLN cc_start: 0.8458 (tt0) cc_final: 0.7928 (tt0) REVERT: G 26 ASP cc_start: 0.8121 (t0) cc_final: 0.7870 (t0) REVERT: G 74 ASP cc_start: 0.7480 (t70) cc_final: 0.7020 (t0) REVERT: G 147 MET cc_start: 0.8107 (OUTLIER) cc_final: 0.7875 (ttm) REVERT: G 297 LYS cc_start: 0.8494 (mttp) cc_final: 0.7723 (tmmt) REVERT: G 332 ASN cc_start: 0.8062 (t0) cc_final: 0.7755 (t0) REVERT: D 74 ASP cc_start: 0.7023 (t70) cc_final: 0.6699 (t0) REVERT: D 103 LYS cc_start: 0.9009 (mttt) cc_final: 0.8749 (mtmt) REVERT: D 330 MET cc_start: 0.8175 (mmm) cc_final: 0.7632 (mtp) REVERT: I 69 GLU cc_start: 0.8084 (pm20) cc_final: 0.7602 (pm20) REVERT: I 74 ASP cc_start: 0.7123 (t70) cc_final: 0.6819 (t0) REVERT: I 225 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8173 (tp) REVERT: I 291 GLN cc_start: 0.8261 (tt0) cc_final: 0.8031 (tp-100) REVERT: I 330 MET cc_start: 0.8324 (mmm) cc_final: 0.7819 (mtp) REVERT: I 332 ASN cc_start: 0.8586 (t0) cc_final: 0.8287 (t0) REVERT: A 80 THR cc_start: 0.8723 (m) cc_final: 0.8462 (t) REVERT: A 124 LYS cc_start: 0.8960 (ttmm) cc_final: 0.8480 (ttpp) REVERT: A 154 MET cc_start: 0.8370 (mmt) cc_final: 0.8060 (mmt) REVERT: A 279 GLU cc_start: 0.8514 (tp30) cc_final: 0.8163 (tp30) REVERT: A 351 PHE cc_start: 0.8899 (m-80) cc_final: 0.8562 (m-80) REVERT: B 167 PHE cc_start: 0.8918 (m-80) cc_final: 0.8339 (m-80) REVERT: B 332 ASN cc_start: 0.8342 (t0) cc_final: 0.8009 (t0) REVERT: H 3 GLU cc_start: 0.7899 (mp0) cc_final: 0.7663 (mp0) REVERT: H 323 MET cc_start: 0.8338 (mmm) cc_final: 0.8104 (mmm) REVERT: H 379 LYS cc_start: 0.8656 (mtpt) cc_final: 0.8263 (tttm) REVERT: E 79 ARG cc_start: 0.9144 (OUTLIER) cc_final: 0.8877 (mtt180) REVERT: E 154 MET cc_start: 0.8685 (mmm) cc_final: 0.8047 (mmt) REVERT: E 170 SER cc_start: 0.9327 (m) cc_final: 0.9098 (t) REVERT: E 319 TYR cc_start: 0.9146 (m-80) cc_final: 0.8603 (m-80) REVERT: E 425 MET cc_start: 0.8475 (tpt) cc_final: 0.8228 (mmm) REVERT: E 430 LYS cc_start: 0.8615 (mmtp) cc_final: 0.8389 (ttpt) REVERT: J 154 MET cc_start: 0.8567 (mmt) cc_final: 0.8242 (mmt) REVERT: J 254 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7579 (tp30) REVERT: J 319 TYR cc_start: 0.9087 (m-80) cc_final: 0.8717 (m-10) REVERT: J 430 LYS cc_start: 0.8702 (mmtp) cc_final: 0.8334 (tttt) REVERT: C 80 THR cc_start: 0.8876 (m) cc_final: 0.8602 (t) REVERT: C 91 GLN cc_start: 0.8413 (mt0) cc_final: 0.8001 (mt0) REVERT: C 254 GLU cc_start: 0.7878 (mp0) cc_final: 0.7079 (mp0) REVERT: C 279 GLU cc_start: 0.8616 (tp30) cc_final: 0.7984 (tt0) REVERT: C 433 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7506 (tp30) REVERT: L 80 THR cc_start: 0.8983 (m) cc_final: 0.8628 (t) REVERT: L 91 GLN cc_start: 0.8334 (mt0) cc_final: 0.7926 (mt0) REVERT: L 120 ASP cc_start: 0.7892 (t70) cc_final: 0.7644 (t0) REVERT: L 154 MET cc_start: 0.8578 (mmm) cc_final: 0.8178 (mmm) REVERT: L 172 TYR cc_start: 0.8178 (t80) cc_final: 0.7419 (t80) REVERT: L 203 MET cc_start: 0.8848 (mmp) cc_final: 0.7819 (mmt) REVERT: L 248 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8097 (tt) REVERT: L 254 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7738 (tp30) REVERT: L 319 TYR cc_start: 0.9100 (m-80) cc_final: 0.8886 (m-80) REVERT: L 339 ARG cc_start: 0.7501 (ptt90) cc_final: 0.7113 (ttp-110) REVERT: L 353 VAL cc_start: 0.9421 (t) cc_final: 0.8790 (m) REVERT: L 377 MET cc_start: 0.8745 (ttp) cc_final: 0.8303 (tmm) REVERT: L 433 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7593 (tp30) REVERT: K 124 LYS cc_start: 0.8902 (ttmm) cc_final: 0.8523 (ttpp) REVERT: K 203 MET cc_start: 0.8652 (mmp) cc_final: 0.8176 (mmp) REVERT: K 433 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7577 (tp30) outliers start: 120 outliers final: 99 residues processed: 727 average time/residue: 0.2385 time to fit residues: 288.9616 Evaluate side-chains 725 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 622 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain F residue 224 ASP Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain G residue 147 MET Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 224 ASP Chi-restraints excluded: chain G residue 326 VAL Chi-restraints excluded: chain D residue 127 CYS Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 239 CYS Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 368 ILE Chi-restraints excluded: chain I residue 127 CYS Chi-restraints excluded: chain I residue 181 GLU Chi-restraints excluded: chain I residue 205 GLU Chi-restraints excluded: chain I residue 225 LEU Chi-restraints excluded: chain I residue 239 CYS Chi-restraints excluded: chain I residue 374 ILE Chi-restraints excluded: chain I residue 415 MET Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain H residue 203 ASP Chi-restraints excluded: chain H residue 219 THR Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain H residue 326 VAL Chi-restraints excluded: chain H residue 375 GLN Chi-restraints excluded: chain E residue 4 CYS Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 79 ARG Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain J residue 4 CYS Chi-restraints excluded: chain J residue 36 MET Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 194 THR Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 285 GLN Chi-restraints excluded: chain J residue 288 VAL Chi-restraints excluded: chain J residue 324 VAL Chi-restraints excluded: chain J residue 335 ILE Chi-restraints excluded: chain J residue 362 VAL Chi-restraints excluded: chain J residue 398 MET Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 36 MET Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 151 SER Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 248 LEU Chi-restraints excluded: chain L residue 252 LEU Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain L residue 288 VAL Chi-restraints excluded: chain L residue 303 VAL Chi-restraints excluded: chain L residue 324 VAL Chi-restraints excluded: chain L residue 362 VAL Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 381 THR Chi-restraints excluded: chain K residue 4 CYS Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 133 GLN Chi-restraints excluded: chain K residue 151 SER Chi-restraints excluded: chain K residue 160 ASP Chi-restraints excluded: chain K residue 218 ASP Chi-restraints excluded: chain K residue 253 THR Chi-restraints excluded: chain K residue 324 VAL Chi-restraints excluded: chain K residue 353 VAL Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 379 SER Chi-restraints excluded: chain K residue 419 SER Chi-restraints excluded: chain K residue 428 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 455 optimal weight: 8.9990 chunk 115 optimal weight: 5.9990 chunk 397 optimal weight: 6.9990 chunk 414 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 355 optimal weight: 3.9990 chunk 429 optimal weight: 6.9990 chunk 145 optimal weight: 0.9980 chunk 130 optimal weight: 9.9990 chunk 184 optimal weight: 6.9990 chunk 321 optimal weight: 8.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 335 ASN ** G 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.096726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.082981 restraints weight = 66459.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.085908 restraints weight = 36418.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.087949 restraints weight = 23665.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.089386 restraints weight = 17060.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.090447 restraints weight = 13193.785| |-----------------------------------------------------------------------------| r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.4638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 41796 Z= 0.152 Angle : 0.553 9.404 56784 Z= 0.277 Chirality : 0.045 0.159 6216 Planarity : 0.003 0.058 7398 Dihedral : 10.232 147.265 5760 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.78 % Allowed : 14.64 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.12), residues: 5130 helix: 0.36 (0.12), residues: 2184 sheet: -0.53 (0.19), residues: 840 loop : -1.25 (0.13), residues: 2106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 339 TYR 0.017 0.001 TYR K 103 PHE 0.027 0.001 PHE H 212 TRP 0.012 0.001 TRP A 21 HIS 0.003 0.001 HIS E 28 Details of bonding type rmsd covalent geometry : bond 0.00359 (41796) covalent geometry : angle 0.55269 (56784) hydrogen bonds : bond 0.03345 ( 1440) hydrogen bonds : angle 4.30687 ( 4284) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 752 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 630 time to evaluate : 1.625 Fit side-chains revert: symmetry clash REVERT: F 65 LEU cc_start: 0.8901 (mp) cc_final: 0.8637 (mt) REVERT: F 150 LEU cc_start: 0.9133 (tp) cc_final: 0.8883 (tp) REVERT: F 292 GLN cc_start: 0.8464 (tt0) cc_final: 0.7949 (tt0) REVERT: G 26 ASP cc_start: 0.8234 (t0) cc_final: 0.7924 (t0) REVERT: G 74 ASP cc_start: 0.7667 (t70) cc_final: 0.7151 (t0) REVERT: G 332 ASN cc_start: 0.8097 (t0) cc_final: 0.7763 (t0) REVERT: D 74 ASP cc_start: 0.7209 (t70) cc_final: 0.6846 (t0) REVERT: D 103 LYS cc_start: 0.9076 (mttt) cc_final: 0.8798 (mtmt) REVERT: D 297 LYS cc_start: 0.8736 (mttt) cc_final: 0.8269 (tmmt) REVERT: D 330 MET cc_start: 0.8254 (mmm) cc_final: 0.7779 (mtp) REVERT: D 335 ASN cc_start: 0.8220 (m-40) cc_final: 0.7918 (m110) REVERT: D 406 MET cc_start: 0.8289 (mmm) cc_final: 0.7585 (mmt) REVERT: I 69 GLU cc_start: 0.8007 (pm20) cc_final: 0.7476 (pm20) REVERT: I 74 ASP cc_start: 0.7320 (t70) cc_final: 0.6988 (t0) REVERT: I 291 GLN cc_start: 0.8394 (tt0) cc_final: 0.8026 (tp-100) REVERT: I 330 MET cc_start: 0.8331 (mmm) cc_final: 0.8073 (mtp) REVERT: A 36 MET cc_start: 0.9048 (ttp) cc_final: 0.8828 (ttp) REVERT: A 80 THR cc_start: 0.8780 (m) cc_final: 0.8498 (t) REVERT: A 124 LYS cc_start: 0.8938 (ttmm) cc_final: 0.8404 (ttpp) REVERT: A 154 MET cc_start: 0.8434 (mmt) cc_final: 0.8090 (mmt) REVERT: A 279 GLU cc_start: 0.8600 (tp30) cc_final: 0.8226 (tp30) REVERT: A 351 PHE cc_start: 0.8998 (m-80) cc_final: 0.8617 (m-80) REVERT: B 332 ASN cc_start: 0.8367 (t0) cc_final: 0.8017 (t0) REVERT: H 3 GLU cc_start: 0.7958 (mp0) cc_final: 0.7709 (mp0) REVERT: H 209 ASP cc_start: 0.8760 (t0) cc_final: 0.8485 (t0) REVERT: H 247 ASN cc_start: 0.8447 (m-40) cc_final: 0.8046 (m110) REVERT: H 257 MET cc_start: 0.8480 (mmm) cc_final: 0.8225 (mmm) REVERT: H 379 LYS cc_start: 0.8621 (mtpt) cc_final: 0.8224 (tttt) REVERT: E 79 ARG cc_start: 0.9073 (OUTLIER) cc_final: 0.8817 (mtt180) REVERT: E 154 MET cc_start: 0.8709 (mmm) cc_final: 0.8072 (mmt) REVERT: E 170 SER cc_start: 0.9326 (m) cc_final: 0.9040 (t) REVERT: E 319 TYR cc_start: 0.9167 (m-80) cc_final: 0.8607 (m-80) REVERT: E 425 MET cc_start: 0.8506 (tpt) cc_final: 0.8290 (mmm) REVERT: J 154 MET cc_start: 0.8634 (mmt) cc_final: 0.8313 (mmt) REVERT: J 254 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7574 (tp30) REVERT: J 319 TYR cc_start: 0.9129 (m-80) cc_final: 0.8726 (m-10) REVERT: J 430 LYS cc_start: 0.8642 (mmtp) cc_final: 0.8268 (tttt) REVERT: C 80 THR cc_start: 0.8947 (m) cc_final: 0.8659 (t) REVERT: C 91 GLN cc_start: 0.8391 (mt0) cc_final: 0.7993 (mt0) REVERT: C 279 GLU cc_start: 0.8682 (tp30) cc_final: 0.7995 (tt0) REVERT: C 433 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7665 (tp30) REVERT: L 80 THR cc_start: 0.9042 (m) cc_final: 0.8671 (t) REVERT: L 91 GLN cc_start: 0.8375 (mt0) cc_final: 0.7955 (mt0) REVERT: L 120 ASP cc_start: 0.7941 (t70) cc_final: 0.7681 (t0) REVERT: L 172 TYR cc_start: 0.8216 (t80) cc_final: 0.7336 (t80) REVERT: L 203 MET cc_start: 0.8902 (mmp) cc_final: 0.7811 (mmt) REVERT: L 207 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7153 (tm-30) REVERT: L 248 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.7937 (tt) REVERT: L 254 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7744 (tp30) REVERT: L 339 ARG cc_start: 0.7630 (ptt90) cc_final: 0.7215 (ttp-110) REVERT: L 353 VAL cc_start: 0.9450 (t) cc_final: 0.8841 (m) REVERT: L 414 GLU cc_start: 0.7610 (tm-30) cc_final: 0.7202 (tm-30) REVERT: L 417 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.7267 (tt0) REVERT: L 433 GLU cc_start: 0.8284 (mm-30) cc_final: 0.7747 (tp30) REVERT: K 3 GLU cc_start: 0.8087 (mp0) cc_final: 0.7835 (mp0) REVERT: K 124 LYS cc_start: 0.8917 (ttmm) cc_final: 0.8515 (ttpp) REVERT: K 433 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7772 (tp30) outliers start: 122 outliers final: 110 residues processed: 704 average time/residue: 0.2406 time to fit residues: 280.7956 Evaluate side-chains 727 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 613 time to evaluate : 1.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 145 SER Chi-restraints excluded: chain F residue 224 ASP Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 147 MET Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 224 ASP Chi-restraints excluded: chain G residue 326 VAL Chi-restraints excluded: chain D residue 127 CYS Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 239 CYS Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain I residue 127 CYS Chi-restraints excluded: chain I residue 181 GLU Chi-restraints excluded: chain I residue 205 GLU Chi-restraints excluded: chain I residue 225 LEU Chi-restraints excluded: chain I residue 239 CYS Chi-restraints excluded: chain I residue 374 ILE Chi-restraints excluded: chain I residue 415 MET Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 239 CYS Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain H residue 219 THR Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain H residue 326 VAL Chi-restraints excluded: chain H residue 375 GLN Chi-restraints excluded: chain E residue 4 CYS Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 79 ARG Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain J residue 4 CYS Chi-restraints excluded: chain J residue 36 MET Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 194 THR Chi-restraints excluded: chain J residue 207 GLU Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 285 GLN Chi-restraints excluded: chain J residue 288 VAL Chi-restraints excluded: chain J residue 324 VAL Chi-restraints excluded: chain J residue 335 ILE Chi-restraints excluded: chain J residue 362 VAL Chi-restraints excluded: chain J residue 398 MET Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 36 MET Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 151 SER Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 207 GLU Chi-restraints excluded: chain L residue 248 LEU Chi-restraints excluded: chain L residue 252 LEU Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain L residue 288 VAL Chi-restraints excluded: chain L residue 303 VAL Chi-restraints excluded: chain L residue 324 VAL Chi-restraints excluded: chain L residue 335 ILE Chi-restraints excluded: chain L residue 362 VAL Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 381 THR Chi-restraints excluded: chain L residue 417 GLU Chi-restraints excluded: chain K residue 4 CYS Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 133 GLN Chi-restraints excluded: chain K residue 151 SER Chi-restraints excluded: chain K residue 160 ASP Chi-restraints excluded: chain K residue 218 ASP Chi-restraints excluded: chain K residue 253 THR Chi-restraints excluded: chain K residue 324 VAL Chi-restraints excluded: chain K residue 335 ILE Chi-restraints excluded: chain K residue 353 VAL Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 379 SER Chi-restraints excluded: chain K residue 419 SER Chi-restraints excluded: chain K residue 428 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 194 optimal weight: 9.9990 chunk 359 optimal weight: 3.9990 chunk 193 optimal weight: 1.9990 chunk 484 optimal weight: 9.9990 chunk 471 optimal weight: 6.9990 chunk 389 optimal weight: 20.0000 chunk 67 optimal weight: 0.9990 chunk 108 optimal weight: 8.9990 chunk 352 optimal weight: 4.9990 chunk 391 optimal weight: 0.7980 chunk 137 optimal weight: 6.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 335 ASN G 57 ASN ** G 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 293 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.112871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.100315 restraints weight = 59900.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.103427 restraints weight = 31455.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.105556 restraints weight = 19642.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.107042 restraints weight = 13598.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.108100 restraints weight = 10064.523| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.4712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 41796 Z= 0.114 Angle : 0.533 9.493 56784 Z= 0.266 Chirality : 0.044 0.157 6216 Planarity : 0.003 0.057 7398 Dihedral : 10.043 145.685 5760 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.44 % Allowed : 15.00 % Favored : 82.56 % 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: -0.59 (0.12), residues: 5130 helix: 0.43 (0.12), residues: 2220 sheet: -0.44 (0.19), residues: 840 loop : -1.19 (0.13), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 339 TYR 0.017 0.001 TYR L 319 PHE 0.029 0.001 PHE H 212 TRP 0.011 0.001 TRP C 346 HIS 0.003 0.001 HIS F 396 Details of bonding type rmsd covalent geometry : bond 0.00265 (41796) covalent geometry : angle 0.53313 (56784) hydrogen bonds : bond 0.03048 ( 1440) hydrogen bonds : angle 4.19806 ( 4284) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 768 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 661 time to evaluate : 1.656 Fit side-chains REVERT: F 65 LEU cc_start: 0.8836 (mp) cc_final: 0.8530 (mt) REVERT: F 163 ILE cc_start: 0.8513 (pt) cc_final: 0.8217 (pt) REVERT: F 292 GLN cc_start: 0.8552 (tt0) cc_final: 0.7765 (tt0) REVERT: G 26 ASP cc_start: 0.8176 (t0) cc_final: 0.7869 (t0) REVERT: G 74 ASP cc_start: 0.7596 (t70) cc_final: 0.7081 (t0) REVERT: G 136 THR cc_start: 0.9342 (m) cc_final: 0.8854 (p) REVERT: G 147 MET cc_start: 0.8097 (ttm) cc_final: 0.7858 (ttm) REVERT: G 332 ASN cc_start: 0.8055 (t0) cc_final: 0.7728 (t0) REVERT: D 51 TYR cc_start: 0.8817 (m-80) cc_final: 0.8466 (m-80) REVERT: D 74 ASP cc_start: 0.7038 (t70) cc_final: 0.6730 (t0) REVERT: D 103 LYS cc_start: 0.9083 (mttt) cc_final: 0.8807 (mtmt) REVERT: D 167 PHE cc_start: 0.8721 (m-80) cc_final: 0.8225 (m-10) REVERT: D 297 LYS cc_start: 0.8715 (mttt) cc_final: 0.8226 (tmmt) REVERT: D 330 MET cc_start: 0.8357 (mmm) cc_final: 0.7920 (mtp) REVERT: D 335 ASN cc_start: 0.8302 (m-40) cc_final: 0.8089 (m110) REVERT: I 69 GLU cc_start: 0.7983 (pm20) cc_final: 0.7451 (pm20) REVERT: I 167 PHE cc_start: 0.8967 (m-80) cc_final: 0.8679 (m-80) REVERT: I 291 GLN cc_start: 0.8369 (tt0) cc_final: 0.8030 (tp-100) REVERT: I 330 MET cc_start: 0.8383 (mmm) cc_final: 0.8019 (mtp) REVERT: A 36 MET cc_start: 0.9034 (ttp) cc_final: 0.8822 (ttp) REVERT: A 80 THR cc_start: 0.8751 (m) cc_final: 0.8469 (t) REVERT: A 124 LYS cc_start: 0.8932 (ttmm) cc_final: 0.8417 (ttpp) REVERT: A 154 MET cc_start: 0.8416 (mmt) cc_final: 0.8128 (mmt) REVERT: A 221 ARG cc_start: 0.7933 (mtt-85) cc_final: 0.7672 (mpp80) REVERT: A 279 GLU cc_start: 0.8628 (tp30) cc_final: 0.8237 (tp30) REVERT: A 351 PHE cc_start: 0.8993 (m-80) cc_final: 0.8615 (m-80) REVERT: B 210 ILE cc_start: 0.9295 (mm) cc_final: 0.9064 (mt) REVERT: B 279 GLN cc_start: 0.8271 (mt0) cc_final: 0.8033 (mt0) REVERT: B 332 ASN cc_start: 0.8336 (t0) cc_final: 0.7996 (t0) REVERT: H 3 GLU cc_start: 0.7960 (mp0) cc_final: 0.7688 (mp0) REVERT: H 247 ASN cc_start: 0.8411 (m-40) cc_final: 0.7973 (m110) REVERT: H 379 LYS cc_start: 0.8590 (mtpt) cc_final: 0.8170 (tttm) REVERT: E 79 ARG cc_start: 0.9083 (OUTLIER) cc_final: 0.8863 (mtt180) REVERT: E 154 MET cc_start: 0.8707 (mmm) cc_final: 0.8053 (mmt) REVERT: E 170 SER cc_start: 0.9336 (m) cc_final: 0.9076 (t) REVERT: E 319 TYR cc_start: 0.9153 (m-80) cc_final: 0.8519 (m-80) REVERT: J 124 LYS cc_start: 0.9019 (ttmm) cc_final: 0.8514 (ttpp) REVERT: J 154 MET cc_start: 0.8612 (mmt) cc_final: 0.8285 (mmt) REVERT: J 254 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7550 (tp30) REVERT: J 319 TYR cc_start: 0.9113 (m-80) cc_final: 0.8695 (m-10) REVERT: J 430 LYS cc_start: 0.8627 (mmtp) cc_final: 0.8264 (tttt) REVERT: C 80 THR cc_start: 0.8850 (m) cc_final: 0.8547 (t) REVERT: C 91 GLN cc_start: 0.8383 (mt0) cc_final: 0.8011 (mt0) REVERT: C 254 GLU cc_start: 0.7894 (mp0) cc_final: 0.6972 (mp0) REVERT: C 279 GLU cc_start: 0.8682 (tp30) cc_final: 0.7999 (tt0) REVERT: C 295 CYS cc_start: 0.8317 (m) cc_final: 0.7970 (m) REVERT: C 433 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7594 (tp30) REVERT: L 80 THR cc_start: 0.9005 (m) cc_final: 0.8635 (t) REVERT: L 91 GLN cc_start: 0.8377 (mt0) cc_final: 0.7972 (mt0) REVERT: L 120 ASP cc_start: 0.7924 (t70) cc_final: 0.7648 (t0) REVERT: L 145 THR cc_start: 0.8917 (m) cc_final: 0.8662 (m) REVERT: L 172 TYR cc_start: 0.8204 (t80) cc_final: 0.7362 (t80) REVERT: L 203 MET cc_start: 0.8839 (mmp) cc_final: 0.7792 (mmt) REVERT: L 207 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7121 (tm-30) REVERT: L 248 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7844 (tt) REVERT: L 254 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7730 (tp30) REVERT: L 339 ARG cc_start: 0.7599 (ptt90) cc_final: 0.7239 (ttp-110) REVERT: L 353 VAL cc_start: 0.9456 (t) cc_final: 0.8838 (m) REVERT: L 377 MET cc_start: 0.8567 (ttp) cc_final: 0.8358 (tmm) REVERT: L 433 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7768 (tp30) REVERT: K 3 GLU cc_start: 0.8056 (mp0) cc_final: 0.7772 (mp0) REVERT: K 124 LYS cc_start: 0.8908 (ttmm) cc_final: 0.8515 (ttpp) REVERT: K 433 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7713 (tp30) outliers start: 107 outliers final: 95 residues processed: 728 average time/residue: 0.2390 time to fit residues: 289.6068 Evaluate side-chains 726 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 628 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 145 SER Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 239 CYS Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain I residue 127 CYS Chi-restraints excluded: chain I residue 181 GLU Chi-restraints excluded: chain I residue 205 GLU Chi-restraints excluded: chain I residue 225 LEU Chi-restraints excluded: chain I residue 239 CYS Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 374 ILE Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain H residue 219 THR Chi-restraints excluded: chain H residue 326 VAL Chi-restraints excluded: chain H residue 375 GLN Chi-restraints excluded: chain E residue 4 CYS Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 79 ARG Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain J residue 4 CYS Chi-restraints excluded: chain J residue 33 ASP Chi-restraints excluded: chain J residue 36 MET Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 194 THR Chi-restraints excluded: chain J residue 207 GLU Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 285 GLN Chi-restraints excluded: chain J residue 288 VAL Chi-restraints excluded: chain J residue 324 VAL Chi-restraints excluded: chain J residue 335 ILE Chi-restraints excluded: chain J residue 362 VAL Chi-restraints excluded: chain J residue 398 MET Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 36 MET Chi-restraints excluded: chain L residue 151 SER Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 207 GLU Chi-restraints excluded: chain L residue 248 LEU Chi-restraints excluded: chain L residue 252 LEU Chi-restraints excluded: chain L residue 288 VAL Chi-restraints excluded: chain L residue 303 VAL Chi-restraints excluded: chain L residue 324 VAL Chi-restraints excluded: chain L residue 362 VAL Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 381 THR Chi-restraints excluded: chain K residue 4 CYS Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 133 GLN Chi-restraints excluded: chain K residue 151 SER Chi-restraints excluded: chain K residue 154 MET Chi-restraints excluded: chain K residue 160 ASP Chi-restraints excluded: chain K residue 218 ASP Chi-restraints excluded: chain K residue 253 THR Chi-restraints excluded: chain K residue 324 VAL Chi-restraints excluded: chain K residue 335 ILE Chi-restraints excluded: chain K residue 353 VAL Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 379 SER Chi-restraints excluded: chain K residue 419 SER Chi-restraints excluded: chain K residue 428 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 485 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 127 optimal weight: 7.9990 chunk 125 optimal weight: 9.9990 chunk 394 optimal weight: 30.0000 chunk 134 optimal weight: 6.9990 chunk 181 optimal weight: 20.0000 chunk 67 optimal weight: 0.8980 chunk 238 optimal weight: 0.0670 chunk 44 optimal weight: 5.9990 chunk 55 optimal weight: 8.9990 overall best weight: 3.7924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 335 ASN F 423 GLN ** G 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 31 GLN ** J 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.097345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.083886 restraints weight = 66468.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.086702 restraints weight = 37179.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.088674 restraints weight = 24483.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.090073 restraints weight = 17807.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.091097 restraints weight = 13833.999| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.4758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 41796 Z= 0.143 Angle : 0.557 9.624 56784 Z= 0.278 Chirality : 0.045 0.328 6216 Planarity : 0.004 0.057 7398 Dihedral : 9.979 146.207 5760 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.50 % Allowed : 15.26 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.12), residues: 5130 helix: 0.46 (0.12), residues: 2220 sheet: -0.46 (0.19), residues: 840 loop : -1.16 (0.13), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 339 TYR 0.016 0.001 TYR K 103 PHE 0.028 0.001 PHE H 212 TRP 0.011 0.001 TRP C 21 HIS 0.003 0.001 HIS H 28 Details of bonding type rmsd covalent geometry : bond 0.00337 (41796) covalent geometry : angle 0.55656 (56784) hydrogen bonds : bond 0.03233 ( 1440) hydrogen bonds : angle 4.24849 ( 4284) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7068.87 seconds wall clock time: 123 minutes 2.17 seconds (7382.17 seconds total)