Starting phenix.real_space_refine on Fri Mar 6 23:05:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7d72_30599/03_2026/7d72_30599.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d72_30599/03_2026/7d72_30599.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7d72_30599/03_2026/7d72_30599.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d72_30599/03_2026/7d72_30599.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7d72_30599/03_2026/7d72_30599.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d72_30599/03_2026/7d72_30599.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 24 5.49 5 Mg 3 5.21 5 S 220 5.16 5 C 22479 2.51 5 N 6205 2.21 5 O 6527 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 331 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35458 Number of models: 1 Model: "" Number of chains: 27 Chain: "K" Number of atoms: 2787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2787 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 337} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 2789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2789 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 22, 'TRANS': 337} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 2 Chain: "A" Number of atoms: 3172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3172 Classifications: {'peptide': 407} Link IDs: {'PTRANS': 31, 'TRANS': 375} Chain breaks: 1 Chain: "B" Number of atoms: 3167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3167 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 31, 'TRANS': 374} Chain breaks: 1 Chain: "C" Number of atoms: 3167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3167 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 31, 'TRANS': 374} Chain breaks: 1 Chain: "D" Number of atoms: 3167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3167 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 31, 'TRANS': 374} Chain breaks: 1 Chain: "E" Number of atoms: 2789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2789 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 22, 'TRANS': 337} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 2 Chain: "F" Number of atoms: 2789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2789 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 22, 'TRANS': 337} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 2 Chain: "G" Number of atoms: 2789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2789 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 22, 'TRANS': 337} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 2 Chain: "H" Number of atoms: 2789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2789 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 22, 'TRANS': 337} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 2 Chain: "J" Number of atoms: 2789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2789 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 22, 'TRANS': 337} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 2 Chain: "L" Number of atoms: 2787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2787 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 337} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'GDD': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'GDD': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'GDD': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'GDD': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'GDD': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'GDD': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {' MG': 1, 'GDD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {' MG': 1, 'GDD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {' MG': 1, 'GDD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'GDD': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'GDD': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'GDD': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 9.26, per 1000 atoms: 0.26 Number of scatterers: 35458 At special positions: 0 Unit cell: (135.296, 198.716, 183.918, 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 220 16.00 P 24 15.00 Mg 3 11.99 O 6527 8.00 N 6205 7.00 C 22479 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS E 289 " - pdb=" SG CYS E 306 " distance=2.03 Simple disulfide: pdb=" SG CYS G 289 " - pdb=" SG CYS G 306 " distance=2.03 Simple disulfide: pdb=" SG CYS J 289 " - pdb=" SG CYS J 306 " distance=2.03 Simple disulfide: pdb=" SG CYS L 289 " - pdb=" SG CYS L 306 " distance=2.03 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.82 Conformation dependent library (CDL) restraints added in 1.5 seconds 8946 Ramachandran restraints generated. 4473 Oldfield, 0 Emsley, 4473 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8274 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 81 sheets defined 28.6% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.95 Creating SS restraints... Processing helix chain 'K' and resid 14 through 19 removed outlier: 3.509A pdb=" N THR K 18 " --> pdb=" O LEU K 14 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 25 Processing helix chain 'K' and resid 33 through 45 Processing helix chain 'K' and resid 56 through 72 removed outlier: 4.751A pdb=" N LEU K 60 " --> pdb=" O MET K 56 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ALA K 66 " --> pdb=" O LYS K 62 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG K 70 " --> pdb=" O ALA K 66 " (cutoff:3.500A) Processing helix chain 'K' and resid 87 through 93 Processing helix chain 'K' and resid 93 through 99 removed outlier: 3.744A pdb=" N LEU K 97 " --> pdb=" O ALA K 93 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU K 99 " --> pdb=" O ASP K 95 " (cutoff:3.500A) Processing helix chain 'K' and resid 116 through 128 removed outlier: 3.516A pdb=" N HIS K 126 " --> pdb=" O GLN K 122 " (cutoff:3.500A) Processing helix chain 'K' and resid 179 through 184 removed outlier: 3.598A pdb=" N LEU K 183 " --> pdb=" O SER K 179 " (cutoff:3.500A) Processing helix chain 'K' and resid 192 through 205 Proline residue: K 199 - end of helix Processing helix chain 'K' and resid 221 through 240 Processing helix chain 'I' and resid 16 through 20 removed outlier: 3.991A pdb=" N LEU I 19 " --> pdb=" O PRO I 16 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N SER I 20 " --> pdb=" O LEU I 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 16 through 20' Processing helix chain 'I' and resid 22 through 25 Processing helix chain 'I' and resid 33 through 45 removed outlier: 3.919A pdb=" N GLN I 37 " --> pdb=" O ILE I 33 " (cutoff:3.500A) Processing helix chain 'I' and resid 57 through 72 removed outlier: 4.345A pdb=" N GLN I 69 " --> pdb=" O LYS I 65 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ARG I 70 " --> pdb=" O ALA I 66 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY I 72 " --> pdb=" O GLU I 68 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 93 removed outlier: 3.548A pdb=" N ALA I 91 " --> pdb=" O ALA I 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 98 Processing helix chain 'I' and resid 116 through 128 Processing helix chain 'I' and resid 140 through 144 removed outlier: 4.299A pdb=" N LYS I 143 " --> pdb=" O GLU I 140 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR I 144 " --> pdb=" O PRO I 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 140 through 144' Processing helix chain 'I' and resid 181 through 186 removed outlier: 3.929A pdb=" N ARG I 185 " --> pdb=" O ALA I 181 " (cutoff:3.500A) Processing helix chain 'I' and resid 192 through 197 Processing helix chain 'I' and resid 197 through 205 removed outlier: 4.416A pdb=" N LYS I 203 " --> pdb=" O PRO I 199 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLU I 204 " --> pdb=" O ILE I 200 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY I 205 " --> pdb=" O MET I 201 " (cutoff:3.500A) Processing helix chain 'I' and resid 221 through 240 removed outlier: 3.815A pdb=" N GLN I 234 " --> pdb=" O CYS I 230 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER I 235 " --> pdb=" O LEU I 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 28 Processing helix chain 'A' and resid 37 through 47 removed outlier: 3.724A pdb=" N VAL A 47 " --> pdb=" O ALA A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 77 Processing helix chain 'A' and resid 89 through 98 removed outlier: 3.693A pdb=" N GLY A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU A 95 " --> pdb=" O THR A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 103 Processing helix chain 'A' and resid 122 through 134 removed outlier: 4.061A pdb=" N GLN A 133 " --> pdb=" O ALA A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 203 removed outlier: 4.174A pdb=" N LEU A 194 " --> pdb=" O ALA A 190 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASP A 196 " --> pdb=" O LYS A 192 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN A 203 " --> pdb=" O GLN A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 230 removed outlier: 3.811A pdb=" N PHE A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N SER A 228 " --> pdb=" O GLN A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 269 removed outlier: 4.522A pdb=" N GLN A 266 " --> pdb=" O LEU A 262 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N ASP A 267 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N THR A 268 " --> pdb=" O ARG A 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 16 removed outlier: 3.716A pdb=" N THR B 15 " --> pdb=" O GLN B 12 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ARG B 16 " --> pdb=" O LYS B 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 12 through 16' Processing helix chain 'B' and resid 17 through 22 Processing helix chain 'B' and resid 25 through 28 Processing helix chain 'B' and resid 37 through 46 Processing helix chain 'B' and resid 62 through 77 removed outlier: 3.663A pdb=" N GLN B 74 " --> pdb=" O GLU B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 98 removed outlier: 4.098A pdb=" N GLY B 94 " --> pdb=" O GLY B 90 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N LEU B 95 " --> pdb=" O THR B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 103 Processing helix chain 'B' and resid 122 through 134 removed outlier: 4.003A pdb=" N ARG B 132 " --> pdb=" O GLU B 128 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLN B 133 " --> pdb=" O ALA B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 151 removed outlier: 3.592A pdb=" N LEU B 150 " --> pdb=" O THR B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 202 removed outlier: 4.034A pdb=" N LEU B 194 " --> pdb=" O ALA B 190 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP B 196 " --> pdb=" O LYS B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 226 Processing helix chain 'B' and resid 252 through 269 removed outlier: 3.912A pdb=" N TYR B 256 " --> pdb=" O GLY B 252 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLN B 266 " --> pdb=" O LEU B 262 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ASP B 267 " --> pdb=" O SER B 263 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR B 268 " --> pdb=" O ARG B 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 15 removed outlier: 3.690A pdb=" N GLY C 14 " --> pdb=" O GLY C 10 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N THR C 15 " --> pdb=" O PRO C 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 10 through 15' Processing helix chain 'C' and resid 25 through 28 Processing helix chain 'C' and resid 36 through 46 removed outlier: 4.250A pdb=" N HIS C 40 " --> pdb=" O MET C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 77 removed outlier: 3.719A pdb=" N GLN C 74 " --> pdb=" O GLU C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 98 Processing helix chain 'C' and resid 98 through 104 Processing helix chain 'C' and resid 122 through 134 Processing helix chain 'C' and resid 147 through 151 removed outlier: 3.591A pdb=" N LEU C 150 " --> pdb=" O THR C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 203 removed outlier: 4.065A pdb=" N LEU C 194 " --> pdb=" O ALA C 190 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN C 203 " --> pdb=" O GLN C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 226 Processing helix chain 'C' and resid 250 through 269 removed outlier: 4.389A pdb=" N GLN C 266 " --> pdb=" O LEU C 262 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N ASP C 267 " --> pdb=" O SER C 263 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR C 268 " --> pdb=" O ARG C 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 16 removed outlier: 4.202A pdb=" N ARG D 16 " --> pdb=" O LYS D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 22 removed outlier: 3.611A pdb=" N PHE D 22 " --> pdb=" O ARG D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 28 Processing helix chain 'D' and resid 36 through 46 removed outlier: 4.178A pdb=" N HIS D 40 " --> pdb=" O MET D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 77 removed outlier: 3.793A pdb=" N GLN D 74 " --> pdb=" O GLU D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 98 removed outlier: 3.792A pdb=" N GLY D 94 " --> pdb=" O GLY D 90 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LEU D 95 " --> pdb=" O THR D 91 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE D 98 " --> pdb=" O GLY D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 103 Processing helix chain 'D' and resid 122 through 134 removed outlier: 3.579A pdb=" N ARG D 132 " --> pdb=" O GLU D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 151 removed outlier: 3.598A pdb=" N ASN D 151 " --> pdb=" O GLN D 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 148 through 151' Processing helix chain 'D' and resid 190 through 203 removed outlier: 4.144A pdb=" N LEU D 194 " --> pdb=" O ALA D 190 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP D 196 " --> pdb=" O LYS D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 231 removed outlier: 3.645A pdb=" N PHE D 227 " --> pdb=" O GLU D 223 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N SER D 228 " --> pdb=" O GLN D 224 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA D 229 " --> pdb=" O ASP D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 269 removed outlier: 4.107A pdb=" N TYR D 256 " --> pdb=" O GLY D 252 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLN D 266 " --> pdb=" O LEU D 262 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N THR D 268 " --> pdb=" O ARG D 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 13 No H-bonds generated for 'chain 'E' and resid 11 through 13' Processing helix chain 'E' and resid 14 through 19 Processing helix chain 'E' and resid 22 through 26 removed outlier: 3.528A pdb=" N VAL E 26 " --> pdb=" O LYS E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 45 Processing helix chain 'E' and resid 60 through 72 removed outlier: 4.059A pdb=" N GLN E 69 " --> pdb=" O LYS E 65 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG E 70 " --> pdb=" O ALA E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 93 removed outlier: 3.940A pdb=" N ALA E 91 " --> pdb=" O ALA E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 99 Processing helix chain 'E' and resid 116 through 128 Processing helix chain 'E' and resid 196 through 205 removed outlier: 3.535A pdb=" N ILE E 200 " --> pdb=" O GLU E 196 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU E 204 " --> pdb=" O ILE E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 240 removed outlier: 3.701A pdb=" N LEU E 226 " --> pdb=" O PRO E 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 19 Processing helix chain 'F' and resid 22 through 26 removed outlier: 3.618A pdb=" N VAL F 26 " --> pdb=" O LYS F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 45 removed outlier: 3.555A pdb=" N GLN F 37 " --> pdb=" O ILE F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 67 removed outlier: 3.632A pdb=" N LEU F 60 " --> pdb=" O MET F 56 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLU F 63 " --> pdb=" O VAL F 59 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLN F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 72 removed outlier: 3.682A pdb=" N LEU F 71 " --> pdb=" O GLN F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 93 Processing helix chain 'F' and resid 93 through 98 Processing helix chain 'F' and resid 116 through 128 Processing helix chain 'F' and resid 140 through 144 removed outlier: 4.310A pdb=" N LYS F 143 " --> pdb=" O GLU F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 186 removed outlier: 4.125A pdb=" N ARG F 185 " --> pdb=" O ALA F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 192 through 205 removed outlier: 3.654A pdb=" N GLU F 196 " --> pdb=" O SER F 192 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N PHE F 198 " --> pdb=" O GLU F 194 " (cutoff:3.500A) Proline residue: F 199 - end of helix removed outlier: 3.514A pdb=" N LYS F 203 " --> pdb=" O PRO F 199 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU F 204 " --> pdb=" O ILE F 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 221 through 240 removed outlier: 4.256A pdb=" N GLN F 234 " --> pdb=" O CYS F 230 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER F 235 " --> pdb=" O LEU F 231 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 19 Processing helix chain 'G' and resid 22 through 26 removed outlier: 3.538A pdb=" N VAL G 26 " --> pdb=" O LYS G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 45 removed outlier: 3.519A pdb=" N GLN G 37 " --> pdb=" O ILE G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 72 removed outlier: 4.101A pdb=" N LYS G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N GLN G 69 " --> pdb=" O LYS G 65 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ARG G 70 " --> pdb=" O ALA G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 93 Processing helix chain 'G' and resid 93 through 99 removed outlier: 3.721A pdb=" N LEU G 97 " --> pdb=" O ALA G 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 128 Processing helix chain 'G' and resid 180 through 185 Processing helix chain 'G' and resid 192 through 205 removed outlier: 5.111A pdb=" N PHE G 198 " --> pdb=" O GLU G 194 " (cutoff:3.500A) Proline residue: G 199 - end of helix removed outlier: 3.601A pdb=" N GLU G 204 " --> pdb=" O ILE G 200 " (cutoff:3.500A) Processing helix chain 'G' and resid 221 through 240 removed outlier: 3.581A pdb=" N THR G 227 " --> pdb=" O LYS G 223 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN G 234 " --> pdb=" O CYS G 230 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 26 removed outlier: 3.583A pdb=" N VAL H 26 " --> pdb=" O LYS H 23 " (cutoff:3.500A) Processing helix chain 'H' and resid 32 through 45 removed outlier: 3.576A pdb=" N HIS H 36 " --> pdb=" O PRO H 32 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLN H 37 " --> pdb=" O ILE H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 72 removed outlier: 3.701A pdb=" N ARG H 70 " --> pdb=" O ALA H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 93 Processing helix chain 'H' and resid 93 through 98 removed outlier: 3.519A pdb=" N LEU H 97 " --> pdb=" O ALA H 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 116 through 128 Processing helix chain 'H' and resid 140 through 144 removed outlier: 4.016A pdb=" N LYS H 143 " --> pdb=" O GLU H 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 192 through 205 Proline residue: H 199 - end of helix Processing helix chain 'H' and resid 221 through 240 removed outlier: 3.681A pdb=" N GLN H 234 " --> pdb=" O CYS H 230 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER H 235 " --> pdb=" O LEU H 231 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 19 Processing helix chain 'J' and resid 22 through 26 removed outlier: 3.669A pdb=" N VAL J 26 " --> pdb=" O LYS J 23 " (cutoff:3.500A) Processing helix chain 'J' and resid 32 through 45 removed outlier: 3.672A pdb=" N GLN J 37 " --> pdb=" O ILE J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 57 through 72 removed outlier: 3.514A pdb=" N GLU J 61 " --> pdb=" O SER J 57 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ARG J 70 " --> pdb=" O ALA J 66 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 93 removed outlier: 3.513A pdb=" N ALA J 91 " --> pdb=" O ALA J 87 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 99 Processing helix chain 'J' and resid 116 through 128 removed outlier: 3.745A pdb=" N GLN J 122 " --> pdb=" O GLN J 118 " (cutoff:3.500A) Processing helix chain 'J' and resid 179 through 183 Processing helix chain 'J' and resid 196 through 205 removed outlier: 3.589A pdb=" N ILE J 200 " --> pdb=" O GLU J 196 " (cutoff:3.500A) Processing helix chain 'J' and resid 221 through 240 removed outlier: 4.416A pdb=" N LEU J 226 " --> pdb=" O PRO J 222 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR J 227 " --> pdb=" O LYS J 223 " (cutoff:3.500A) Processing helix chain 'L' and resid 14 through 19 Processing helix chain 'L' and resid 32 through 45 removed outlier: 3.609A pdb=" N HIS L 36 " --> pdb=" O PRO L 32 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN L 37 " --> pdb=" O ILE L 33 " (cutoff:3.500A) Processing helix chain 'L' and resid 57 through 72 removed outlier: 4.165A pdb=" N GLU L 63 " --> pdb=" O VAL L 59 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLN L 69 " --> pdb=" O LYS L 65 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ARG L 70 " --> pdb=" O ALA L 66 " (cutoff:3.500A) Processing helix chain 'L' and resid 87 through 93 removed outlier: 3.594A pdb=" N ALA L 91 " --> pdb=" O ALA L 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 93 through 99 Processing helix chain 'L' and resid 116 through 128 Processing helix chain 'L' and resid 179 through 186 removed outlier: 4.131A pdb=" N LEU L 183 " --> pdb=" O SER L 179 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLN L 184 " --> pdb=" O PRO L 180 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG L 185 " --> pdb=" O ALA L 181 " (cutoff:3.500A) Processing helix chain 'L' and resid 192 through 205 removed outlier: 3.991A pdb=" N GLU L 196 " --> pdb=" O SER L 192 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N PHE L 198 " --> pdb=" O GLU L 194 " (cutoff:3.500A) Proline residue: L 199 - end of helix Processing helix chain 'L' and resid 221 through 240 removed outlier: 4.278A pdb=" N GLN L 234 " --> pdb=" O CYS L 230 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N SER L 235 " --> pdb=" O LEU L 231 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 74 through 79 removed outlier: 5.902A pdb=" N VAL K 49 " --> pdb=" O SER K 76 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N SER K 78 " --> pdb=" O VAL K 49 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LEU K 51 " --> pdb=" O SER K 78 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ALA K 3 " --> pdb=" O ILE K 50 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ALA K 52 " --> pdb=" O ALA K 3 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ILE K 5 " --> pdb=" O ALA K 52 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASN K 108 " --> pdb=" O GLY K 174 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N GLY K 174 " --> pdb=" O ASN K 108 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU K 134 " --> pdb=" O ALA K 173 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N MET K 175 " --> pdb=" O SER K 132 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N SER K 132 " --> pdb=" O MET K 175 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 27 through 28 removed outlier: 3.607A pdb=" N LYS K 31 " --> pdb=" O PHE K 28 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'K' and resid 111 through 112 Processing sheet with id=AA4, first strand: chain 'K' and resid 146 through 147 removed outlier: 3.743A pdb=" N VAL K 160 " --> pdb=" O VAL K 146 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'K' and resid 254 through 256 removed outlier: 6.843A pdb=" N LEU K 255 " --> pdb=" O LEU K 274 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N SER K 273 " --> pdb=" O VAL K 291 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N THR K 290 " --> pdb=" O VAL K 308 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE K 307 " --> pdb=" O LEU K 326 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'K' and resid 261 through 262 removed outlier: 6.503A pdb=" N ARG K 261 " --> pdb=" O VAL K 280 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL K 279 " --> pdb=" O ILE K 297 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ARG K 296 " --> pdb=" O VAL K 314 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ARG K 313 " --> pdb=" O VAL K 332 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ILE K 331 " --> pdb=" O ILE K 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'K' and resid 285 through 287 removed outlier: 6.337A pdb=" N CYS K 285 " --> pdb=" O LEU K 303 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ARG K 319 " --> pdb=" O LEU K 338 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 74 through 79 removed outlier: 6.327A pdb=" N VAL I 49 " --> pdb=" O SER I 76 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N SER I 78 " --> pdb=" O VAL I 49 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N LEU I 51 " --> pdb=" O SER I 78 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ALA I 3 " --> pdb=" O ILE I 50 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ALA I 52 " --> pdb=" O ALA I 3 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N ILE I 5 " --> pdb=" O ALA I 52 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N GLY I 174 " --> pdb=" O ASN I 108 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N LEU I 134 " --> pdb=" O ALA I 173 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N MET I 175 " --> pdb=" O SER I 132 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N SER I 132 " --> pdb=" O MET I 175 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 27 through 28 Processing sheet with id=AB1, first strand: chain 'I' and resid 111 through 112 Processing sheet with id=AB2, first strand: chain 'I' and resid 254 through 256 removed outlier: 6.571A pdb=" N SER I 273 " --> pdb=" O VAL I 291 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N THR I 290 " --> pdb=" O VAL I 308 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 261 through 262 removed outlier: 6.476A pdb=" N ARG I 261 " --> pdb=" O VAL I 280 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N VAL I 279 " --> pdb=" O ILE I 297 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ARG I 296 " --> pdb=" O VAL I 314 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ARG I 313 " --> pdb=" O VAL I 332 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ILE I 331 " --> pdb=" O ILE I 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'I' and resid 285 through 287 removed outlier: 6.382A pdb=" N CYS I 285 " --> pdb=" O LEU I 303 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ARG I 319 " --> pdb=" O LEU I 338 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 80 through 83 removed outlier: 8.451A pdb=" N ARG A 81 " --> pdb=" O GLN A 51 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ILE A 53 " --> pdb=" O ARG A 81 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N LEU A 83 " --> pdb=" O ILE A 53 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N LEU A 55 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N LEU A 2 " --> pdb=" O GLN A 51 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE A 53 " --> pdb=" O LEU A 2 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ALA A 4 " --> pdb=" O ILE A 53 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N LEU A 55 " --> pdb=" O ALA A 4 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE A 6 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LYS A 3 " --> pdb=" O ALA A 109 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N GLY A 182 " --> pdb=" O ASN A 114 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ILE A 178 " --> pdb=" O ILE A 155 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N GLY A 153 " --> pdb=" O ASN A 180 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N CYS A 154 " --> pdb=" O TYR A 167 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N TYR A 167 " --> pdb=" O CYS A 154 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL A 156 " --> pdb=" O LEU A 165 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 80 through 83 removed outlier: 8.451A pdb=" N ARG A 81 " --> pdb=" O GLN A 51 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ILE A 53 " --> pdb=" O ARG A 81 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N LEU A 83 " --> pdb=" O ILE A 53 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N LEU A 55 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N LEU A 2 " --> pdb=" O GLN A 51 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE A 53 " --> pdb=" O LEU A 2 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ALA A 4 " --> pdb=" O ILE A 53 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N LEU A 55 " --> pdb=" O ALA A 4 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE A 6 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LYS A 3 " --> pdb=" O ALA A 109 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N GLY A 182 " --> pdb=" O ASN A 114 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N LEU A 140 " --> pdb=" O CYS A 181 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ILE A 183 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LEU A 138 " --> pdb=" O ILE A 183 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 30 through 31 removed outlier: 3.793A pdb=" N VAL A 34 " --> pdb=" O VAL A 31 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 117 through 119 Processing sheet with id=AB9, first strand: chain 'A' and resid 282 through 283 removed outlier: 7.062A pdb=" N TRP A 282 " --> pdb=" O LEU A 301 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N VAL A 300 " --> pdb=" O LEU A 319 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ARG A 318 " --> pdb=" O VAL A 336 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 287 through 289 removed outlier: 6.537A pdb=" N SER A 306 " --> pdb=" O VAL A 324 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ILE A 323 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE A 386 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ILE A 403 " --> pdb=" O ILE A 419 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 294 through 295 removed outlier: 6.420A pdb=" N LYS A 294 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N THR A 312 " --> pdb=" O LEU A 330 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N THR A 329 " --> pdb=" O VAL A 347 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N THR A 346 " --> pdb=" O ILE A 393 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'B' and resid 80 through 84 removed outlier: 3.583A pdb=" N GLY B 57 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N LEU B 2 " --> pdb=" O MET B 50 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLU B 52 " --> pdb=" O LEU B 2 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N GLY B 182 " --> pdb=" O ASN B 114 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N LEU B 140 " --> pdb=" O CYS B 181 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE B 183 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N LEU B 138 " --> pdb=" O ILE B 183 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 30 through 31 removed outlier: 3.640A pdb=" N VAL B 34 " --> pdb=" O VAL B 31 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 117 through 119 Processing sheet with id=AC6, first strand: chain 'B' and resid 154 through 157 Processing sheet with id=AC7, first strand: chain 'B' and resid 282 through 283 removed outlier: 6.578A pdb=" N TRP B 282 " --> pdb=" O LEU B 301 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL B 300 " --> pdb=" O LEU B 319 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ARG B 318 " --> pdb=" O VAL B 336 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ARG B 352 " --> pdb=" O ILE B 399 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 287 through 289 removed outlier: 6.706A pdb=" N TYR B 288 " --> pdb=" O ILE B 307 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N SER B 306 " --> pdb=" O VAL B 324 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE B 323 " --> pdb=" O VAL B 341 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE B 340 " --> pdb=" O LEU B 387 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE B 386 " --> pdb=" O VAL B 404 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ILE B 403 " --> pdb=" O ILE B 419 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 294 through 295 removed outlier: 6.772A pdb=" N LYS B 294 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N THR B 312 " --> pdb=" O LEU B 330 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N THR B 329 " --> pdb=" O VAL B 347 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N THR B 346 " --> pdb=" O ILE B 393 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'C' and resid 80 through 83 removed outlier: 8.785A pdb=" N ARG C 81 " --> pdb=" O GLN C 51 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE C 53 " --> pdb=" O ARG C 81 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N LEU C 83 " --> pdb=" O ILE C 53 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N LEU C 55 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU C 2 " --> pdb=" O MET C 50 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLU C 52 " --> pdb=" O LEU C 2 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYS C 3 " --> pdb=" O ALA C 109 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N GLY C 182 " --> pdb=" O ASN C 114 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LEU C 140 " --> pdb=" O CYS C 181 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ILE C 183 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LEU C 138 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N PHE C 137 " --> pdb=" O TYR C 237 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N HIS C 239 " --> pdb=" O PHE C 137 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N LEU C 139 " --> pdb=" O HIS C 239 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 30 through 31 removed outlier: 3.661A pdb=" N VAL C 34 " --> pdb=" O VAL C 31 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 117 through 119 Processing sheet with id=AD4, first strand: chain 'C' and resid 153 through 158 removed outlier: 5.935A pdb=" N ASN C 158 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N VAL C 164 " --> pdb=" O ASN C 158 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 282 through 283 removed outlier: 6.718A pdb=" N TRP C 282 " --> pdb=" O LEU C 301 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N VAL C 300 " --> pdb=" O LEU C 319 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 287 through 288 removed outlier: 6.666A pdb=" N TYR C 288 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N SER C 306 " --> pdb=" O VAL C 324 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE C 323 " --> pdb=" O VAL C 341 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILE C 386 " --> pdb=" O VAL C 404 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ILE C 403 " --> pdb=" O ILE C 419 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 294 through 295 removed outlier: 6.484A pdb=" N LYS C 294 " --> pdb=" O VAL C 313 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N THR C 312 " --> pdb=" O LEU C 330 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N THR C 329 " --> pdb=" O VAL C 347 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N THR C 346 " --> pdb=" O ILE C 393 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'D' and resid 80 through 84 removed outlier: 7.905A pdb=" N LEU D 2 " --> pdb=" O GLN D 51 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ILE D 53 " --> pdb=" O LEU D 2 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ALA D 4 " --> pdb=" O ILE D 53 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N LEU D 55 " --> pdb=" O ALA D 4 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE D 6 " --> pdb=" O LEU D 55 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N GLY D 57 " --> pdb=" O ILE D 6 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS D 3 " --> pdb=" O ALA D 109 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N GLY D 182 " --> pdb=" O ASN D 114 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N LEU D 140 " --> pdb=" O CYS D 181 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILE D 183 " --> pdb=" O LEU D 138 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N LEU D 138 " --> pdb=" O ILE D 183 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N PHE D 137 " --> pdb=" O TYR D 237 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N HIS D 239 " --> pdb=" O PHE D 137 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N LEU D 139 " --> pdb=" O HIS D 239 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 30 through 31 removed outlier: 3.599A pdb=" N VAL D 34 " --> pdb=" O VAL D 31 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 117 through 119 Processing sheet with id=AE2, first strand: chain 'D' and resid 153 through 158 removed outlier: 6.482A pdb=" N ASN D 158 " --> pdb=" O VAL D 164 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL D 164 " --> pdb=" O ASN D 158 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 282 through 283 removed outlier: 7.188A pdb=" N TRP D 282 " --> pdb=" O LEU D 301 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL D 300 " --> pdb=" O LEU D 319 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ARG D 318 " --> pdb=" O VAL D 336 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ARG D 352 " --> pdb=" O ILE D 399 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 287 through 289 removed outlier: 6.466A pdb=" N SER D 306 " --> pdb=" O VAL D 324 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ILE D 323 " --> pdb=" O VAL D 341 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ILE D 340 " --> pdb=" O LEU D 387 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ILE D 386 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE D 403 " --> pdb=" O ILE D 419 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 294 through 295 removed outlier: 6.943A pdb=" N LYS D 294 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N THR D 312 " --> pdb=" O LEU D 330 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N THR D 329 " --> pdb=" O VAL D 347 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N THR D 346 " --> pdb=" O ILE D 393 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'E' and resid 74 through 78 removed outlier: 6.118A pdb=" N VAL E 49 " --> pdb=" O SER E 76 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N SER E 78 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N LEU E 51 " --> pdb=" O SER E 78 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ALA E 3 " --> pdb=" O ILE E 50 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N ALA E 52 " --> pdb=" O ALA E 3 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ILE E 5 " --> pdb=" O ALA E 52 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE E 105 " --> pdb=" O LYS E 2 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN E 108 " --> pdb=" O GLY E 174 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N GLY E 174 " --> pdb=" O ASN E 108 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU E 134 " --> pdb=" O ALA E 173 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N MET E 175 " --> pdb=" O SER E 132 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N SER E 132 " --> pdb=" O MET E 175 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 111 through 112 Processing sheet with id=AE8, first strand: chain 'E' and resid 146 through 147 Processing sheet with id=AE9, first strand: chain 'E' and resid 254 through 256 removed outlier: 6.761A pdb=" N LEU E 255 " --> pdb=" O LEU E 274 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N SER E 273 " --> pdb=" O VAL E 291 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N THR E 290 " --> pdb=" O VAL E 308 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N CYS E 285 " --> pdb=" O LEU E 303 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N SER E 305 " --> pdb=" O CYS E 285 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N ARG E 287 " --> pdb=" O SER E 305 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N ILE E 307 " --> pdb=" O ARG E 287 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N SER E 267 " --> pdb=" O ILE E 286 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'E' and resid 254 through 256 removed outlier: 6.761A pdb=" N LEU E 255 " --> pdb=" O LEU E 274 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N SER E 273 " --> pdb=" O VAL E 291 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N THR E 290 " --> pdb=" O VAL E 308 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N CYS E 306 " --> pdb=" O ASN E 322 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N THR E 324 " --> pdb=" O CYS E 306 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N VAL E 308 " --> pdb=" O THR E 324 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ARG E 319 " --> pdb=" O LEU E 338 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 261 through 262 removed outlier: 6.412A pdb=" N ARG E 261 " --> pdb=" O VAL E 280 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL E 279 " --> pdb=" O ILE E 297 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ARG E 296 " --> pdb=" O VAL E 314 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ARG E 313 " --> pdb=" O VAL E 332 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ILE E 331 " --> pdb=" O ILE E 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'E' and resid 342 through 343 removed outlier: 6.494A pdb=" N SER E 342 " --> pdb=" O ILE E 359 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'F' and resid 74 through 79 removed outlier: 6.733A pdb=" N VAL F 49 " --> pdb=" O SER F 76 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N SER F 78 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LEU F 51 " --> pdb=" O SER F 78 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ALA F 3 " --> pdb=" O ILE F 50 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ALA F 52 " --> pdb=" O ALA F 3 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N ILE F 5 " --> pdb=" O ALA F 52 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN F 108 " --> pdb=" O GLY F 174 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N GLY F 174 " --> pdb=" O ASN F 108 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LEU F 134 " --> pdb=" O ALA F 173 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N MET F 175 " --> pdb=" O SER F 132 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N SER F 132 " --> pdb=" O MET F 175 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 111 through 112 Processing sheet with id=AF6, first strand: chain 'F' and resid 146 through 149 removed outlier: 6.644A pdb=" N VAL F 146 " --> pdb=" O PHE F 159 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N PHE F 159 " --> pdb=" O VAL F 146 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL F 148 " --> pdb=" O HIS F 157 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 254 through 256 removed outlier: 6.658A pdb=" N LEU F 255 " --> pdb=" O LEU F 274 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N SER F 273 " --> pdb=" O VAL F 291 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N THR F 290 " --> pdb=" O VAL F 308 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'F' and resid 261 through 262 removed outlier: 6.498A pdb=" N ARG F 261 " --> pdb=" O VAL F 280 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL F 279 " --> pdb=" O ILE F 297 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ARG F 296 " --> pdb=" O VAL F 314 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ARG F 313 " --> pdb=" O VAL F 332 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE F 331 " --> pdb=" O ILE F 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'F' and resid 302 through 303 removed outlier: 6.370A pdb=" N TRP F 302 " --> pdb=" O MET F 320 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ARG F 319 " --> pdb=" O LEU F 338 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'G' and resid 75 through 78 removed outlier: 6.372A pdb=" N VAL G 49 " --> pdb=" O SER G 76 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N SER G 78 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEU G 51 " --> pdb=" O SER G 78 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ALA G 3 " --> pdb=" O ILE G 50 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N ALA G 52 " --> pdb=" O ALA G 3 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ILE G 5 " --> pdb=" O ALA G 52 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASN G 108 " --> pdb=" O GLY G 174 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N GLY G 174 " --> pdb=" O ASN G 108 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LEU G 134 " --> pdb=" O ALA G 173 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N MET G 175 " --> pdb=" O SER G 132 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N SER G 132 " --> pdb=" O MET G 175 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'G' and resid 111 through 112 Processing sheet with id=AG3, first strand: chain 'G' and resid 146 through 149 removed outlier: 4.249A pdb=" N ARG G 158 " --> pdb=" O VAL G 148 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'G' and resid 254 through 256 removed outlier: 6.856A pdb=" N LEU G 255 " --> pdb=" O LEU G 274 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N SER G 273 " --> pdb=" O VAL G 291 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N THR G 290 " --> pdb=" O VAL G 308 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'G' and resid 261 through 262 removed outlier: 6.492A pdb=" N ARG G 261 " --> pdb=" O VAL G 280 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL G 279 " --> pdb=" O ILE G 297 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ARG G 296 " --> pdb=" O VAL G 314 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ARG G 313 " --> pdb=" O VAL G 332 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ILE G 331 " --> pdb=" O ILE G 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG5 Processing sheet with id=AG6, first strand: chain 'G' and resid 285 through 287 removed outlier: 6.242A pdb=" N CYS G 285 " --> pdb=" O LEU G 303 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ARG G 319 " --> pdb=" O LEU G 338 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'G' and resid 342 through 343 removed outlier: 6.452A pdb=" N SER G 342 " --> pdb=" O ILE G 359 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG7 Processing sheet with id=AG8, first strand: chain 'H' and resid 74 through 79 removed outlier: 3.536A pdb=" N VAL H 49 " --> pdb=" O ARG H 74 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N ALA H 3 " --> pdb=" O ILE H 50 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N ALA H 52 " --> pdb=" O ALA H 3 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ILE H 5 " --> pdb=" O ALA H 52 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN H 108 " --> pdb=" O GLY H 174 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N GLY H 174 " --> pdb=" O ASN H 108 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU H 134 " --> pdb=" O ALA H 173 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N MET H 175 " --> pdb=" O SER H 132 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N SER H 132 " --> pdb=" O MET H 175 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'H' and resid 111 through 112 Processing sheet with id=AH1, first strand: chain 'H' and resid 146 through 149 removed outlier: 3.717A pdb=" N ARG H 158 " --> pdb=" O VAL H 148 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'H' and resid 254 through 256 removed outlier: 6.475A pdb=" N SER H 273 " --> pdb=" O VAL H 291 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N THR H 290 " --> pdb=" O VAL H 308 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ILE H 307 " --> pdb=" O LEU H 326 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'H' and resid 261 through 262 removed outlier: 6.661A pdb=" N ARG H 261 " --> pdb=" O VAL H 280 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N VAL H 279 " --> pdb=" O ILE H 297 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ARG H 296 " --> pdb=" O VAL H 314 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ARG H 313 " --> pdb=" O VAL H 332 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ILE H 331 " --> pdb=" O ILE H 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH3 Processing sheet with id=AH4, first strand: chain 'H' and resid 285 through 287 removed outlier: 6.348A pdb=" N ARG H 319 " --> pdb=" O LEU H 338 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'J' and resid 75 through 79 removed outlier: 6.110A pdb=" N ALA J 3 " --> pdb=" O ILE J 50 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N ALA J 52 " --> pdb=" O ALA J 3 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ILE J 5 " --> pdb=" O ALA J 52 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN J 108 " --> pdb=" O GLY J 174 " (cutoff:3.500A) removed outlier: 8.490A pdb=" N GLY J 174 " --> pdb=" O ASN J 108 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N LEU J 134 " --> pdb=" O ALA J 173 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N MET J 175 " --> pdb=" O SER J 132 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N SER J 132 " --> pdb=" O MET J 175 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'J' and resid 111 through 112 Processing sheet with id=AH7, first strand: chain 'J' and resid 146 through 148 removed outlier: 4.042A pdb=" N ARG J 158 " --> pdb=" O VAL J 148 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'J' and resid 254 through 256 removed outlier: 6.524A pdb=" N SER J 273 " --> pdb=" O VAL J 291 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N THR J 290 " --> pdb=" O VAL J 308 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'J' and resid 261 through 262 removed outlier: 6.526A pdb=" N ARG J 261 " --> pdb=" O VAL J 280 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL J 279 " --> pdb=" O ILE J 297 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ARG J 296 " --> pdb=" O VAL J 314 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ARG J 313 " --> pdb=" O VAL J 332 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ILE J 331 " --> pdb=" O ILE J 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH9 Processing sheet with id=AI1, first strand: chain 'J' and resid 285 through 287 removed outlier: 6.674A pdb=" N ARG J 319 " --> pdb=" O LEU J 338 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'L' and resid 74 through 75 removed outlier: 4.093A pdb=" N VAL L 49 " --> pdb=" O ARG L 74 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N ALA L 3 " --> pdb=" O ILE L 50 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU L 6 " --> pdb=" O LEU L 107 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASN L 108 " --> pdb=" O GLY L 174 " (cutoff:3.500A) removed outlier: 8.651A pdb=" N GLY L 174 " --> pdb=" O ASN L 108 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU L 134 " --> pdb=" O ALA L 173 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N MET L 175 " --> pdb=" O SER L 132 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N SER L 132 " --> pdb=" O MET L 175 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'L' and resid 111 through 112 Processing sheet with id=AI4, first strand: chain 'L' and resid 146 through 149 Processing sheet with id=AI5, first strand: chain 'L' and resid 254 through 255 Processing sheet with id=AI6, first strand: chain 'L' and resid 261 through 262 removed outlier: 6.563A pdb=" N ARG L 261 " --> pdb=" O VAL L 280 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL L 279 " --> pdb=" O ILE L 297 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ARG L 296 " --> pdb=" O VAL L 314 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ARG L 313 " --> pdb=" O VAL L 332 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE L 331 " --> pdb=" O ILE L 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI6 Processing sheet with id=AI7, first strand: chain 'L' and resid 285 through 287 removed outlier: 6.286A pdb=" N CYS L 285 " --> pdb=" O LEU L 303 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N TRP L 302 " --> pdb=" O MET L 320 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ARG L 319 " --> pdb=" O LEU L 338 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI7 Processing sheet with id=AI8, first strand: chain 'L' and resid 290 through 291 removed outlier: 6.703A pdb=" N THR L 290 " --> pdb=" O VAL L 308 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI8 Processing sheet with id=AI9, first strand: chain 'L' and resid 342 through 343 removed outlier: 6.496A pdb=" N SER L 342 " --> pdb=" O ILE L 359 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI9 978 hydrogen bonds defined for protein. 2787 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: 9.37 Time building geometry restraints manager: 3.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8917 1.33 - 1.45: 6764 1.45 - 1.57: 20159 1.57 - 1.70: 73 1.70 - 1.82: 336 Bond restraints: 36249 Sorted by residual: bond pdb=" O2A GDD J 401 " pdb=" PA GDD J 401 " ideal model delta sigma weight residual 1.496 1.609 -0.113 2.00e-02 2.50e+03 3.20e+01 bond pdb=" O2A GDD F 401 " pdb=" PA GDD F 401 " ideal model delta sigma weight residual 1.496 1.609 -0.113 2.00e-02 2.50e+03 3.17e+01 bond pdb=" O2B GDD I 401 " pdb=" PB GDD I 401 " ideal model delta sigma weight residual 1.496 1.608 -0.112 2.00e-02 2.50e+03 3.15e+01 bond pdb=" O2A GDD I 401 " pdb=" PA GDD I 401 " ideal model delta sigma weight residual 1.496 1.608 -0.112 2.00e-02 2.50e+03 3.13e+01 bond pdb=" O2A GDD L 401 " pdb=" PA GDD L 401 " ideal model delta sigma weight residual 1.496 1.606 -0.110 2.00e-02 2.50e+03 3.04e+01 ... (remaining 36244 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.66: 48382 3.66 - 7.33: 713 7.33 - 10.99: 172 10.99 - 14.66: 14 14.66 - 18.32: 12 Bond angle restraints: 49293 Sorted by residual: angle pdb=" N SER L 57 " pdb=" CA SER L 57 " pdb=" C SER L 57 " ideal model delta sigma weight residual 111.28 119.85 -8.57 1.09e+00 8.42e-01 6.18e+01 angle pdb=" N ARG D 18 " pdb=" CA ARG D 18 " pdb=" C ARG D 18 " ideal model delta sigma weight residual 113.16 123.56 -10.40 1.42e+00 4.96e-01 5.36e+01 angle pdb=" C ARG K 15 " pdb=" N PRO K 16 " pdb=" CA PRO K 16 " ideal model delta sigma weight residual 119.19 112.02 7.17 1.06e+00 8.90e-01 4.58e+01 angle pdb=" N LEU E 60 " pdb=" CA LEU E 60 " pdb=" C LEU E 60 " ideal model delta sigma weight residual 114.04 105.66 8.38 1.24e+00 6.50e-01 4.57e+01 angle pdb=" C ASP C 359 " pdb=" N PRO C 360 " pdb=" CA PRO C 360 " ideal model delta sigma weight residual 119.84 128.19 -8.35 1.25e+00 6.40e-01 4.46e+01 ... (remaining 49288 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 19167 18.00 - 36.00: 2296 36.00 - 54.00: 651 54.00 - 71.99: 149 71.99 - 89.99: 46 Dihedral angle restraints: 22309 sinusoidal: 9454 harmonic: 12855 Sorted by residual: dihedral pdb=" C VAL K 165 " pdb=" N VAL K 165 " pdb=" CA VAL K 165 " pdb=" CB VAL K 165 " ideal model delta harmonic sigma weight residual -122.00 -138.65 16.65 0 2.50e+00 1.60e-01 4.43e+01 dihedral pdb=" CA ASP F 95 " pdb=" C ASP F 95 " pdb=" N LEU F 96 " pdb=" CA LEU F 96 " ideal model delta harmonic sigma weight residual 180.00 151.81 28.19 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" N PHE K 166 " pdb=" C PHE K 166 " pdb=" CA PHE K 166 " pdb=" CB PHE K 166 " ideal model delta harmonic sigma weight residual 122.80 136.82 -14.02 0 2.50e+00 1.60e-01 3.15e+01 ... (remaining 22306 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 5067 0.113 - 0.226: 492 0.226 - 0.340: 42 0.340 - 0.453: 8 0.453 - 0.566: 2 Chirality restraints: 5611 Sorted by residual: chirality pdb=" CA PHE K 166 " pdb=" N PHE K 166 " pdb=" C PHE K 166 " pdb=" CB PHE K 166 " both_signs ideal model delta sigma weight residual False 2.51 1.94 0.57 2.00e-01 2.50e+01 8.00e+00 chirality pdb=" CB VAL K 165 " pdb=" CA VAL K 165 " pdb=" CG1 VAL K 165 " pdb=" CG2 VAL K 165 " both_signs ideal model delta sigma weight residual False -2.63 -2.15 -0.48 2.00e-01 2.50e+01 5.79e+00 chirality pdb=" CA VAL K 165 " pdb=" N VAL K 165 " pdb=" C VAL K 165 " pdb=" CB VAL K 165 " both_signs ideal model delta sigma weight residual False 2.44 2.03 0.41 2.00e-01 2.50e+01 4.21e+00 ... (remaining 5608 not shown) Planarity restraints: 6325 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS E 79 " -0.043 2.00e-02 2.50e+03 3.81e-02 2.17e+01 pdb=" CG HIS E 79 " 0.080 2.00e-02 2.50e+03 pdb=" ND1 HIS E 79 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS E 79 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 HIS E 79 " -0.017 2.00e-02 2.50e+03 pdb=" NE2 HIS E 79 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY G 88 " -0.061 5.00e-02 4.00e+02 9.19e-02 1.35e+01 pdb=" N PRO G 89 " 0.159 5.00e-02 4.00e+02 pdb=" CA PRO G 89 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO G 89 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY I 88 " -0.056 5.00e-02 4.00e+02 8.50e-02 1.15e+01 pdb=" N PRO I 89 " 0.147 5.00e-02 4.00e+02 pdb=" CA PRO I 89 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO I 89 " -0.047 5.00e-02 4.00e+02 ... (remaining 6322 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.29: 38 2.29 - 2.94: 15009 2.94 - 3.60: 50682 3.60 - 4.25: 82543 4.25 - 4.90: 141722 Nonbonded interactions: 289994 Sorted by model distance: nonbonded pdb=" OD1 ASP I 110 " pdb=" O3' GDD I 401 " model vdw 1.640 3.040 nonbonded pdb=" CB LEU H 344 " pdb=" O MET H 360 " model vdw 1.695 3.440 nonbonded pdb=" NH2 ARG K 15 " pdb=" O PRO L 345 " model vdw 1.900 3.120 nonbonded pdb=" O PRO A 406 " pdb=" NH2 ARG B 18 " model vdw 1.990 3.120 nonbonded pdb=" O3B GDD F 401 " pdb="MG MG F 402 " model vdw 2.002 2.170 ... (remaining 289989 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 203 or resid 218 through 501)) selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = (chain 'E' and (resid 1 through 166 or (resid 167 and (name N or name CA or name \ C or name O or name CB )) or resid 168 through 401)) selection = (chain 'F' and (resid 1 through 166 or (resid 167 and (name N or name CA or name \ C or name O or name CB )) or resid 168 through 401)) selection = (chain 'G' and (resid 1 through 166 or (resid 167 and (name N or name CA or name \ C or name O or name CB )) or resid 168 through 401)) selection = (chain 'H' and (resid 1 through 166 or (resid 167 and (name N or name CA or name \ C or name O or name CB )) or resid 168 through 401)) selection = (chain 'I' and (resid 1 through 166 or (resid 167 and (name N or name CA or name \ C or name O or name CB )) or resid 168 through 401)) selection = (chain 'J' and (resid 1 through 166 or (resid 167 and (name N or name CA or name \ C or name O or name CB )) or resid 168 through 401)) selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.30 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.160 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: 0.030 Extract box with map and model: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 36.210 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.070 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: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 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 : 0.010 0.855 36254 Z= 0.612 Angle : 1.230 18.325 49301 Z= 0.641 Chirality : 0.071 0.566 5611 Planarity : 0.009 0.092 6325 Dihedral : 17.319 89.993 14023 Min Nonbonded Distance : 1.640 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.92 % Favored : 94.84 % Rotamer: Outliers : 8.56 % Allowed : 16.76 % Favored : 74.68 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % 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: -2.44 (0.11), residues: 4473 helix: -2.88 (0.12), residues: 955 sheet: -1.05 (0.17), residues: 803 loop : -1.29 (0.11), residues: 2715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 264 TYR 0.018 0.002 TYR A 167 PHE 0.039 0.003 PHE G 215 TRP 0.017 0.002 TRP C 343 HIS 0.031 0.002 HIS E 79 Details of bonding type rmsd covalent geometry : bond 0.00948 (36249) covalent geometry : angle 1.23023 (49293) SS BOND : bond 0.00270 ( 4) SS BOND : angle 1.15758 ( 8) hydrogen bonds : bond 0.18718 ( 969) hydrogen bonds : angle 8.07095 ( 2787) Misc. bond : bond 0.85528 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8946 Ramachandran restraints generated. 4473 Oldfield, 0 Emsley, 4473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8946 Ramachandran restraints generated. 4473 Oldfield, 0 Emsley, 4473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1192 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 336 poor density : 856 time to evaluate : 1.453 Fit side-chains revert: symmetry clash Corrupt residue: chain: I residue: PRO 199 >>> skipping revert: symmetry clash revert: symmetry clash Corrupt residue: chain: E residue: PRO 199 >>> skipping revert: symmetry clash Corrupt residue: chain: F residue: PRO 199 >>> skipping revert: symmetry clash revert: symmetry clash Corrupt residue: chain: H residue: PRO 199 >>> skipping revert: symmetry clash Corrupt residue: chain: J residue: PRO 199 >>> skipping revert: symmetry clash Corrupt residue: chain: L residue: PRO 199 >>> skipping REVERT: K 65 LYS cc_start: 0.8678 (mmtt) cc_final: 0.8174 (mmtt) REVERT: K 80 GLU cc_start: 0.6698 (OUTLIER) cc_final: 0.5998 (pt0) REVERT: K 86 THR cc_start: 0.7051 (OUTLIER) cc_final: 0.6739 (t) REVERT: K 331 ILE cc_start: 0.8794 (mm) cc_final: 0.8457 (tt) REVERT: I 63 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7323 (mm-30) REVERT: I 124 HIS cc_start: 0.7005 (t70) cc_final: 0.6301 (t70) REVERT: I 195 LYS cc_start: 0.7848 (tmtt) cc_final: 0.7629 (tptp) REVERT: I 201 MET cc_start: 0.6760 (ttt) cc_final: 0.6501 (ttt) REVERT: I 210 MET cc_start: 0.4872 (ttt) cc_final: 0.4480 (ttt) REVERT: I 224 ASP cc_start: 0.7907 (m-30) cc_final: 0.7523 (m-30) REVERT: I 229 MET cc_start: 0.8226 (tmm) cc_final: 0.8005 (tmm) REVERT: C 70 GLU cc_start: 0.7551 (mm-30) cc_final: 0.6923 (mm-30) REVERT: C 319 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8455 (mt) REVERT: C 332 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7436 (mm-30) REVERT: C 369 MET cc_start: 0.8418 (OUTLIER) cc_final: 0.8182 (tmm) REVERT: D 118 CYS cc_start: 0.8284 (OUTLIER) cc_final: 0.7945 (t) REVERT: D 177 ASP cc_start: 0.7290 (t70) cc_final: 0.7004 (t70) REVERT: D 261 TYR cc_start: 0.8573 (m-10) cc_final: 0.7151 (m-10) REVERT: E 63 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7688 (mm-30) REVERT: E 185 ARG cc_start: 0.6119 (ttm170) cc_final: 0.5860 (mtm-85) REVERT: E 223 LYS cc_start: 0.8430 (ttpp) cc_final: 0.8115 (tptt) REVERT: E 229 MET cc_start: 0.8509 (tmm) cc_final: 0.8250 (tmm) REVERT: F 166 PHE cc_start: 0.5944 (t80) cc_final: 0.5702 (t80) REVERT: F 229 MET cc_start: 0.7938 (tmm) cc_final: 0.7719 (tmm) REVERT: G 15 ARG cc_start: 0.6770 (OUTLIER) cc_final: 0.6192 (tpt-90) REVERT: G 19 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8739 (mm) REVERT: G 20 SER cc_start: 0.8005 (m) cc_final: 0.7754 (p) REVERT: G 64 MET cc_start: 0.7019 (ptm) cc_final: 0.6676 (ptm) REVERT: G 68 GLU cc_start: 0.8364 (pt0) cc_final: 0.8039 (pt0) REVERT: G 114 ASP cc_start: 0.7639 (t0) cc_final: 0.7091 (t0) REVERT: G 147 VAL cc_start: 0.8523 (OUTLIER) cc_final: 0.8285 (p) REVERT: G 304 GLU cc_start: 0.8173 (tm-30) cc_final: 0.7874 (tm-30) REVERT: H 84 LEU cc_start: 0.5669 (mm) cc_final: 0.5131 (mm) REVERT: J 65 LYS cc_start: 0.8130 (mtpt) cc_final: 0.7772 (tptp) REVERT: J 99 GLU cc_start: 0.5071 (OUTLIER) cc_final: 0.4827 (pm20) REVERT: J 143 LYS cc_start: 0.8744 (mttt) cc_final: 0.8540 (mmtt) REVERT: J 161 GLU cc_start: 0.6614 (tm-30) cc_final: 0.6327 (tm-30) REVERT: J 167 VAL cc_start: 0.8634 (OUTLIER) cc_final: 0.8424 (p) REVERT: J 207 LEU cc_start: 0.7828 (mt) cc_final: 0.7451 (mt) REVERT: J 215 PHE cc_start: 0.7848 (p90) cc_final: 0.7503 (p90) REVERT: J 301 SER cc_start: 0.9205 (t) cc_final: 0.8961 (m) REVERT: J 328 GLU cc_start: 0.7245 (tp30) cc_final: 0.6963 (tp30) REVERT: L 71 LEU cc_start: 0.7346 (OUTLIER) cc_final: 0.6938 (mt) REVERT: L 194 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.6688 (mt-10) REVERT: L 210 MET cc_start: 0.5605 (ttt) cc_final: 0.4962 (ttt) REVERT: L 321 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.6431 (mm-30) REVERT: L 334 ASP cc_start: 0.7741 (OUTLIER) cc_final: 0.6507 (t70) outliers start: 336 outliers final: 190 residues processed: 1118 average time/residue: 0.2442 time to fit residues: 428.7017 Evaluate side-chains 723 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 205 poor density : 518 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 15 ARG Chi-restraints excluded: chain K residue 27 ASP Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 50 ILE Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 80 GLU Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 153 THR Chi-restraints excluded: chain K residue 189 GLN Chi-restraints excluded: chain K residue 191 THR Chi-restraints excluded: chain K residue 253 ASN Chi-restraints excluded: chain K residue 266 CYS Chi-restraints excluded: chain K residue 267 SER Chi-restraints excluded: chain K residue 273 SER Chi-restraints excluded: chain K residue 324 THR Chi-restraints excluded: chain K residue 342 SER Chi-restraints excluded: chain I residue 27 ASP Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 77 MET Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 112 ILE Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 167 VAL Chi-restraints excluded: chain I residue 176 TYR Chi-restraints excluded: chain I residue 199 PRO Chi-restraints excluded: chain I residue 253 ASN Chi-restraints excluded: chain I residue 267 SER Chi-restraints excluded: chain I residue 273 SER Chi-restraints excluded: chain I residue 306 CYS Chi-restraints excluded: chain I residue 312 CYS Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 363 ASN Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 118 CYS Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 326 HIS Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 408 LYS Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 332 GLU Chi-restraints excluded: chain C residue 339 SER Chi-restraints excluded: chain C residue 363 ASN Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 118 CYS Chi-restraints excluded: chain D residue 135 HIS Chi-restraints excluded: chain D residue 151 ASN Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 258 SER Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 265 TYR Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 339 SER Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 413 SER Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 95 ASP Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 129 GLN Chi-restraints excluded: chain E residue 132 SER Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 199 PRO Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 286 ILE Chi-restraints excluded: chain E residue 348 SER Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 144 TYR Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 193 ILE Chi-restraints excluded: chain F residue 197 VAL Chi-restraints excluded: chain F residue 199 PRO Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 253 ASN Chi-restraints excluded: chain F residue 273 SER Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 289 CYS Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain F residue 334 ASP Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 15 ARG Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 191 THR Chi-restraints excluded: chain G residue 192 SER Chi-restraints excluded: chain G residue 193 ILE Chi-restraints excluded: chain G residue 197 VAL Chi-restraints excluded: chain G residue 227 THR Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain G residue 257 ASP Chi-restraints excluded: chain G residue 259 SER Chi-restraints excluded: chain G residue 267 SER Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain G residue 353 VAL Chi-restraints excluded: chain H residue 35 LEU Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 74 ARG Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 95 ASP Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 153 THR Chi-restraints excluded: chain H residue 182 VAL Chi-restraints excluded: chain H residue 193 ILE Chi-restraints excluded: chain H residue 199 PRO Chi-restraints excluded: chain H residue 201 MET Chi-restraints excluded: chain H residue 267 SER Chi-restraints excluded: chain H residue 278 VAL Chi-restraints excluded: chain H residue 321 GLU Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain H residue 335 GLU Chi-restraints excluded: chain H residue 360 MET Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 7 VAL Chi-restraints excluded: chain J residue 10 TYR Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 78 SER Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 95 ASP Chi-restraints excluded: chain J residue 99 GLU Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 147 VAL Chi-restraints excluded: chain J residue 153 THR Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 186 ILE Chi-restraints excluded: chain J residue 191 THR Chi-restraints excluded: chain J residue 197 VAL Chi-restraints excluded: chain J residue 199 PRO Chi-restraints excluded: chain J residue 227 THR Chi-restraints excluded: chain J residue 278 VAL Chi-restraints excluded: chain J residue 324 THR Chi-restraints excluded: chain L residue 20 SER Chi-restraints excluded: chain L residue 29 CYS Chi-restraints excluded: chain L residue 51 LEU Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain L residue 60 LEU Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 153 THR Chi-restraints excluded: chain L residue 183 LEU Chi-restraints excluded: chain L residue 191 THR Chi-restraints excluded: chain L residue 194 GLU Chi-restraints excluded: chain L residue 199 PRO Chi-restraints excluded: chain L residue 256 VAL Chi-restraints excluded: chain L residue 278 VAL Chi-restraints excluded: chain L residue 321 GLU Chi-restraints excluded: chain L residue 334 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 432 optimal weight: 10.0000 chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 30.0000 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.0870 chunk 248 optimal weight: 0.4980 chunk 207 optimal weight: 0.9990 chunk 401 optimal weight: 0.0070 chunk 424 optimal weight: 7.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 30 ASN ** K 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 67 GLN K 118 GLN K 164 GLN K 221 GLN K 238 GLN I 30 ASN I 69 GLN ** I 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 271 ASN A 40 HIS A 199 GLN A 286 ASN A 401 ASN B 40 HIS B 151 ASN B 199 GLN B 202 GLN B 286 ASN B 331 GLN B 338 HIS B 401 ASN C 40 HIS C 160 GLN C 199 GLN C 201 ASN C 202 GLN C 286 ASN C 304 ASN C 401 ASN D 51 GLN D 97 HIS D 199 GLN D 201 ASN D 338 HIS D 401 ASN ** E 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 221 GLN E 333 ASN E 346 HIS ** F 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 108 ASN F 122 GLN F 126 HIS ** F 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 129 GLN F 169 ASN F 316 GLN G 126 HIS ** G 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 206 GLN G 238 GLN H 30 ASN H 67 GLN H 69 GLN H 108 ASN ** H 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 157 HIS ** J 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 108 ASN ** J 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 157 HIS J 169 ASN J 234 GLN ** J 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 333 ASN L 79 HIS ** L 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 169 ASN L 234 GLN L 265 ASN L 346 HIS Total number of N/Q/H flips: 62 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.161183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.111937 restraints weight = 56175.862| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.47 r_work: 0.3201 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3057 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3045 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 36254 Z= 0.139 Angle : 0.687 15.708 49301 Z= 0.351 Chirality : 0.050 0.248 5611 Planarity : 0.006 0.075 6325 Dihedral : 9.809 68.105 5795 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.14 % Favored : 95.77 % Rotamer: Outliers : 4.90 % Allowed : 20.91 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.55 (0.12), residues: 4473 helix: -1.48 (0.14), residues: 978 sheet: -0.76 (0.15), residues: 1168 loop : -0.86 (0.12), residues: 2327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E 185 TYR 0.014 0.001 TYR G 144 PHE 0.051 0.002 PHE L 215 TRP 0.014 0.001 TRP E 216 HIS 0.011 0.001 HIS F 124 Details of bonding type rmsd covalent geometry : bond 0.00306 (36249) covalent geometry : angle 0.68663 (49293) SS BOND : bond 0.01883 ( 4) SS BOND : angle 0.98275 ( 8) hydrogen bonds : bond 0.04711 ( 969) hydrogen bonds : angle 6.30701 ( 2787) Misc. bond : bond 0.00684 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8946 Ramachandran restraints generated. 4473 Oldfield, 0 Emsley, 4473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8946 Ramachandran restraints generated. 4473 Oldfield, 0 Emsley, 4473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 819 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 196 poor density : 623 time to evaluate : 1.387 Fit side-chains Corrupt residue: chain: K residue: PRO 199 >>> skipping Corrupt residue: chain: I residue: PRO 199 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: E residue: PRO 199 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: F residue: PRO 199 >>> skipping revert: symmetry clash revert: symmetry clash Corrupt residue: chain: H residue: PRO 199 >>> skipping Corrupt residue: chain: J residue: PRO 199 >>> skipping revert: symmetry clash Corrupt residue: chain: L residue: PRO 199 >>> skipping REVERT: K 22 PRO cc_start: 0.8323 (Cg_exo) cc_final: 0.7927 (Cg_endo) REVERT: K 27 ASP cc_start: 0.8332 (m-30) cc_final: 0.7385 (t0) REVERT: K 139 GLU cc_start: 0.8261 (pp20) cc_final: 0.7671 (pp20) REVERT: K 194 GLU cc_start: 0.7335 (pm20) cc_final: 0.7098 (pt0) REVERT: K 201 MET cc_start: 0.6734 (tpp) cc_final: 0.6509 (tpp) REVERT: K 329 ASP cc_start: 0.8608 (t0) cc_final: 0.8325 (t0) REVERT: K 331 ILE cc_start: 0.8923 (mm) cc_final: 0.8335 (tt) REVERT: I 63 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7225 (mm-30) REVERT: I 195 LYS cc_start: 0.8213 (tmtt) cc_final: 0.7753 (tptp) REVERT: I 224 ASP cc_start: 0.8260 (m-30) cc_final: 0.7824 (m-30) REVERT: I 229 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.8229 (tmm) REVERT: I 261 ARG cc_start: 0.8068 (ttm110) cc_final: 0.7135 (tpp80) REVERT: I 265 ASN cc_start: 0.7559 (t0) cc_final: 0.7248 (t0) REVERT: I 360 MET cc_start: 0.6793 (mmt) cc_final: 0.5335 (mtm) REVERT: A 51 GLN cc_start: 0.8450 (tt0) cc_final: 0.8146 (tt0) REVERT: A 368 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.7685 (mtp85) REVERT: A 376 LYS cc_start: 0.8558 (tppt) cc_final: 0.7777 (ptpt) REVERT: C 295 VAL cc_start: 0.9331 (t) cc_final: 0.9058 (m) REVERT: C 332 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8039 (mm-30) REVERT: C 376 LYS cc_start: 0.8005 (tppt) cc_final: 0.7666 (tppt) REVERT: D 23 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7679 (mm-30) REVERT: D 118 CYS cc_start: 0.9184 (OUTLIER) cc_final: 0.8662 (t) REVERT: D 146 ARG cc_start: 0.8556 (ttt180) cc_final: 0.8201 (mtp180) REVERT: D 169 GLU cc_start: 0.8496 (tp30) cc_final: 0.8277 (tp30) REVERT: D 261 TYR cc_start: 0.8797 (m-10) cc_final: 0.7531 (m-10) REVERT: D 294 LYS cc_start: 0.8263 (ttmm) cc_final: 0.8012 (tppp) REVERT: E 55 TYR cc_start: 0.7195 (t80) cc_final: 0.6910 (t80) REVERT: E 70 ARG cc_start: 0.7798 (mtp85) cc_final: 0.7480 (mmm160) REVERT: E 162 LYS cc_start: 0.7461 (tptt) cc_final: 0.5437 (tmtt) REVERT: E 201 MET cc_start: 0.7960 (OUTLIER) cc_final: 0.7635 (mmp) REVERT: E 210 MET cc_start: 0.6690 (OUTLIER) cc_final: 0.6197 (tpp) REVERT: E 304 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7677 (tm-30) REVERT: E 311 ARG cc_start: 0.7931 (ttp-110) cc_final: 0.7604 (ttp80) REVERT: E 329 ASP cc_start: 0.8336 (t0) cc_final: 0.8033 (t0) REVERT: F 60 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8395 (tp) REVERT: F 166 PHE cc_start: 0.6342 (t80) cc_final: 0.5696 (t80) REVERT: F 201 MET cc_start: 0.8225 (tpp) cc_final: 0.7594 (tpp) REVERT: F 208 TYR cc_start: 0.6505 (m-80) cc_final: 0.6244 (m-10) REVERT: F 231 LEU cc_start: 0.8765 (tp) cc_final: 0.8544 (tp) REVERT: G 64 MET cc_start: 0.7540 (ptm) cc_final: 0.6822 (ptm) REVERT: G 65 LYS cc_start: 0.8056 (ptpt) cc_final: 0.7578 (mmmm) REVERT: G 68 GLU cc_start: 0.8423 (pt0) cc_final: 0.7714 (pt0) REVERT: G 114 ASP cc_start: 0.7817 (t0) cc_final: 0.7199 (t0) REVERT: G 120 MET cc_start: 0.8766 (tpp) cc_final: 0.8507 (tpt) REVERT: H 144 TYR cc_start: 0.7479 (OUTLIER) cc_final: 0.6558 (m-80) REVERT: H 171 ILE cc_start: 0.8237 (mp) cc_final: 0.7951 (mp) REVERT: J 1 MET cc_start: 0.5640 (tpp) cc_final: 0.4312 (pmm) REVERT: J 77 MET cc_start: 0.7339 (pmm) cc_final: 0.6720 (ptp) REVERT: J 301 SER cc_start: 0.9424 (t) cc_final: 0.9073 (m) REVERT: J 312 CYS cc_start: 0.8931 (t) cc_final: 0.8382 (m) REVERT: J 316 GLN cc_start: 0.7924 (OUTLIER) cc_final: 0.6995 (mm110) REVERT: L 48 HIS cc_start: 0.5619 (OUTLIER) cc_final: 0.5333 (t-90) REVERT: L 77 MET cc_start: 0.7884 (pmm) cc_final: 0.7488 (ppp) REVERT: L 317 TRP cc_start: 0.8630 (m-10) cc_final: 0.8011 (m-10) REVERT: L 321 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7406 (tm-30) outliers start: 196 outliers final: 121 residues processed: 773 average time/residue: 0.2142 time to fit residues: 272.8140 Evaluate side-chains 655 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 522 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 41 LEU Chi-restraints excluded: chain K residue 50 ILE Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 153 THR Chi-restraints excluded: chain K residue 189 GLN Chi-restraints excluded: chain K residue 199 PRO Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 176 TYR Chi-restraints excluded: chain I residue 193 ILE Chi-restraints excluded: chain I residue 199 PRO Chi-restraints excluded: chain I residue 200 ILE Chi-restraints excluded: chain I residue 229 MET Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 368 ARG Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 326 HIS Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 408 LYS Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 332 GLU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 118 CYS Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 265 TYR Chi-restraints excluded: chain D residue 304 ASN Chi-restraints excluded: chain D residue 339 SER Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 199 PRO Chi-restraints excluded: chain E residue 201 MET Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 266 CYS Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 286 ILE Chi-restraints excluded: chain E residue 304 GLU Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 348 SER Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 95 ASP Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 144 TYR Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 169 ASN Chi-restraints excluded: chain F residue 193 ILE Chi-restraints excluded: chain F residue 197 VAL Chi-restraints excluded: chain F residue 199 PRO Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 213 GLN Chi-restraints excluded: chain F residue 242 GLU Chi-restraints excluded: chain F residue 273 SER Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 77 MET Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 168 SER Chi-restraints excluded: chain G residue 193 ILE Chi-restraints excluded: chain G residue 215 PHE Chi-restraints excluded: chain G residue 257 ASP Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain G residue 328 GLU Chi-restraints excluded: chain H residue 30 ASN Chi-restraints excluded: chain H residue 35 LEU Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 74 ARG Chi-restraints excluded: chain H residue 108 ASN Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 126 HIS Chi-restraints excluded: chain H residue 144 TYR Chi-restraints excluded: chain H residue 182 VAL Chi-restraints excluded: chain H residue 199 PRO Chi-restraints excluded: chain H residue 278 VAL Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain H residue 335 GLU Chi-restraints excluded: chain H residue 359 ILE Chi-restraints excluded: chain H residue 360 MET Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 10 TYR Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 147 VAL Chi-restraints excluded: chain J residue 153 THR Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 186 ILE Chi-restraints excluded: chain J residue 191 THR Chi-restraints excluded: chain J residue 199 PRO Chi-restraints excluded: chain J residue 316 GLN Chi-restraints excluded: chain J residue 324 THR Chi-restraints excluded: chain L residue 48 HIS Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 169 ASN Chi-restraints excluded: chain L residue 191 THR Chi-restraints excluded: chain L residue 199 PRO Chi-restraints excluded: chain L residue 265 ASN Chi-restraints excluded: chain L residue 321 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 290 optimal weight: 4.9990 chunk 50 optimal weight: 20.0000 chunk 137 optimal weight: 0.6980 chunk 4 optimal weight: 10.0000 chunk 266 optimal weight: 7.9990 chunk 318 optimal weight: 5.9990 chunk 223 optimal weight: 0.7980 chunk 205 optimal weight: 6.9990 chunk 60 optimal weight: 0.0060 chunk 316 optimal weight: 8.9990 chunk 354 optimal weight: 8.9990 overall best weight: 2.5000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 36 HIS ** K 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 238 GLN I 69 GLN I 79 HIS ** I 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 346 HIS B 338 HIS C 338 HIS D 40 HIS D 51 GLN D 135 HIS E 126 HIS ** E 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 79 HIS ** F 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 126 HIS ** G 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 339 ASN J 108 ASN ** J 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 234 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.158456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.110123 restraints weight = 55784.364| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.56 r_work: 0.3151 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3018 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3018 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 36254 Z= 0.164 Angle : 0.649 15.645 49301 Z= 0.328 Chirality : 0.050 0.257 5611 Planarity : 0.005 0.067 6325 Dihedral : 8.633 74.038 5625 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.52 % Favored : 95.39 % Rotamer: Outliers : 5.24 % Allowed : 21.04 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.98 (0.12), residues: 4473 helix: -0.44 (0.16), residues: 933 sheet: -0.61 (0.15), residues: 1182 loop : -0.64 (0.13), residues: 2358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 287 TYR 0.026 0.001 TYR J 55 PHE 0.046 0.002 PHE L 215 TRP 0.008 0.001 TRP B 343 HIS 0.008 0.001 HIS E 127 Details of bonding type rmsd covalent geometry : bond 0.00388 (36249) covalent geometry : angle 0.64823 (49293) SS BOND : bond 0.00487 ( 4) SS BOND : angle 1.70705 ( 8) hydrogen bonds : bond 0.04250 ( 969) hydrogen bonds : angle 5.86844 ( 2787) Misc. bond : bond 0.00697 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8946 Ramachandran restraints generated. 4473 Oldfield, 0 Emsley, 4473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8946 Ramachandran restraints generated. 4473 Oldfield, 0 Emsley, 4473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 769 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 209 poor density : 560 time to evaluate : 1.381 Fit side-chains Corrupt residue: chain: K residue: PRO 199 >>> skipping Corrupt residue: chain: I residue: PRO 199 >>> skipping revert: symmetry clash revert: symmetry clash Corrupt residue: chain: E residue: PRO 199 >>> skipping revert: symmetry clash Corrupt residue: chain: F residue: PRO 199 >>> skipping revert: symmetry clash revert: symmetry clash Corrupt residue: chain: H residue: PRO 199 >>> skipping Corrupt residue: chain: J residue: PRO 199 >>> skipping Corrupt residue: chain: L residue: PRO 199 >>> skipping REVERT: K 22 PRO cc_start: 0.8171 (Cg_exo) cc_final: 0.7948 (Cg_endo) REVERT: K 27 ASP cc_start: 0.8327 (m-30) cc_final: 0.7390 (t0) REVERT: K 139 GLU cc_start: 0.8277 (pp20) cc_final: 0.7642 (pp20) REVERT: K 194 GLU cc_start: 0.7497 (pm20) cc_final: 0.7257 (pt0) REVERT: K 201 MET cc_start: 0.6820 (tpp) cc_final: 0.6538 (tpp) REVERT: K 329 ASP cc_start: 0.8587 (t0) cc_final: 0.8323 (t0) REVERT: K 331 ILE cc_start: 0.8998 (mm) cc_final: 0.8382 (tt) REVERT: I 63 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7423 (mm-30) REVERT: I 124 HIS cc_start: 0.6880 (t70) cc_final: 0.6612 (t70) REVERT: I 195 LYS cc_start: 0.8204 (tmtt) cc_final: 0.7656 (tptp) REVERT: I 224 ASP cc_start: 0.8342 (m-30) cc_final: 0.7846 (m-30) REVERT: I 229 MET cc_start: 0.8482 (tmm) cc_final: 0.8218 (tmm) REVERT: I 265 ASN cc_start: 0.7613 (t0) cc_final: 0.7219 (t0) REVERT: I 322 ASN cc_start: 0.8039 (t0) cc_final: 0.7763 (t0) REVERT: I 360 MET cc_start: 0.6908 (mmt) cc_final: 0.6254 (mmm) REVERT: A 51 GLN cc_start: 0.8487 (tt0) cc_final: 0.8177 (tt0) REVERT: A 81 ARG cc_start: 0.8710 (mtt-85) cc_final: 0.7716 (mtp180) REVERT: A 368 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.7221 (mtp85) REVERT: A 376 LYS cc_start: 0.8726 (tppt) cc_final: 0.7790 (ptpt) REVERT: C 228 SER cc_start: 0.9045 (OUTLIER) cc_final: 0.8831 (p) REVERT: C 295 VAL cc_start: 0.9343 (t) cc_final: 0.9070 (m) REVERT: C 332 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.8593 (mp0) REVERT: C 369 MET cc_start: 0.8845 (OUTLIER) cc_final: 0.8550 (tmm) REVERT: C 376 LYS cc_start: 0.8184 (tppt) cc_final: 0.7860 (tppt) REVERT: D 118 CYS cc_start: 0.9260 (OUTLIER) cc_final: 0.8630 (t) REVERT: D 146 ARG cc_start: 0.8659 (ttt180) cc_final: 0.8259 (mtp180) REVERT: D 230 LEU cc_start: 0.8812 (mt) cc_final: 0.8238 (mp) REVERT: D 261 TYR cc_start: 0.8831 (m-10) cc_final: 0.7597 (m-10) REVERT: D 294 LYS cc_start: 0.8268 (ttmm) cc_final: 0.8046 (tppp) REVERT: D 315 GLU cc_start: 0.7487 (tp30) cc_final: 0.7087 (tm-30) REVERT: E 15 ARG cc_start: 0.6904 (OUTLIER) cc_final: 0.6485 (tpp80) REVERT: E 55 TYR cc_start: 0.7055 (t80) cc_final: 0.6842 (t80) REVERT: E 98 SER cc_start: 0.5791 (OUTLIER) cc_final: 0.5474 (p) REVERT: E 138 VAL cc_start: 0.6897 (t) cc_final: 0.6695 (t) REVERT: E 162 LYS cc_start: 0.7513 (tptt) cc_final: 0.5392 (tmtt) REVERT: E 210 MET cc_start: 0.6611 (OUTLIER) cc_final: 0.6104 (tpp) REVERT: E 233 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8395 (mm) REVERT: E 304 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7783 (tm-30) REVERT: E 329 ASP cc_start: 0.8262 (t0) cc_final: 0.7886 (t0) REVERT: F 95 ASP cc_start: 0.5624 (OUTLIER) cc_final: 0.5413 (m-30) REVERT: F 110 ASP cc_start: 0.8608 (p0) cc_final: 0.8212 (p0) REVERT: F 166 PHE cc_start: 0.6464 (t80) cc_final: 0.5821 (t80) REVERT: F 172 ASN cc_start: 0.8809 (t0) cc_final: 0.8473 (t0) REVERT: F 201 MET cc_start: 0.8226 (tpp) cc_final: 0.7566 (tpp) REVERT: F 216 TRP cc_start: 0.8351 (t60) cc_final: 0.7939 (t60) REVERT: F 223 LYS cc_start: 0.8877 (tptm) cc_final: 0.8497 (tptp) REVERT: F 231 LEU cc_start: 0.8817 (tp) cc_final: 0.8606 (tp) REVERT: G 56 MET cc_start: 0.6362 (mmt) cc_final: 0.4846 (ptp) REVERT: G 64 MET cc_start: 0.7582 (ptm) cc_final: 0.6885 (ptm) REVERT: G 65 LYS cc_start: 0.8125 (ptpt) cc_final: 0.7639 (mmmm) REVERT: G 68 GLU cc_start: 0.8294 (pt0) cc_final: 0.7703 (pt0) REVERT: G 114 ASP cc_start: 0.7931 (t0) cc_final: 0.7580 (t0) REVERT: G 120 MET cc_start: 0.8690 (tpp) cc_final: 0.8427 (tpt) REVERT: G 144 TYR cc_start: 0.9040 (m-10) cc_final: 0.8686 (m-10) REVERT: H 144 TYR cc_start: 0.7569 (OUTLIER) cc_final: 0.6522 (m-80) REVERT: H 171 ILE cc_start: 0.8237 (mp) cc_final: 0.7938 (mp) REVERT: J 1 MET cc_start: 0.5472 (tpp) cc_final: 0.4656 (pmm) REVERT: J 64 MET cc_start: 0.8065 (ppp) cc_final: 0.7729 (ppp) REVERT: J 161 GLU cc_start: 0.7118 (tp30) cc_final: 0.6830 (tp30) REVERT: J 271 ASN cc_start: 0.8204 (m-40) cc_final: 0.7984 (m110) REVERT: J 301 SER cc_start: 0.9369 (t) cc_final: 0.9012 (m) REVERT: J 312 CYS cc_start: 0.8834 (t) cc_final: 0.8424 (m) REVERT: J 322 ASN cc_start: 0.8445 (t0) cc_final: 0.7588 (t0) REVERT: L 48 HIS cc_start: 0.5614 (OUTLIER) cc_final: 0.5381 (t-90) REVERT: L 77 MET cc_start: 0.7979 (pmm) cc_final: 0.7209 (ppp) REVERT: L 106 VAL cc_start: 0.8340 (t) cc_final: 0.8092 (m) REVERT: L 297 ILE cc_start: 0.9047 (mp) cc_final: 0.8756 (tt) REVERT: L 317 TRP cc_start: 0.8679 (m-10) cc_final: 0.8094 (m-10) REVERT: L 321 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7396 (tm-30) outliers start: 209 outliers final: 147 residues processed: 716 average time/residue: 0.2016 time to fit residues: 240.9724 Evaluate side-chains 659 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 498 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 41 LEU Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 50 ILE Chi-restraints excluded: chain K residue 106 VAL Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 136 THR Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 153 THR Chi-restraints excluded: chain K residue 189 GLN Chi-restraints excluded: chain K residue 199 PRO Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 69 GLN Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 176 TYR Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 193 ILE Chi-restraints excluded: chain I residue 199 PRO Chi-restraints excluded: chain I residue 312 CYS Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 368 ARG Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 118 CYS Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 326 HIS Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 408 LYS Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 332 GLU Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 3 LYS Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 118 CYS Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 265 TYR Chi-restraints excluded: chain D residue 339 SER Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 15 ARG Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 117 PHE Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 176 TYR Chi-restraints excluded: chain E residue 199 PRO Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 266 CYS Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 286 ILE Chi-restraints excluded: chain E residue 304 GLU Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 348 SER Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 95 ASP Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 153 THR Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 193 ILE Chi-restraints excluded: chain F residue 197 VAL Chi-restraints excluded: chain F residue 199 PRO Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 289 CYS Chi-restraints excluded: chain F residue 306 CYS Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 77 MET Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 168 SER Chi-restraints excluded: chain G residue 193 ILE Chi-restraints excluded: chain G residue 197 VAL Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain G residue 257 ASP Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain G residue 353 VAL Chi-restraints excluded: chain G residue 359 ILE Chi-restraints excluded: chain H residue 35 LEU Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 74 ARG Chi-restraints excluded: chain H residue 144 TYR Chi-restraints excluded: chain H residue 175 MET Chi-restraints excluded: chain H residue 199 PRO Chi-restraints excluded: chain H residue 278 VAL Chi-restraints excluded: chain H residue 299 SER Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain H residue 335 GLU Chi-restraints excluded: chain H residue 359 ILE Chi-restraints excluded: chain H residue 360 MET Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 7 VAL Chi-restraints excluded: chain J residue 10 TYR Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 147 VAL Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 186 ILE Chi-restraints excluded: chain J residue 199 PRO Chi-restraints excluded: chain J residue 227 THR Chi-restraints excluded: chain J residue 230 CYS Chi-restraints excluded: chain J residue 278 VAL Chi-restraints excluded: chain J residue 324 THR Chi-restraints excluded: chain L residue 48 HIS Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 153 THR Chi-restraints excluded: chain L residue 183 LEU Chi-restraints excluded: chain L residue 191 THR Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain L residue 199 PRO Chi-restraints excluded: chain L residue 278 VAL Chi-restraints excluded: chain L residue 321 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 291 optimal weight: 7.9990 chunk 91 optimal weight: 0.7980 chunk 284 optimal weight: 5.9990 chunk 323 optimal weight: 5.9990 chunk 439 optimal weight: 0.0470 chunk 103 optimal weight: 3.9990 chunk 376 optimal weight: 20.0000 chunk 101 optimal weight: 0.7980 chunk 183 optimal weight: 5.9990 chunk 174 optimal weight: 7.9990 chunk 428 optimal weight: 0.0870 overall best weight: 1.1458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 69 GLN I 79 HIS ** I 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 HIS B 151 ASN ** E 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 126 HIS ** E 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 126 HIS ** G 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 30 ASN H 108 ASN ** H 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 221 GLN H 265 ASN J 30 ASN J 36 HIS J 108 ASN ** J 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 265 ASN ** L 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 169 ASN L 234 GLN L 265 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.159606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.111364 restraints weight = 55731.060| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.44 r_work: 0.3173 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3038 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3038 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 36254 Z= 0.117 Angle : 0.605 13.708 49301 Z= 0.305 Chirality : 0.049 0.255 5611 Planarity : 0.005 0.064 6325 Dihedral : 8.050 73.050 5617 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.20 % Favored : 95.71 % Rotamer: Outliers : 4.83 % Allowed : 21.87 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.67 (0.12), residues: 4473 helix: 0.09 (0.17), residues: 933 sheet: -0.54 (0.15), residues: 1235 loop : -0.50 (0.13), residues: 2305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 287 TYR 0.016 0.001 TYR F 208 PHE 0.044 0.002 PHE L 215 TRP 0.019 0.001 TRP E 216 HIS 0.009 0.001 HIS I 127 Details of bonding type rmsd covalent geometry : bond 0.00266 (36249) covalent geometry : angle 0.60503 (49293) SS BOND : bond 0.00578 ( 4) SS BOND : angle 1.79609 ( 8) hydrogen bonds : bond 0.03658 ( 969) hydrogen bonds : angle 5.57223 ( 2787) Misc. bond : bond 0.00214 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8946 Ramachandran restraints generated. 4473 Oldfield, 0 Emsley, 4473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8946 Ramachandran restraints generated. 4473 Oldfield, 0 Emsley, 4473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 746 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 193 poor density : 553 time to evaluate : 1.395 Fit side-chains Corrupt residue: chain: K residue: PRO 199 >>> skipping Corrupt residue: chain: I residue: PRO 199 >>> skipping revert: symmetry clash Corrupt residue: chain: E residue: PRO 199 >>> skipping revert: symmetry clash revert: symmetry clash Corrupt residue: chain: F residue: PRO 199 >>> skipping revert: symmetry clash revert: symmetry clash Corrupt residue: chain: H residue: PRO 199 >>> skipping Corrupt residue: chain: J residue: PRO 199 >>> skipping Corrupt residue: chain: L residue: PRO 199 >>> skipping REVERT: K 139 GLU cc_start: 0.8335 (pp20) cc_final: 0.7745 (pp20) REVERT: K 201 MET cc_start: 0.6773 (tpp) cc_final: 0.6528 (tpp) REVERT: K 329 ASP cc_start: 0.8565 (t0) cc_final: 0.8251 (t0) REVERT: K 331 ILE cc_start: 0.8971 (mm) cc_final: 0.8370 (tt) REVERT: I 63 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7521 (mm-30) REVERT: I 124 HIS cc_start: 0.6938 (t70) cc_final: 0.6616 (t70) REVERT: I 195 LYS cc_start: 0.8212 (tmtt) cc_final: 0.7692 (tptp) REVERT: I 224 ASP cc_start: 0.8187 (m-30) cc_final: 0.7829 (m-30) REVERT: I 229 MET cc_start: 0.8434 (OUTLIER) cc_final: 0.8178 (tmm) REVERT: I 265 ASN cc_start: 0.7618 (t0) cc_final: 0.7166 (t0) REVERT: I 360 MET cc_start: 0.6776 (mmt) cc_final: 0.6148 (mmm) REVERT: A 51 GLN cc_start: 0.8558 (tt0) cc_final: 0.8038 (tt0) REVERT: A 81 ARG cc_start: 0.8695 (mtt-85) cc_final: 0.7721 (mtp180) REVERT: A 368 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.7604 (mtp85) REVERT: A 376 LYS cc_start: 0.8722 (tppt) cc_final: 0.7786 (ptpt) REVERT: C 59 TYR cc_start: 0.8915 (m-80) cc_final: 0.8696 (m-80) REVERT: C 295 VAL cc_start: 0.9319 (t) cc_final: 0.9056 (m) REVERT: C 332 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8549 (mp0) REVERT: C 369 MET cc_start: 0.8832 (OUTLIER) cc_final: 0.8549 (tmm) REVERT: C 376 LYS cc_start: 0.8213 (tppt) cc_final: 0.7914 (tppt) REVERT: D 118 CYS cc_start: 0.9197 (OUTLIER) cc_final: 0.8488 (t) REVERT: D 146 ARG cc_start: 0.8629 (ttt180) cc_final: 0.8231 (mtp180) REVERT: D 230 LEU cc_start: 0.8816 (mt) cc_final: 0.8583 (mp) REVERT: D 261 TYR cc_start: 0.8816 (m-10) cc_final: 0.7441 (m-10) REVERT: D 294 LYS cc_start: 0.8256 (ttmm) cc_final: 0.8050 (tppp) REVERT: D 315 GLU cc_start: 0.7577 (tp30) cc_final: 0.7346 (tm-30) REVERT: D 364 ASP cc_start: 0.8461 (t0) cc_final: 0.8174 (t0) REVERT: E 15 ARG cc_start: 0.6733 (OUTLIER) cc_final: 0.6472 (tpp80) REVERT: E 70 ARG cc_start: 0.7915 (tpt90) cc_final: 0.7506 (mmt180) REVERT: E 77 MET cc_start: 0.6744 (mpp) cc_final: 0.6524 (mpp) REVERT: E 98 SER cc_start: 0.5710 (OUTLIER) cc_final: 0.5414 (p) REVERT: E 162 LYS cc_start: 0.7425 (tptt) cc_final: 0.5423 (tmtt) REVERT: E 210 MET cc_start: 0.6696 (OUTLIER) cc_final: 0.6157 (tpp) REVERT: E 229 MET cc_start: 0.8801 (tmm) cc_final: 0.8576 (tmm) REVERT: E 233 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8389 (mm) REVERT: E 304 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7709 (tm-30) REVERT: E 311 ARG cc_start: 0.7976 (ttp-110) cc_final: 0.7688 (ttp80) REVERT: E 329 ASP cc_start: 0.8344 (t0) cc_final: 0.7923 (t0) REVERT: F 60 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8305 (tp) REVERT: F 166 PHE cc_start: 0.6466 (t80) cc_final: 0.5844 (t80) REVERT: F 172 ASN cc_start: 0.8809 (t0) cc_final: 0.8588 (t0) REVERT: F 201 MET cc_start: 0.8168 (tpp) cc_final: 0.7619 (tpp) REVERT: F 216 TRP cc_start: 0.8356 (t60) cc_final: 0.8035 (t60) REVERT: F 223 LYS cc_start: 0.8862 (tptm) cc_final: 0.8512 (tptp) REVERT: G 56 MET cc_start: 0.6421 (mmt) cc_final: 0.5016 (ptp) REVERT: G 64 MET cc_start: 0.7565 (ptm) cc_final: 0.7128 (ptm) REVERT: G 68 GLU cc_start: 0.8298 (pt0) cc_final: 0.7956 (pt0) REVERT: G 114 ASP cc_start: 0.7984 (t0) cc_final: 0.7658 (t0) REVERT: G 120 MET cc_start: 0.8622 (tpp) cc_final: 0.8353 (tpt) REVERT: G 144 TYR cc_start: 0.8956 (m-10) cc_final: 0.8621 (m-10) REVERT: J 1 MET cc_start: 0.5403 (tpp) cc_final: 0.5075 (pmm) REVERT: J 161 GLU cc_start: 0.7051 (tp30) cc_final: 0.6713 (tp30) REVERT: J 208 TYR cc_start: 0.7579 (m-80) cc_final: 0.7340 (m-80) REVERT: J 312 CYS cc_start: 0.8740 (t) cc_final: 0.8407 (m) REVERT: J 322 ASN cc_start: 0.8486 (t0) cc_final: 0.7644 (t0) REVERT: L 70 ARG cc_start: 0.7962 (ttp-170) cc_final: 0.7628 (ptm160) REVERT: L 77 MET cc_start: 0.7977 (pmm) cc_final: 0.7073 (ppp) REVERT: L 160 VAL cc_start: 0.7313 (p) cc_final: 0.7053 (m) REVERT: L 227 THR cc_start: 0.8120 (t) cc_final: 0.7912 (t) REVERT: L 317 TRP cc_start: 0.8680 (m-10) cc_final: 0.8062 (m-10) REVERT: L 321 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7286 (tm-30) REVERT: L 351 GLU cc_start: 0.7940 (pm20) cc_final: 0.7711 (pm20) outliers start: 193 outliers final: 134 residues processed: 691 average time/residue: 0.2022 time to fit residues: 234.4795 Evaluate side-chains 651 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 505 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 41 LEU Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 50 ILE Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 127 HIS Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 153 THR Chi-restraints excluded: chain K residue 199 PRO Chi-restraints excluded: chain K residue 245 CYS Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 176 TYR Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 193 ILE Chi-restraints excluded: chain I residue 199 PRO Chi-restraints excluded: chain I residue 229 MET Chi-restraints excluded: chain I residue 233 LEU Chi-restraints excluded: chain I residue 312 CYS Chi-restraints excluded: chain A residue 166 HIS Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 368 ARG Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 118 CYS Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 326 HIS Chi-restraints excluded: chain B residue 408 LYS Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 332 GLU Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 118 CYS Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 304 ASN Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 15 ARG Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 117 PHE Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 176 TYR Chi-restraints excluded: chain E residue 199 PRO Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 266 CYS Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 286 ILE Chi-restraints excluded: chain E residue 304 GLU Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 144 TYR Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 193 ILE Chi-restraints excluded: chain F residue 197 VAL Chi-restraints excluded: chain F residue 199 PRO Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 289 CYS Chi-restraints excluded: chain F residue 306 CYS Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 77 MET Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 193 ILE Chi-restraints excluded: chain G residue 197 VAL Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain G residue 257 ASP Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain G residue 328 GLU Chi-restraints excluded: chain G residue 353 VAL Chi-restraints excluded: chain H residue 35 LEU Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 79 HIS Chi-restraints excluded: chain H residue 108 ASN Chi-restraints excluded: chain H residue 193 ILE Chi-restraints excluded: chain H residue 199 PRO Chi-restraints excluded: chain H residue 278 VAL Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain H residue 335 GLU Chi-restraints excluded: chain H residue 359 ILE Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 10 TYR Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 147 VAL Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 186 ILE Chi-restraints excluded: chain J residue 199 PRO Chi-restraints excluded: chain J residue 278 VAL Chi-restraints excluded: chain J residue 324 THR Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain L residue 60 LEU Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 153 THR Chi-restraints excluded: chain L residue 169 ASN Chi-restraints excluded: chain L residue 191 THR Chi-restraints excluded: chain L residue 194 GLU Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain L residue 199 PRO Chi-restraints excluded: chain L residue 256 VAL Chi-restraints excluded: chain L residue 278 VAL Chi-restraints excluded: chain L residue 321 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 29 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 235 optimal weight: 6.9990 chunk 129 optimal weight: 10.0000 chunk 441 optimal weight: 20.0000 chunk 122 optimal weight: 3.9990 chunk 79 optimal weight: 0.2980 chunk 366 optimal weight: 20.0000 chunk 35 optimal weight: 0.8980 chunk 409 optimal weight: 1.9990 chunk 237 optimal weight: 20.0000 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 79 HIS ** I 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 269 HIS D 407 HIS E 126 HIS ** E 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 48 HIS ** F 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 206 GLN G 126 HIS ** G 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 36 HIS J 108 ASN ** J 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 30 ASN L 48 HIS ** L 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 169 ASN L 234 GLN L 265 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.158282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.111692 restraints weight = 55623.808| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.41 r_work: 0.3150 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3024 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3024 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 36254 Z= 0.151 Angle : 0.615 10.975 49301 Z= 0.309 Chirality : 0.049 0.224 5611 Planarity : 0.005 0.063 6325 Dihedral : 7.811 74.347 5598 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.90 % Favored : 95.04 % Rotamer: Outliers : 5.22 % Allowed : 22.52 % Favored : 72.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.53 (0.12), residues: 4473 helix: 0.35 (0.17), residues: 934 sheet: -0.48 (0.15), residues: 1228 loop : -0.46 (0.13), residues: 2311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 287 TYR 0.015 0.001 TYR F 208 PHE 0.043 0.002 PHE L 215 TRP 0.021 0.001 TRP E 216 HIS 0.009 0.001 HIS I 127 Details of bonding type rmsd covalent geometry : bond 0.00357 (36249) covalent geometry : angle 0.61451 (49293) SS BOND : bond 0.00506 ( 4) SS BOND : angle 1.57136 ( 8) hydrogen bonds : bond 0.03614 ( 969) hydrogen bonds : angle 5.45361 ( 2787) Misc. bond : bond 0.00182 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8946 Ramachandran restraints generated. 4473 Oldfield, 0 Emsley, 4473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8946 Ramachandran restraints generated. 4473 Oldfield, 0 Emsley, 4473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 735 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 208 poor density : 527 time to evaluate : 1.414 Fit side-chains Corrupt residue: chain: K residue: PRO 199 >>> skipping Corrupt residue: chain: I residue: PRO 199 >>> skipping revert: symmetry clash Corrupt residue: chain: E residue: PRO 199 >>> skipping revert: symmetry clash revert: symmetry clash Corrupt residue: chain: F residue: PRO 199 >>> skipping revert: symmetry clash revert: symmetry clash Corrupt residue: chain: H residue: PRO 199 >>> skipping Corrupt residue: chain: J residue: PRO 199 >>> skipping revert: symmetry clash Corrupt residue: chain: L residue: PRO 199 >>> skipping REVERT: K 64 MET cc_start: 0.8597 (tpt) cc_final: 0.8351 (tpt) REVERT: K 139 GLU cc_start: 0.8321 (pp20) cc_final: 0.7703 (pp20) REVERT: K 201 MET cc_start: 0.6695 (tpp) cc_final: 0.6457 (tpp) REVERT: K 329 ASP cc_start: 0.8556 (t0) cc_final: 0.8292 (t0) REVERT: K 331 ILE cc_start: 0.8986 (mm) cc_final: 0.8376 (tt) REVERT: I 195 LYS cc_start: 0.8231 (tmtt) cc_final: 0.7766 (tptp) REVERT: I 224 ASP cc_start: 0.8205 (m-30) cc_final: 0.7864 (m-30) REVERT: I 229 MET cc_start: 0.8430 (OUTLIER) cc_final: 0.8188 (tmm) REVERT: I 265 ASN cc_start: 0.7659 (t0) cc_final: 0.7221 (t0) REVERT: I 360 MET cc_start: 0.6765 (mmt) cc_final: 0.5505 (mtm) REVERT: A 1 MET cc_start: 0.7945 (tmm) cc_final: 0.7640 (tmm) REVERT: A 51 GLN cc_start: 0.8571 (tt0) cc_final: 0.8068 (tt0) REVERT: A 81 ARG cc_start: 0.8659 (mtt-85) cc_final: 0.7705 (mtp180) REVERT: A 368 ARG cc_start: 0.8776 (OUTLIER) cc_final: 0.6973 (mtp85) REVERT: C 228 SER cc_start: 0.9030 (OUTLIER) cc_final: 0.8827 (p) REVERT: C 295 VAL cc_start: 0.9316 (t) cc_final: 0.9063 (m) REVERT: C 369 MET cc_start: 0.8885 (OUTLIER) cc_final: 0.8618 (tmm) REVERT: C 376 LYS cc_start: 0.8316 (tppt) cc_final: 0.7998 (tppt) REVERT: D 1 MET cc_start: 0.7481 (tmm) cc_final: 0.7268 (tmm) REVERT: D 118 CYS cc_start: 0.9181 (OUTLIER) cc_final: 0.8488 (t) REVERT: D 146 ARG cc_start: 0.8633 (ttt180) cc_final: 0.8245 (mtp180) REVERT: D 230 LEU cc_start: 0.8895 (mt) cc_final: 0.8682 (mp) REVERT: D 261 TYR cc_start: 0.8855 (m-10) cc_final: 0.7494 (m-10) REVERT: D 294 LYS cc_start: 0.8346 (ttmm) cc_final: 0.8138 (tppp) REVERT: D 364 ASP cc_start: 0.8530 (t0) cc_final: 0.8181 (t0) REVERT: E 15 ARG cc_start: 0.6755 (OUTLIER) cc_final: 0.6394 (tpp80) REVERT: E 64 MET cc_start: 0.7816 (ptp) cc_final: 0.7531 (ptp) REVERT: E 98 SER cc_start: 0.5717 (OUTLIER) cc_final: 0.5388 (p) REVERT: E 138 VAL cc_start: 0.6814 (t) cc_final: 0.6575 (t) REVERT: E 162 LYS cc_start: 0.7442 (tptt) cc_final: 0.5416 (tmtt) REVERT: E 210 MET cc_start: 0.6732 (OUTLIER) cc_final: 0.6189 (tpp) REVERT: E 233 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8441 (mm) REVERT: E 329 ASP cc_start: 0.8408 (t0) cc_final: 0.7972 (t0) REVERT: F 60 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8343 (tp) REVERT: F 96 LEU cc_start: 0.6896 (OUTLIER) cc_final: 0.6570 (mp) REVERT: F 166 PHE cc_start: 0.6587 (t80) cc_final: 0.5968 (t80) REVERT: F 201 MET cc_start: 0.8093 (tpp) cc_final: 0.7586 (tpp) REVERT: F 210 MET cc_start: 0.5521 (ttm) cc_final: 0.5296 (ttm) REVERT: F 216 TRP cc_start: 0.8416 (t60) cc_final: 0.8029 (t60) REVERT: F 223 LYS cc_start: 0.8897 (tptm) cc_final: 0.8535 (tptp) REVERT: G 56 MET cc_start: 0.6449 (mmt) cc_final: 0.4978 (ptp) REVERT: G 64 MET cc_start: 0.7599 (ptm) cc_final: 0.7189 (ptm) REVERT: G 68 GLU cc_start: 0.8304 (pt0) cc_final: 0.8080 (pt0) REVERT: G 69 GLN cc_start: 0.7990 (OUTLIER) cc_final: 0.7784 (pm20) REVERT: G 114 ASP cc_start: 0.8014 (t0) cc_final: 0.7705 (t0) REVERT: G 120 MET cc_start: 0.8634 (tpp) cc_final: 0.8365 (tpt) REVERT: G 144 TYR cc_start: 0.8950 (m-80) cc_final: 0.8737 (m-10) REVERT: H 144 TYR cc_start: 0.7575 (OUTLIER) cc_final: 0.6327 (m-80) REVERT: J 1 MET cc_start: 0.5638 (tpp) cc_final: 0.5173 (pmm) REVERT: J 73 ILE cc_start: 0.7422 (OUTLIER) cc_final: 0.7101 (mm) REVERT: J 208 TYR cc_start: 0.7618 (m-80) cc_final: 0.7386 (m-80) REVERT: J 301 SER cc_start: 0.9361 (t) cc_final: 0.9042 (m) REVERT: J 312 CYS cc_start: 0.8719 (t) cc_final: 0.8420 (m) REVERT: J 322 ASN cc_start: 0.8536 (t0) cc_final: 0.7721 (t0) REVERT: L 70 ARG cc_start: 0.7940 (ttp-170) cc_final: 0.7543 (ptm160) REVERT: L 77 MET cc_start: 0.8016 (pmm) cc_final: 0.7554 (ppp) REVERT: L 160 VAL cc_start: 0.7348 (p) cc_final: 0.7126 (m) REVERT: L 317 TRP cc_start: 0.8708 (m-10) cc_final: 0.8104 (m-10) REVERT: L 321 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7389 (tm-30) REVERT: L 351 GLU cc_start: 0.7986 (pm20) cc_final: 0.7742 (pm20) outliers start: 208 outliers final: 149 residues processed: 680 average time/residue: 0.1988 time to fit residues: 226.7483 Evaluate side-chains 655 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 491 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 41 LEU Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 50 ILE Chi-restraints excluded: chain K residue 106 VAL Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 112 ILE Chi-restraints excluded: chain K residue 136 THR Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 153 THR Chi-restraints excluded: chain K residue 199 PRO Chi-restraints excluded: chain K residue 306 CYS Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 176 TYR Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 193 ILE Chi-restraints excluded: chain I residue 199 PRO Chi-restraints excluded: chain I residue 229 MET Chi-restraints excluded: chain I residue 233 LEU Chi-restraints excluded: chain I residue 306 CYS Chi-restraints excluded: chain I residue 312 CYS Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 166 HIS Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 368 ARG Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 118 CYS Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 326 HIS Chi-restraints excluded: chain B residue 408 LYS Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 118 CYS Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 304 ASN Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 15 ARG Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 117 PHE Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 176 TYR Chi-restraints excluded: chain E residue 199 PRO Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 266 CYS Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 286 ILE Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 144 TYR Chi-restraints excluded: chain F residue 153 THR Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 193 ILE Chi-restraints excluded: chain F residue 197 VAL Chi-restraints excluded: chain F residue 199 PRO Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 231 LEU Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 289 CYS Chi-restraints excluded: chain F residue 306 CYS Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 69 GLN Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 77 MET Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 193 ILE Chi-restraints excluded: chain G residue 197 VAL Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain G residue 257 ASP Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain G residue 328 GLU Chi-restraints excluded: chain G residue 353 VAL Chi-restraints excluded: chain H residue 35 LEU Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 79 HIS Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 126 HIS Chi-restraints excluded: chain H residue 144 TYR Chi-restraints excluded: chain H residue 193 ILE Chi-restraints excluded: chain H residue 199 PRO Chi-restraints excluded: chain H residue 278 VAL Chi-restraints excluded: chain H residue 299 SER Chi-restraints excluded: chain H residue 322 ASN Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain H residue 335 GLU Chi-restraints excluded: chain H residue 359 ILE Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 10 TYR Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 36 HIS Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 73 ILE Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 147 VAL Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 186 ILE Chi-restraints excluded: chain J residue 199 PRO Chi-restraints excluded: chain J residue 278 VAL Chi-restraints excluded: chain J residue 304 GLU Chi-restraints excluded: chain J residue 324 THR Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain L residue 60 LEU Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 153 THR Chi-restraints excluded: chain L residue 169 ASN Chi-restraints excluded: chain L residue 183 LEU Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain L residue 199 PRO Chi-restraints excluded: chain L residue 256 VAL Chi-restraints excluded: chain L residue 278 VAL Chi-restraints excluded: chain L residue 321 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 72 optimal weight: 6.9990 chunk 159 optimal weight: 2.9990 chunk 269 optimal weight: 5.9990 chunk 163 optimal weight: 7.9990 chunk 385 optimal weight: 7.9990 chunk 358 optimal weight: 0.0070 chunk 219 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 chunk 264 optimal weight: 10.0000 chunk 110 optimal weight: 6.9990 chunk 340 optimal weight: 40.0000 overall best weight: 4.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 157 HIS I 79 HIS ** I 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 51 GLN D 276 HIS E 126 HIS ** E 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 339 ASN ** F 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 221 GLN F 271 ASN G 126 HIS ** G 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 108 ASN ** H 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 265 ASN J 36 HIS J 79 HIS J 108 ASN ** J 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 234 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.156235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.106044 restraints weight = 55721.440| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.28 r_work: 0.3129 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3004 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3004 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 36254 Z= 0.210 Angle : 0.653 15.373 49301 Z= 0.327 Chirality : 0.051 0.229 5611 Planarity : 0.005 0.063 6325 Dihedral : 7.865 76.288 5591 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.30 % Favored : 94.63 % Rotamer: Outliers : 5.76 % Allowed : 22.21 % Favored : 72.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.12), residues: 4473 helix: 0.36 (0.17), residues: 970 sheet: -0.53 (0.15), residues: 1221 loop : -0.52 (0.13), residues: 2282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 287 TYR 0.015 0.001 TYR B 261 PHE 0.043 0.002 PHE L 215 TRP 0.023 0.001 TRP A 343 HIS 0.027 0.001 HIS J 36 Details of bonding type rmsd covalent geometry : bond 0.00507 (36249) covalent geometry : angle 0.65308 (49293) SS BOND : bond 0.00166 ( 4) SS BOND : angle 1.43445 ( 8) hydrogen bonds : bond 0.03827 ( 969) hydrogen bonds : angle 5.44655 ( 2787) Misc. bond : bond 0.00200 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8946 Ramachandran restraints generated. 4473 Oldfield, 0 Emsley, 4473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8946 Ramachandran restraints generated. 4473 Oldfield, 0 Emsley, 4473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 730 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 229 poor density : 501 time to evaluate : 1.386 Fit side-chains Corrupt residue: chain: K residue: PRO 199 >>> skipping Corrupt residue: chain: I residue: PRO 199 >>> skipping revert: symmetry clash revert: symmetry clash Corrupt residue: chain: E residue: PRO 199 >>> skipping revert: symmetry clash Corrupt residue: chain: F residue: PRO 199 >>> skipping revert: symmetry clash Corrupt residue: chain: H residue: PRO 199 >>> skipping Corrupt residue: chain: J residue: PRO 199 >>> skipping Corrupt residue: chain: L residue: PRO 199 >>> skipping revert: symmetry clash REVERT: K 39 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7647 (mt-10) REVERT: K 64 MET cc_start: 0.8646 (tpt) cc_final: 0.8402 (tpt) REVERT: K 117 PHE cc_start: 0.7032 (m-10) cc_final: 0.6789 (m-10) REVERT: K 139 GLU cc_start: 0.8327 (pp20) cc_final: 0.7653 (pp20) REVERT: K 201 MET cc_start: 0.6710 (tpp) cc_final: 0.6482 (tpp) REVERT: K 331 ILE cc_start: 0.8986 (mm) cc_final: 0.8381 (tt) REVERT: I 1 MET cc_start: 0.5746 (pmm) cc_final: 0.4368 (pmm) REVERT: I 63 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7448 (mm-30) REVERT: I 124 HIS cc_start: 0.6687 (t70) cc_final: 0.6268 (t70) REVERT: I 195 LYS cc_start: 0.8294 (tmtt) cc_final: 0.7767 (tptp) REVERT: I 224 ASP cc_start: 0.8146 (m-30) cc_final: 0.7819 (m-30) REVERT: I 229 MET cc_start: 0.8478 (OUTLIER) cc_final: 0.8193 (tmm) REVERT: I 322 ASN cc_start: 0.8245 (t0) cc_final: 0.7846 (t0) REVERT: A 1 MET cc_start: 0.7985 (tmm) cc_final: 0.7697 (tmm) REVERT: A 51 GLN cc_start: 0.8601 (tt0) cc_final: 0.8070 (tt0) REVERT: A 321 GLU cc_start: 0.8549 (mm-30) cc_final: 0.8235 (tp30) REVERT: A 368 ARG cc_start: 0.8897 (OUTLIER) cc_final: 0.7027 (mtp85) REVERT: B 133 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.8185 (tp40) REVERT: C 295 VAL cc_start: 0.9340 (t) cc_final: 0.9096 (m) REVERT: C 369 MET cc_start: 0.8961 (OUTLIER) cc_final: 0.8696 (tmm) REVERT: C 376 LYS cc_start: 0.8340 (tppt) cc_final: 0.8060 (tppt) REVERT: C 412 ARG cc_start: 0.8847 (OUTLIER) cc_final: 0.8418 (ptt90) REVERT: D 118 CYS cc_start: 0.9174 (OUTLIER) cc_final: 0.8482 (t) REVERT: D 230 LEU cc_start: 0.8960 (mt) cc_final: 0.8732 (mp) REVERT: D 261 TYR cc_start: 0.8857 (m-10) cc_final: 0.7593 (m-10) REVERT: D 364 ASP cc_start: 0.8504 (t0) cc_final: 0.8156 (t0) REVERT: E 15 ARG cc_start: 0.7075 (OUTLIER) cc_final: 0.6764 (tpp80) REVERT: E 138 VAL cc_start: 0.6787 (t) cc_final: 0.6568 (t) REVERT: E 162 LYS cc_start: 0.7216 (tptt) cc_final: 0.5270 (tmtt) REVERT: E 210 MET cc_start: 0.6727 (OUTLIER) cc_final: 0.6263 (tpp) REVERT: E 233 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8410 (mm) REVERT: E 312 CYS cc_start: 0.7812 (m) cc_final: 0.7367 (m) REVERT: E 329 ASP cc_start: 0.8410 (t0) cc_final: 0.7988 (t0) REVERT: F 60 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8338 (tp) REVERT: F 96 LEU cc_start: 0.6875 (OUTLIER) cc_final: 0.6529 (mp) REVERT: F 166 PHE cc_start: 0.6597 (t80) cc_final: 0.6025 (t80) REVERT: F 175 MET cc_start: 0.8169 (ptm) cc_final: 0.7912 (ptm) REVERT: F 188 LEU cc_start: 0.5036 (tp) cc_final: 0.4555 (mp) REVERT: F 201 MET cc_start: 0.8107 (tpp) cc_final: 0.7550 (tpp) REVERT: F 210 MET cc_start: 0.5485 (ttm) cc_final: 0.5277 (ttm) REVERT: F 216 TRP cc_start: 0.8511 (t60) cc_final: 0.8099 (t60) REVERT: F 223 LYS cc_start: 0.8828 (tptm) cc_final: 0.8526 (tptp) REVERT: G 56 MET cc_start: 0.6404 (mmt) cc_final: 0.4692 (ptp) REVERT: G 64 MET cc_start: 0.7667 (ptm) cc_final: 0.7243 (ptm) REVERT: G 68 GLU cc_start: 0.8379 (pt0) cc_final: 0.8055 (pt0) REVERT: G 114 ASP cc_start: 0.7951 (t0) cc_final: 0.7722 (t0) REVERT: G 120 MET cc_start: 0.8645 (tpp) cc_final: 0.8341 (tpt) REVERT: G 144 TYR cc_start: 0.8893 (m-80) cc_final: 0.8692 (m-10) REVERT: H 144 TYR cc_start: 0.7622 (OUTLIER) cc_final: 0.6377 (m-80) REVERT: J 73 ILE cc_start: 0.7313 (OUTLIER) cc_final: 0.7000 (mm) REVERT: J 120 MET cc_start: 0.8528 (OUTLIER) cc_final: 0.8309 (ttp) REVERT: J 208 TYR cc_start: 0.7608 (m-80) cc_final: 0.6405 (t80) REVERT: J 223 LYS cc_start: 0.8737 (tttt) cc_final: 0.8383 (ptpp) REVERT: J 301 SER cc_start: 0.9308 (t) cc_final: 0.9006 (m) REVERT: J 312 CYS cc_start: 0.8776 (t) cc_final: 0.8468 (m) REVERT: J 322 ASN cc_start: 0.8650 (t0) cc_final: 0.7905 (t0) REVERT: L 70 ARG cc_start: 0.7986 (ttp-170) cc_final: 0.7604 (ptm160) REVERT: L 77 MET cc_start: 0.8154 (pmm) cc_final: 0.7598 (ppp) REVERT: L 160 VAL cc_start: 0.7459 (p) cc_final: 0.7227 (m) REVERT: L 317 TRP cc_start: 0.8761 (m-10) cc_final: 0.8523 (m-10) outliers start: 229 outliers final: 169 residues processed: 668 average time/residue: 0.1961 time to fit residues: 223.2690 Evaluate side-chains 655 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 472 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 50 ILE Chi-restraints excluded: chain K residue 106 VAL Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 112 ILE Chi-restraints excluded: chain K residue 127 HIS Chi-restraints excluded: chain K residue 136 THR Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 153 THR Chi-restraints excluded: chain K residue 199 PRO Chi-restraints excluded: chain K residue 306 CYS Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 167 VAL Chi-restraints excluded: chain I residue 176 TYR Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 193 ILE Chi-restraints excluded: chain I residue 199 PRO Chi-restraints excluded: chain I residue 221 GLN Chi-restraints excluded: chain I residue 229 MET Chi-restraints excluded: chain I residue 233 LEU Chi-restraints excluded: chain I residue 306 CYS Chi-restraints excluded: chain I residue 312 CYS Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 166 HIS Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 368 ARG Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 118 CYS Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 326 HIS Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 408 LYS Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 412 ARG Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 118 CYS Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 265 TYR Chi-restraints excluded: chain D residue 304 ASN Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 15 ARG Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 117 PHE Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 176 TYR Chi-restraints excluded: chain E residue 199 PRO Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 266 CYS Chi-restraints excluded: chain E residue 286 ILE Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 144 TYR Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 153 THR Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 193 ILE Chi-restraints excluded: chain F residue 197 VAL Chi-restraints excluded: chain F residue 199 PRO Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 231 LEU Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 289 CYS Chi-restraints excluded: chain F residue 306 CYS Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 77 MET Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 193 ILE Chi-restraints excluded: chain G residue 197 VAL Chi-restraints excluded: chain G residue 215 PHE Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain G residue 257 ASP Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain G residue 344 LEU Chi-restraints excluded: chain G residue 353 VAL Chi-restraints excluded: chain G residue 359 ILE Chi-restraints excluded: chain H residue 30 ASN Chi-restraints excluded: chain H residue 35 LEU Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 79 HIS Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 108 ASN Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 126 HIS Chi-restraints excluded: chain H residue 144 TYR Chi-restraints excluded: chain H residue 153 THR Chi-restraints excluded: chain H residue 193 ILE Chi-restraints excluded: chain H residue 199 PRO Chi-restraints excluded: chain H residue 278 VAL Chi-restraints excluded: chain H residue 299 SER Chi-restraints excluded: chain H residue 322 ASN Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain H residue 335 GLU Chi-restraints excluded: chain H residue 359 ILE Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 7 VAL Chi-restraints excluded: chain J residue 10 TYR Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 73 ILE Chi-restraints excluded: chain J residue 120 MET Chi-restraints excluded: chain J residue 121 VAL Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 147 VAL Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 186 ILE Chi-restraints excluded: chain J residue 193 ILE Chi-restraints excluded: chain J residue 199 PRO Chi-restraints excluded: chain J residue 278 VAL Chi-restraints excluded: chain J residue 304 GLU Chi-restraints excluded: chain J residue 324 THR Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain L residue 60 LEU Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 153 THR Chi-restraints excluded: chain L residue 169 ASN Chi-restraints excluded: chain L residue 176 TYR Chi-restraints excluded: chain L residue 183 LEU Chi-restraints excluded: chain L residue 191 THR Chi-restraints excluded: chain L residue 193 ILE Chi-restraints excluded: chain L residue 194 GLU Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain L residue 199 PRO Chi-restraints excluded: chain L residue 256 VAL Chi-restraints excluded: chain L residue 278 VAL Chi-restraints excluded: chain L residue 321 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 312 optimal weight: 0.4980 chunk 416 optimal weight: 40.0000 chunk 254 optimal weight: 6.9990 chunk 410 optimal weight: 6.9990 chunk 419 optimal weight: 20.0000 chunk 187 optimal weight: 6.9990 chunk 188 optimal weight: 4.9990 chunk 393 optimal weight: 10.0000 chunk 137 optimal weight: 4.9990 chunk 163 optimal weight: 0.9980 chunk 253 optimal weight: 3.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 79 HIS ** I 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 126 HIS ** E 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 126 HIS ** G 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 265 ASN J 108 ASN ** J 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 234 GLN L 265 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.156510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.108277 restraints weight = 55887.172| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.37 r_work: 0.3124 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2998 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2998 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 36254 Z= 0.175 Angle : 0.642 14.722 49301 Z= 0.320 Chirality : 0.050 0.226 5611 Planarity : 0.005 0.062 6325 Dihedral : 7.745 76.937 5587 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.25 % Favored : 94.70 % Rotamer: Outliers : 5.14 % Allowed : 23.35 % Favored : 71.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.61 (0.13), residues: 4473 helix: 0.49 (0.17), residues: 970 sheet: -0.54 (0.14), residues: 1338 loop : -0.62 (0.13), residues: 2165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 366 TYR 0.016 0.001 TYR B 261 PHE 0.049 0.002 PHE F 215 TRP 0.022 0.001 TRP E 216 HIS 0.009 0.001 HIS E 127 Details of bonding type rmsd covalent geometry : bond 0.00421 (36249) covalent geometry : angle 0.64152 (49293) SS BOND : bond 0.00146 ( 4) SS BOND : angle 1.12562 ( 8) hydrogen bonds : bond 0.03637 ( 969) hydrogen bonds : angle 5.40854 ( 2787) Misc. bond : bond 0.00199 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8946 Ramachandran restraints generated. 4473 Oldfield, 0 Emsley, 4473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8946 Ramachandran restraints generated. 4473 Oldfield, 0 Emsley, 4473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 702 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 205 poor density : 497 time to evaluate : 1.298 Fit side-chains Corrupt residue: chain: K residue: PRO 199 >>> skipping Corrupt residue: chain: I residue: PRO 199 >>> skipping revert: symmetry clash Corrupt residue: chain: E residue: PRO 199 >>> skipping Corrupt residue: chain: F residue: PRO 199 >>> skipping revert: symmetry clash Corrupt residue: chain: H residue: PRO 199 >>> skipping Corrupt residue: chain: J residue: PRO 199 >>> skipping Corrupt residue: chain: L residue: PRO 199 >>> skipping revert: symmetry clash REVERT: K 39 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7688 (mt-10) REVERT: K 64 MET cc_start: 0.8660 (tpt) cc_final: 0.8426 (tpt) REVERT: K 117 PHE cc_start: 0.7063 (m-10) cc_final: 0.6645 (m-10) REVERT: K 139 GLU cc_start: 0.8301 (pp20) cc_final: 0.7572 (pp20) REVERT: K 201 MET cc_start: 0.6772 (tpp) cc_final: 0.6568 (tpp) REVERT: K 331 ILE cc_start: 0.8980 (mm) cc_final: 0.8363 (tt) REVERT: I 1 MET cc_start: 0.5821 (pmm) cc_final: 0.4456 (pmm) REVERT: I 63 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7468 (mm-30) REVERT: I 124 HIS cc_start: 0.6745 (t70) cc_final: 0.6282 (t70) REVERT: I 195 LYS cc_start: 0.8290 (tmtt) cc_final: 0.7771 (tptp) REVERT: I 224 ASP cc_start: 0.8169 (m-30) cc_final: 0.7852 (m-30) REVERT: I 229 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.8189 (tmm) REVERT: I 322 ASN cc_start: 0.8268 (t0) cc_final: 0.7882 (t0) REVERT: A 51 GLN cc_start: 0.8635 (tt0) cc_final: 0.8088 (tt0) REVERT: A 81 ARG cc_start: 0.8665 (mtt-85) cc_final: 0.7705 (mtp180) REVERT: A 321 GLU cc_start: 0.8527 (mm-30) cc_final: 0.8194 (tp30) REVERT: A 368 ARG cc_start: 0.8840 (OUTLIER) cc_final: 0.7264 (mtp85) REVERT: B 133 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.8166 (tp40) REVERT: C 295 VAL cc_start: 0.9335 (t) cc_final: 0.9106 (m) REVERT: C 369 MET cc_start: 0.8974 (OUTLIER) cc_final: 0.8716 (tmm) REVERT: C 376 LYS cc_start: 0.8356 (tppt) cc_final: 0.8068 (tppt) REVERT: C 412 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.8246 (ptt90) REVERT: D 118 CYS cc_start: 0.9210 (OUTLIER) cc_final: 0.8537 (t) REVERT: D 230 LEU cc_start: 0.8978 (mt) cc_final: 0.8748 (mp) REVERT: D 261 TYR cc_start: 0.8855 (m-10) cc_final: 0.7616 (m-10) REVERT: D 315 GLU cc_start: 0.8538 (tm-30) cc_final: 0.8286 (tp30) REVERT: D 364 ASP cc_start: 0.8497 (t0) cc_final: 0.8111 (t0) REVERT: E 4 LEU cc_start: 0.5861 (OUTLIER) cc_final: 0.5296 (tt) REVERT: E 15 ARG cc_start: 0.7171 (OUTLIER) cc_final: 0.6857 (tpp80) REVERT: E 162 LYS cc_start: 0.7198 (tptt) cc_final: 0.5271 (tmtt) REVERT: E 210 MET cc_start: 0.6837 (OUTLIER) cc_final: 0.6333 (tpp) REVERT: E 233 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8369 (mm) REVERT: E 311 ARG cc_start: 0.7911 (ttp-110) cc_final: 0.7570 (ttp80) REVERT: E 329 ASP cc_start: 0.8398 (t0) cc_final: 0.7958 (t0) REVERT: F 60 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8291 (tp) REVERT: F 96 LEU cc_start: 0.6924 (OUTLIER) cc_final: 0.6592 (mp) REVERT: F 110 ASP cc_start: 0.8601 (p0) cc_final: 0.8148 (p0) REVERT: F 166 PHE cc_start: 0.6602 (t80) cc_final: 0.6052 (t80) REVERT: F 188 LEU cc_start: 0.5369 (tp) cc_final: 0.4824 (mp) REVERT: F 201 MET cc_start: 0.8117 (tpp) cc_final: 0.7541 (tpp) REVERT: F 210 MET cc_start: 0.5583 (ttm) cc_final: 0.5362 (ttm) REVERT: F 223 LYS cc_start: 0.8872 (tptm) cc_final: 0.8551 (tptp) REVERT: G 56 MET cc_start: 0.6424 (mmt) cc_final: 0.4847 (ptp) REVERT: G 64 MET cc_start: 0.7745 (ptm) cc_final: 0.7362 (ptm) REVERT: G 68 GLU cc_start: 0.8482 (pt0) cc_final: 0.8101 (pt0) REVERT: G 114 ASP cc_start: 0.7916 (t0) cc_final: 0.7695 (t0) REVERT: G 120 MET cc_start: 0.8629 (tpp) cc_final: 0.8341 (tpt) REVERT: G 144 TYR cc_start: 0.8892 (m-80) cc_final: 0.8671 (m-10) REVERT: G 304 GLU cc_start: 0.8690 (tm-30) cc_final: 0.8282 (tm-30) REVERT: H 31 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.8107 (ttpp) REVERT: H 144 TYR cc_start: 0.7631 (OUTLIER) cc_final: 0.6372 (m-80) REVERT: H 194 GLU cc_start: 0.8126 (mp0) cc_final: 0.7918 (mp0) REVERT: J 1 MET cc_start: 0.5459 (tpp) cc_final: 0.4934 (pmm) REVERT: J 73 ILE cc_start: 0.7320 (OUTLIER) cc_final: 0.7007 (mm) REVERT: J 77 MET cc_start: 0.7767 (OUTLIER) cc_final: 0.7527 (mpp) REVERT: J 120 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.8390 (ttp) REVERT: J 208 TYR cc_start: 0.7583 (m-80) cc_final: 0.6385 (t80) REVERT: J 223 LYS cc_start: 0.8739 (tttt) cc_final: 0.8387 (ptpp) REVERT: J 301 SER cc_start: 0.9322 (t) cc_final: 0.9014 (m) REVERT: J 312 CYS cc_start: 0.8837 (t) cc_final: 0.8450 (m) REVERT: J 322 ASN cc_start: 0.8707 (t0) cc_final: 0.7982 (t0) REVERT: L 70 ARG cc_start: 0.8099 (ttp-170) cc_final: 0.7690 (ptm160) REVERT: L 77 MET cc_start: 0.8020 (pmm) cc_final: 0.7557 (ppp) REVERT: L 160 VAL cc_start: 0.7469 (p) cc_final: 0.7240 (m) REVERT: L 317 TRP cc_start: 0.8762 (m-10) cc_final: 0.8517 (m-10) outliers start: 205 outliers final: 166 residues processed: 650 average time/residue: 0.2032 time to fit residues: 222.0247 Evaluate side-chains 648 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 465 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 50 ILE Chi-restraints excluded: chain K residue 106 VAL Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 112 ILE Chi-restraints excluded: chain K residue 127 HIS Chi-restraints excluded: chain K residue 136 THR Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 153 THR Chi-restraints excluded: chain K residue 199 PRO Chi-restraints excluded: chain K residue 215 PHE Chi-restraints excluded: chain K residue 306 CYS Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 167 VAL Chi-restraints excluded: chain I residue 176 TYR Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 193 ILE Chi-restraints excluded: chain I residue 199 PRO Chi-restraints excluded: chain I residue 221 GLN Chi-restraints excluded: chain I residue 229 MET Chi-restraints excluded: chain I residue 233 LEU Chi-restraints excluded: chain I residue 306 CYS Chi-restraints excluded: chain I residue 312 CYS Chi-restraints excluded: chain A residue 166 HIS Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 368 ARG Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 118 CYS Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 326 HIS Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 408 LYS Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 412 ARG Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 3 LYS Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 118 CYS Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 157 GLU Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 265 TYR Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 304 ASN Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 15 ARG Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 117 PHE Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 176 TYR Chi-restraints excluded: chain E residue 199 PRO Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 266 CYS Chi-restraints excluded: chain E residue 286 ILE Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 153 THR Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 193 ILE Chi-restraints excluded: chain F residue 197 VAL Chi-restraints excluded: chain F residue 199 PRO Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 231 LEU Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 289 CYS Chi-restraints excluded: chain F residue 306 CYS Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 193 ILE Chi-restraints excluded: chain G residue 197 VAL Chi-restraints excluded: chain G residue 215 PHE Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain G residue 257 ASP Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain G residue 328 GLU Chi-restraints excluded: chain G residue 344 LEU Chi-restraints excluded: chain G residue 353 VAL Chi-restraints excluded: chain G residue 359 ILE Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 35 LEU Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 79 HIS Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 108 ASN Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 126 HIS Chi-restraints excluded: chain H residue 144 TYR Chi-restraints excluded: chain H residue 193 ILE Chi-restraints excluded: chain H residue 199 PRO Chi-restraints excluded: chain H residue 278 VAL Chi-restraints excluded: chain H residue 299 SER Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain H residue 335 GLU Chi-restraints excluded: chain H residue 359 ILE Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 7 VAL Chi-restraints excluded: chain J residue 10 TYR Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 73 ILE Chi-restraints excluded: chain J residue 77 MET Chi-restraints excluded: chain J residue 120 MET Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 147 VAL Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 186 ILE Chi-restraints excluded: chain J residue 193 ILE Chi-restraints excluded: chain J residue 199 PRO Chi-restraints excluded: chain J residue 230 CYS Chi-restraints excluded: chain J residue 278 VAL Chi-restraints excluded: chain J residue 304 GLU Chi-restraints excluded: chain J residue 324 THR Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain L residue 60 LEU Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 153 THR Chi-restraints excluded: chain L residue 176 TYR Chi-restraints excluded: chain L residue 183 LEU Chi-restraints excluded: chain L residue 191 THR Chi-restraints excluded: chain L residue 193 ILE Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain L residue 199 PRO Chi-restraints excluded: chain L residue 256 VAL Chi-restraints excluded: chain L residue 278 VAL Chi-restraints excluded: chain L residue 321 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 105 optimal weight: 4.9990 chunk 312 optimal weight: 0.0050 chunk 185 optimal weight: 7.9990 chunk 363 optimal weight: 9.9990 chunk 284 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 294 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 412 optimal weight: 30.0000 chunk 247 optimal weight: 20.0000 chunk 316 optimal weight: 20.0000 overall best weight: 3.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 271 ASN I 79 HIS A 304 ASN ** E 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 126 HIS ** E 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 126 HIS ** G 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 108 ASN ** H 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 265 ASN J 36 HIS J 108 ASN ** J 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 234 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.155814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.105579 restraints weight = 55783.431| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.31 r_work: 0.3130 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3000 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 36254 Z= 0.196 Angle : 0.655 15.247 49301 Z= 0.327 Chirality : 0.051 0.229 5611 Planarity : 0.005 0.063 6325 Dihedral : 7.801 77.343 5586 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.68 % Favored : 94.30 % Rotamer: Outliers : 5.50 % Allowed : 23.38 % Favored : 71.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.61 (0.13), residues: 4473 helix: 0.55 (0.17), residues: 974 sheet: -0.57 (0.14), residues: 1314 loop : -0.63 (0.13), residues: 2185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 287 TYR 0.016 0.001 TYR B 261 PHE 0.041 0.002 PHE F 215 TRP 0.018 0.001 TRP A 343 HIS 0.009 0.001 HIS E 127 Details of bonding type rmsd covalent geometry : bond 0.00475 (36249) covalent geometry : angle 0.65457 (49293) SS BOND : bond 0.00135 ( 4) SS BOND : angle 1.06031 ( 8) hydrogen bonds : bond 0.03651 ( 969) hydrogen bonds : angle 5.39746 ( 2787) Misc. bond : bond 0.00201 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8946 Ramachandran restraints generated. 4473 Oldfield, 0 Emsley, 4473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8946 Ramachandran restraints generated. 4473 Oldfield, 0 Emsley, 4473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 718 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 219 poor density : 499 time to evaluate : 1.350 Fit side-chains Corrupt residue: chain: K residue: PRO 199 >>> skipping Corrupt residue: chain: I residue: PRO 199 >>> skipping revert: symmetry clash Corrupt residue: chain: E residue: PRO 199 >>> skipping revert: symmetry clash Corrupt residue: chain: F residue: PRO 199 >>> skipping revert: symmetry clash Corrupt residue: chain: H residue: PRO 199 >>> skipping Corrupt residue: chain: J residue: PRO 199 >>> skipping Corrupt residue: chain: L residue: PRO 199 >>> skipping revert: symmetry clash REVERT: K 39 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7688 (mt-10) REVERT: K 64 MET cc_start: 0.8667 (tpt) cc_final: 0.8438 (tpt) REVERT: K 139 GLU cc_start: 0.8262 (pp20) cc_final: 0.7531 (pp20) REVERT: K 201 MET cc_start: 0.6804 (tpp) cc_final: 0.6596 (tpp) REVERT: K 331 ILE cc_start: 0.8971 (mm) cc_final: 0.8369 (tt) REVERT: I 1 MET cc_start: 0.5793 (pmm) cc_final: 0.4413 (pmm) REVERT: I 63 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7508 (mm-30) REVERT: I 124 HIS cc_start: 0.6750 (t70) cc_final: 0.6377 (t70) REVERT: I 176 TYR cc_start: 0.6258 (OUTLIER) cc_final: 0.4359 (m-80) REVERT: I 195 LYS cc_start: 0.8292 (tmtt) cc_final: 0.7781 (tptp) REVERT: I 224 ASP cc_start: 0.8107 (m-30) cc_final: 0.7860 (m-30) REVERT: I 229 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.8175 (tmm) REVERT: I 234 GLN cc_start: 0.8145 (tp-100) cc_final: 0.7822 (tp-100) REVERT: I 322 ASN cc_start: 0.8323 (t0) cc_final: 0.7907 (t0) REVERT: A 1 MET cc_start: 0.7994 (tmm) cc_final: 0.7793 (tmm) REVERT: A 51 GLN cc_start: 0.8669 (tt0) cc_final: 0.8107 (tt0) REVERT: A 304 ASN cc_start: 0.8505 (m-40) cc_final: 0.8251 (t0) REVERT: A 321 GLU cc_start: 0.8458 (mm-30) cc_final: 0.8088 (tp30) REVERT: A 368 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.6923 (mtp85) REVERT: B 133 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.8070 (tp40) REVERT: C 283 ILE cc_start: 0.9368 (OUTLIER) cc_final: 0.9137 (mp) REVERT: C 295 VAL cc_start: 0.9350 (t) cc_final: 0.9127 (m) REVERT: C 369 MET cc_start: 0.8992 (OUTLIER) cc_final: 0.8736 (tmm) REVERT: C 376 LYS cc_start: 0.8381 (tppt) cc_final: 0.8114 (tppt) REVERT: C 412 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.8245 (ptt90) REVERT: D 118 CYS cc_start: 0.9184 (OUTLIER) cc_final: 0.8492 (t) REVERT: D 261 TYR cc_start: 0.8867 (m-10) cc_final: 0.7629 (m-10) REVERT: D 364 ASP cc_start: 0.8490 (t0) cc_final: 0.8073 (t0) REVERT: E 4 LEU cc_start: 0.5722 (OUTLIER) cc_final: 0.5223 (tt) REVERT: E 15 ARG cc_start: 0.7261 (OUTLIER) cc_final: 0.6902 (tpp80) REVERT: E 162 LYS cc_start: 0.7130 (tptt) cc_final: 0.5238 (tmtt) REVERT: E 210 MET cc_start: 0.6766 (OUTLIER) cc_final: 0.6305 (tpp) REVERT: E 233 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8351 (mm) REVERT: E 311 ARG cc_start: 0.7865 (ttp-110) cc_final: 0.7528 (ttp80) REVERT: E 312 CYS cc_start: 0.7825 (m) cc_final: 0.7398 (m) REVERT: E 329 ASP cc_start: 0.8326 (t0) cc_final: 0.7917 (t0) REVERT: F 166 PHE cc_start: 0.6642 (t80) cc_final: 0.6089 (t80) REVERT: F 175 MET cc_start: 0.8063 (ppp) cc_final: 0.7854 (ptm) REVERT: F 188 LEU cc_start: 0.5653 (tp) cc_final: 0.5076 (mp) REVERT: F 201 MET cc_start: 0.8167 (tpp) cc_final: 0.7574 (tpp) REVERT: F 223 LYS cc_start: 0.8885 (tptm) cc_final: 0.8576 (tptp) REVERT: G 56 MET cc_start: 0.6334 (mmt) cc_final: 0.4728 (ptp) REVERT: G 64 MET cc_start: 0.7673 (ptm) cc_final: 0.7291 (ptm) REVERT: G 68 GLU cc_start: 0.8560 (pt0) cc_final: 0.8282 (pt0) REVERT: G 114 ASP cc_start: 0.7962 (t0) cc_final: 0.7690 (t0) REVERT: G 120 MET cc_start: 0.8642 (tpp) cc_final: 0.8353 (tpt) REVERT: G 144 TYR cc_start: 0.8888 (m-80) cc_final: 0.8653 (m-10) REVERT: H 31 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8220 (ttpp) REVERT: H 144 TYR cc_start: 0.7567 (OUTLIER) cc_final: 0.6198 (m-80) REVERT: H 194 GLU cc_start: 0.8013 (mp0) cc_final: 0.7804 (mp0) REVERT: J 1 MET cc_start: 0.5621 (tpp) cc_final: 0.5039 (pmm) REVERT: J 73 ILE cc_start: 0.7328 (OUTLIER) cc_final: 0.7028 (mm) REVERT: J 77 MET cc_start: 0.7762 (OUTLIER) cc_final: 0.7524 (mpp) REVERT: J 208 TYR cc_start: 0.7543 (m-80) cc_final: 0.6364 (t80) REVERT: J 223 LYS cc_start: 0.8749 (tttt) cc_final: 0.8422 (ptpp) REVERT: J 301 SER cc_start: 0.9333 (t) cc_final: 0.9022 (m) REVERT: J 312 CYS cc_start: 0.8839 (t) cc_final: 0.8470 (m) REVERT: J 322 ASN cc_start: 0.8744 (t0) cc_final: 0.7911 (t0) REVERT: L 70 ARG cc_start: 0.8132 (ttp-170) cc_final: 0.7749 (ptm160) REVERT: L 77 MET cc_start: 0.8096 (pmm) cc_final: 0.7672 (ppp) REVERT: L 184 GLN cc_start: 0.6417 (tm-30) cc_final: 0.5991 (pt0) REVERT: L 194 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.6712 (mt-10) REVERT: L 317 TRP cc_start: 0.8790 (m-10) cc_final: 0.8579 (m-10) outliers start: 219 outliers final: 178 residues processed: 659 average time/residue: 0.2004 time to fit residues: 223.7097 Evaluate side-chains 665 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 195 poor density : 470 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 50 ILE Chi-restraints excluded: chain K residue 106 VAL Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 112 ILE Chi-restraints excluded: chain K residue 136 THR Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 153 THR Chi-restraints excluded: chain K residue 199 PRO Chi-restraints excluded: chain K residue 215 PHE Chi-restraints excluded: chain K residue 245 CYS Chi-restraints excluded: chain K residue 306 CYS Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 144 TYR Chi-restraints excluded: chain I residue 167 VAL Chi-restraints excluded: chain I residue 176 TYR Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 193 ILE Chi-restraints excluded: chain I residue 199 PRO Chi-restraints excluded: chain I residue 221 GLN Chi-restraints excluded: chain I residue 229 MET Chi-restraints excluded: chain I residue 233 LEU Chi-restraints excluded: chain I residue 306 CYS Chi-restraints excluded: chain I residue 312 CYS Chi-restraints excluded: chain A residue 2 LEU Chi-restraints excluded: chain A residue 166 HIS Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 368 ARG Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 118 CYS Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 326 HIS Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 408 LYS Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 412 ARG Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 3 LYS Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 118 CYS Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 166 HIS Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 253 SER Chi-restraints excluded: chain D residue 265 TYR Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 304 ASN Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 15 ARG Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 117 PHE Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 176 TYR Chi-restraints excluded: chain E residue 199 PRO Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 266 CYS Chi-restraints excluded: chain E residue 286 ILE Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 153 THR Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 193 ILE Chi-restraints excluded: chain F residue 197 VAL Chi-restraints excluded: chain F residue 199 PRO Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 215 PHE Chi-restraints excluded: chain F residue 231 LEU Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 289 CYS Chi-restraints excluded: chain F residue 306 CYS Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 77 MET Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 193 ILE Chi-restraints excluded: chain G residue 197 VAL Chi-restraints excluded: chain G residue 215 PHE Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain G residue 257 ASP Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain G residue 328 GLU Chi-restraints excluded: chain G residue 344 LEU Chi-restraints excluded: chain G residue 353 VAL Chi-restraints excluded: chain G residue 359 ILE Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 35 LEU Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 79 HIS Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 126 HIS Chi-restraints excluded: chain H residue 144 TYR Chi-restraints excluded: chain H residue 153 THR Chi-restraints excluded: chain H residue 193 ILE Chi-restraints excluded: chain H residue 199 PRO Chi-restraints excluded: chain H residue 278 VAL Chi-restraints excluded: chain H residue 299 SER Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain H residue 335 GLU Chi-restraints excluded: chain H residue 359 ILE Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 7 VAL Chi-restraints excluded: chain J residue 10 TYR Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 36 HIS Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 73 ILE Chi-restraints excluded: chain J residue 77 MET Chi-restraints excluded: chain J residue 121 VAL Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 147 VAL Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 186 ILE Chi-restraints excluded: chain J residue 191 THR Chi-restraints excluded: chain J residue 193 ILE Chi-restraints excluded: chain J residue 199 PRO Chi-restraints excluded: chain J residue 230 CYS Chi-restraints excluded: chain J residue 278 VAL Chi-restraints excluded: chain J residue 304 GLU Chi-restraints excluded: chain J residue 324 THR Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain L residue 60 LEU Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 153 THR Chi-restraints excluded: chain L residue 176 TYR Chi-restraints excluded: chain L residue 183 LEU Chi-restraints excluded: chain L residue 191 THR Chi-restraints excluded: chain L residue 193 ILE Chi-restraints excluded: chain L residue 194 GLU Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain L residue 199 PRO Chi-restraints excluded: chain L residue 200 ILE Chi-restraints excluded: chain L residue 256 VAL Chi-restraints excluded: chain L residue 278 VAL Chi-restraints excluded: chain L residue 321 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 157 optimal weight: 2.9990 chunk 158 optimal weight: 0.9980 chunk 131 optimal weight: 1.9990 chunk 261 optimal weight: 9.9990 chunk 320 optimal weight: 1.9990 chunk 433 optimal weight: 10.0000 chunk 268 optimal weight: 30.0000 chunk 216 optimal weight: 0.9990 chunk 15 optimal weight: 30.0000 chunk 413 optimal weight: 3.9990 chunk 442 optimal weight: 7.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 79 HIS ** I 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 GLN D 269 HIS ** E 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 126 HIS ** E 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 264 GLN E 265 ASN F 79 HIS ** F 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 126 HIS ** G 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 265 ASN J 108 ASN ** J 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 234 GLN L 265 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.157378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.111402 restraints weight = 55509.424| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.44 r_work: 0.3143 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3013 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3013 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 36254 Z= 0.131 Angle : 0.630 14.786 49301 Z= 0.312 Chirality : 0.049 0.238 5611 Planarity : 0.005 0.065 6325 Dihedral : 7.528 76.986 5586 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.99 % Favored : 94.99 % Rotamer: Outliers : 4.64 % Allowed : 24.44 % Favored : 70.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.51 (0.13), residues: 4473 helix: 0.70 (0.17), residues: 980 sheet: -0.56 (0.14), residues: 1319 loop : -0.57 (0.13), residues: 2174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 366 TYR 0.015 0.001 TYR B 261 PHE 0.047 0.002 PHE L 215 TRP 0.018 0.001 TRP A 343 HIS 0.012 0.001 HIS J 36 Details of bonding type rmsd covalent geometry : bond 0.00307 (36249) covalent geometry : angle 0.63000 (49293) SS BOND : bond 0.00148 ( 4) SS BOND : angle 1.56815 ( 8) hydrogen bonds : bond 0.03409 ( 969) hydrogen bonds : angle 5.26052 ( 2787) Misc. bond : bond 0.00168 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8946 Ramachandran restraints generated. 4473 Oldfield, 0 Emsley, 4473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8946 Ramachandran restraints generated. 4473 Oldfield, 0 Emsley, 4473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 706 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 186 poor density : 520 time to evaluate : 1.276 Fit side-chains Corrupt residue: chain: K residue: PRO 199 >>> skipping Corrupt residue: chain: I residue: PRO 199 >>> skipping revert: symmetry clash Corrupt residue: chain: E residue: PRO 199 >>> skipping revert: symmetry clash Corrupt residue: chain: F residue: PRO 199 >>> skipping revert: symmetry clash Corrupt residue: chain: H residue: PRO 199 >>> skipping Corrupt residue: chain: J residue: PRO 199 >>> skipping Corrupt residue: chain: L residue: PRO 199 >>> skipping REVERT: K 39 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7619 (mt-10) REVERT: K 64 MET cc_start: 0.8687 (tpt) cc_final: 0.8464 (tpt) REVERT: K 139 GLU cc_start: 0.8229 (pp20) cc_final: 0.7532 (pp20) REVERT: K 201 MET cc_start: 0.6794 (tpp) cc_final: 0.6580 (tpp) REVERT: K 331 ILE cc_start: 0.8968 (mm) cc_final: 0.8378 (tt) REVERT: I 1 MET cc_start: 0.5790 (pmm) cc_final: 0.4519 (pmm) REVERT: I 63 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7447 (mm-30) REVERT: I 124 HIS cc_start: 0.6835 (t70) cc_final: 0.6481 (t70) REVERT: I 172 ASN cc_start: 0.7702 (t0) cc_final: 0.7502 (t0) REVERT: I 176 TYR cc_start: 0.6201 (OUTLIER) cc_final: 0.4493 (m-80) REVERT: I 195 LYS cc_start: 0.8276 (tmtt) cc_final: 0.7771 (tptp) REVERT: I 224 ASP cc_start: 0.8061 (m-30) cc_final: 0.7832 (m-30) REVERT: I 229 MET cc_start: 0.8433 (OUTLIER) cc_final: 0.8194 (tmm) REVERT: I 322 ASN cc_start: 0.8237 (t0) cc_final: 0.7815 (t0) REVERT: A 51 GLN cc_start: 0.8664 (tt0) cc_final: 0.8102 (tt0) REVERT: A 81 ARG cc_start: 0.8634 (mtt-85) cc_final: 0.7695 (mtp180) REVERT: A 304 ASN cc_start: 0.8505 (m-40) cc_final: 0.8255 (t0) REVERT: A 315 GLU cc_start: 0.8268 (mp0) cc_final: 0.7987 (mp0) REVERT: A 321 GLU cc_start: 0.8529 (mm-30) cc_final: 0.8166 (tp30) REVERT: A 368 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.7456 (mtp85) REVERT: B 133 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.8129 (tp40) REVERT: C 283 ILE cc_start: 0.9374 (OUTLIER) cc_final: 0.9130 (mp) REVERT: C 295 VAL cc_start: 0.9346 (t) cc_final: 0.9137 (m) REVERT: C 369 MET cc_start: 0.8966 (OUTLIER) cc_final: 0.8708 (tmm) REVERT: C 376 LYS cc_start: 0.8359 (tppt) cc_final: 0.8087 (tppt) REVERT: C 412 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.8289 (ptt90) REVERT: D 118 CYS cc_start: 0.9174 (OUTLIER) cc_final: 0.8439 (t) REVERT: D 261 TYR cc_start: 0.8839 (m-10) cc_final: 0.7476 (m-10) REVERT: D 364 ASP cc_start: 0.8436 (t0) cc_final: 0.7968 (t0) REVERT: E 15 ARG cc_start: 0.7123 (OUTLIER) cc_final: 0.6866 (tpp80) REVERT: E 134 LEU cc_start: 0.5355 (OUTLIER) cc_final: 0.5061 (tt) REVERT: E 162 LYS cc_start: 0.7089 (tptt) cc_final: 0.5321 (tmtt) REVERT: E 210 MET cc_start: 0.6916 (OUTLIER) cc_final: 0.6505 (tpp) REVERT: E 233 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8367 (mm) REVERT: E 311 ARG cc_start: 0.7859 (ttp-110) cc_final: 0.7487 (ttp80) REVERT: E 312 CYS cc_start: 0.7810 (m) cc_final: 0.7486 (m) REVERT: E 329 ASP cc_start: 0.8332 (t0) cc_final: 0.8002 (t0) REVERT: F 166 PHE cc_start: 0.6606 (t80) cc_final: 0.6078 (t80) REVERT: F 188 LEU cc_start: 0.5746 (tp) cc_final: 0.5119 (mp) REVERT: F 201 MET cc_start: 0.8174 (tpp) cc_final: 0.7558 (tpp) REVERT: F 223 LYS cc_start: 0.8887 (tptm) cc_final: 0.8571 (tptp) REVERT: G 56 MET cc_start: 0.6366 (mmt) cc_final: 0.4829 (ptp) REVERT: G 64 MET cc_start: 0.7716 (ptm) cc_final: 0.7360 (ptm) REVERT: G 68 GLU cc_start: 0.8643 (pt0) cc_final: 0.8307 (pt0) REVERT: G 114 ASP cc_start: 0.7981 (t0) cc_final: 0.7700 (t0) REVERT: G 120 MET cc_start: 0.8598 (tpp) cc_final: 0.8311 (tpt) REVERT: G 313 ARG cc_start: 0.8000 (mtp-110) cc_final: 0.7129 (mmt-90) REVERT: H 31 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.8173 (ttpp) REVERT: H 84 LEU cc_start: 0.5509 (mm) cc_final: 0.5075 (mm) REVERT: H 144 TYR cc_start: 0.7645 (OUTLIER) cc_final: 0.6260 (m-80) REVERT: J 1 MET cc_start: 0.5379 (tpp) cc_final: 0.4815 (pmm) REVERT: J 36 HIS cc_start: 0.7901 (OUTLIER) cc_final: 0.7601 (t-90) REVERT: J 73 ILE cc_start: 0.7280 (OUTLIER) cc_final: 0.6987 (mm) REVERT: J 95 ASP cc_start: 0.8267 (m-30) cc_final: 0.8054 (p0) REVERT: J 208 TYR cc_start: 0.7391 (m-80) cc_final: 0.6258 (t80) REVERT: J 223 LYS cc_start: 0.8756 (tttt) cc_final: 0.8414 (ptpp) REVERT: J 301 SER cc_start: 0.9327 (t) cc_final: 0.9026 (m) REVERT: J 312 CYS cc_start: 0.8830 (t) cc_final: 0.8407 (m) REVERT: J 322 ASN cc_start: 0.8773 (t0) cc_final: 0.8218 (t0) REVERT: L 70 ARG cc_start: 0.8123 (ttp-170) cc_final: 0.7757 (ptm160) REVERT: L 77 MET cc_start: 0.8047 (pmm) cc_final: 0.7648 (ppp) REVERT: L 156 ILE cc_start: 0.6966 (mp) cc_final: 0.6718 (mt) REVERT: L 184 GLN cc_start: 0.6388 (tm-30) cc_final: 0.5989 (pt0) REVERT: L 194 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.6764 (mt-10) REVERT: L 317 TRP cc_start: 0.8766 (m-10) cc_final: 0.8553 (m-10) REVERT: L 321 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7384 (tm-30) outliers start: 186 outliers final: 148 residues processed: 656 average time/residue: 0.2071 time to fit residues: 226.9245 Evaluate side-chains 648 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 482 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 50 ILE Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 112 ILE Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 153 THR Chi-restraints excluded: chain K residue 199 PRO Chi-restraints excluded: chain K residue 215 PHE Chi-restraints excluded: chain K residue 306 CYS Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 144 TYR Chi-restraints excluded: chain I residue 167 VAL Chi-restraints excluded: chain I residue 176 TYR Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 193 ILE Chi-restraints excluded: chain I residue 199 PRO Chi-restraints excluded: chain I residue 221 GLN Chi-restraints excluded: chain I residue 229 MET Chi-restraints excluded: chain I residue 233 LEU Chi-restraints excluded: chain I residue 306 CYS Chi-restraints excluded: chain I residue 312 CYS Chi-restraints excluded: chain A residue 2 LEU Chi-restraints excluded: chain A residue 166 HIS Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 368 ARG Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 118 CYS Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 326 HIS Chi-restraints excluded: chain B residue 408 LYS Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 412 ARG Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 3 LYS Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 118 CYS Chi-restraints excluded: chain D residue 166 HIS Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 265 TYR Chi-restraints excluded: chain D residue 304 ASN Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 15 ARG Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 79 HIS Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 176 TYR Chi-restraints excluded: chain E residue 199 PRO Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 266 CYS Chi-restraints excluded: chain E residue 286 ILE Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 153 THR Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 193 ILE Chi-restraints excluded: chain F residue 197 VAL Chi-restraints excluded: chain F residue 199 PRO Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 215 PHE Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 289 CYS Chi-restraints excluded: chain F residue 306 CYS Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 77 MET Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 193 ILE Chi-restraints excluded: chain G residue 197 VAL Chi-restraints excluded: chain G residue 215 PHE Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain G residue 257 ASP Chi-restraints excluded: chain G residue 328 GLU Chi-restraints excluded: chain G residue 353 VAL Chi-restraints excluded: chain G residue 359 ILE Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 35 LEU Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 79 HIS Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 126 HIS Chi-restraints excluded: chain H residue 144 TYR Chi-restraints excluded: chain H residue 153 THR Chi-restraints excluded: chain H residue 193 ILE Chi-restraints excluded: chain H residue 199 PRO Chi-restraints excluded: chain H residue 278 VAL Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain H residue 335 GLU Chi-restraints excluded: chain H residue 359 ILE Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 7 VAL Chi-restraints excluded: chain J residue 10 TYR Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 36 HIS Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 73 ILE Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 147 VAL Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 186 ILE Chi-restraints excluded: chain J residue 191 THR Chi-restraints excluded: chain J residue 199 PRO Chi-restraints excluded: chain J residue 230 CYS Chi-restraints excluded: chain J residue 278 VAL Chi-restraints excluded: chain J residue 304 GLU Chi-restraints excluded: chain J residue 324 THR Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain L residue 60 LEU Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 153 THR Chi-restraints excluded: chain L residue 176 TYR Chi-restraints excluded: chain L residue 191 THR Chi-restraints excluded: chain L residue 193 ILE Chi-restraints excluded: chain L residue 194 GLU Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain L residue 199 PRO Chi-restraints excluded: chain L residue 256 VAL Chi-restraints excluded: chain L residue 278 VAL Chi-restraints excluded: chain L residue 321 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 370 optimal weight: 10.0000 chunk 290 optimal weight: 6.9990 chunk 135 optimal weight: 4.9990 chunk 418 optimal weight: 6.9990 chunk 307 optimal weight: 0.7980 chunk 312 optimal weight: 4.9990 chunk 296 optimal weight: 2.9990 chunk 333 optimal weight: 9.9990 chunk 387 optimal weight: 5.9990 chunk 386 optimal weight: 20.0000 chunk 429 optimal weight: 20.0000 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 79 HIS B 67 GLN C 51 GLN ** D 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 126 HIS ** E 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 265 ASN ** F 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 126 HIS ** G 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 265 ASN J 36 HIS J 79 HIS J 108 ASN ** J 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 234 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.155477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.104066 restraints weight = 56044.099| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.31 r_work: 0.3117 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2988 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2988 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 36254 Z= 0.211 Angle : 0.680 15.533 49301 Z= 0.338 Chirality : 0.051 0.231 5611 Planarity : 0.005 0.064 6325 Dihedral : 7.740 77.090 5583 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.04 % Favored : 93.94 % Rotamer: Outliers : 4.70 % Allowed : 24.65 % Favored : 70.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.60 (0.13), residues: 4473 helix: 0.69 (0.17), residues: 968 sheet: -0.64 (0.14), residues: 1332 loop : -0.64 (0.13), residues: 2173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 132 TYR 0.015 0.001 TYR B 261 PHE 0.039 0.002 PHE F 215 TRP 0.015 0.001 TRP A 343 HIS 0.012 0.001 HIS G 124 Details of bonding type rmsd covalent geometry : bond 0.00513 (36249) covalent geometry : angle 0.67919 (49293) SS BOND : bond 0.00274 ( 4) SS BOND : angle 2.48398 ( 8) hydrogen bonds : bond 0.03635 ( 969) hydrogen bonds : angle 5.34904 ( 2787) Misc. bond : bond 0.00210 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8946 Ramachandran restraints generated. 4473 Oldfield, 0 Emsley, 4473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8946 Ramachandran restraints generated. 4473 Oldfield, 0 Emsley, 4473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 188 poor density : 487 time to evaluate : 1.426 Fit side-chains Corrupt residue: chain: K residue: PRO 199 >>> skipping Corrupt residue: chain: I residue: PRO 199 >>> skipping revert: symmetry clash revert: symmetry clash Corrupt residue: chain: E residue: PRO 199 >>> skipping revert: symmetry clash Corrupt residue: chain: F residue: PRO 199 >>> skipping Corrupt residue: chain: H residue: PRO 199 >>> skipping Corrupt residue: chain: J residue: PRO 199 >>> skipping Corrupt residue: chain: L residue: PRO 199 >>> skipping revert: symmetry clash REVERT: K 39 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7679 (mt-10) REVERT: K 64 MET cc_start: 0.8695 (tpt) cc_final: 0.8482 (tpt) REVERT: K 139 GLU cc_start: 0.8232 (pp20) cc_final: 0.7504 (pp20) REVERT: K 201 MET cc_start: 0.6803 (tpp) cc_final: 0.6594 (tpp) REVERT: K 331 ILE cc_start: 0.8977 (mm) cc_final: 0.8377 (tt) REVERT: I 1 MET cc_start: 0.6157 (pmm) cc_final: 0.4831 (pmm) REVERT: I 63 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7515 (mm-30) REVERT: I 176 TYR cc_start: 0.6286 (OUTLIER) cc_final: 0.4376 (m-80) REVERT: I 195 LYS cc_start: 0.8282 (tmtt) cc_final: 0.7763 (tptp) REVERT: I 224 ASP cc_start: 0.8110 (m-30) cc_final: 0.7903 (m-30) REVERT: I 229 MET cc_start: 0.8436 (OUTLIER) cc_final: 0.8184 (tmm) REVERT: I 322 ASN cc_start: 0.8276 (t0) cc_final: 0.7854 (t0) REVERT: A 51 GLN cc_start: 0.8667 (tt0) cc_final: 0.8167 (tt0) REVERT: A 304 ASN cc_start: 0.8517 (m-40) cc_final: 0.8251 (t0) REVERT: A 321 GLU cc_start: 0.8502 (mm-30) cc_final: 0.8102 (tp30) REVERT: A 368 ARG cc_start: 0.8786 (OUTLIER) cc_final: 0.7050 (mtp85) REVERT: B 133 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.8117 (tp40) REVERT: C 283 ILE cc_start: 0.9372 (OUTLIER) cc_final: 0.9139 (mp) REVERT: C 295 VAL cc_start: 0.9350 (t) cc_final: 0.9130 (m) REVERT: C 369 MET cc_start: 0.9007 (OUTLIER) cc_final: 0.8749 (tmm) REVERT: C 376 LYS cc_start: 0.8404 (tppt) cc_final: 0.8161 (tppt) REVERT: C 412 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.8442 (ptt90) REVERT: D 118 CYS cc_start: 0.9193 (OUTLIER) cc_final: 0.8515 (t) REVERT: D 261 TYR cc_start: 0.8862 (m-10) cc_final: 0.7630 (m-10) REVERT: D 364 ASP cc_start: 0.8527 (t0) cc_final: 0.8022 (t0) REVERT: E 4 LEU cc_start: 0.5653 (OUTLIER) cc_final: 0.5115 (tt) REVERT: E 15 ARG cc_start: 0.7266 (OUTLIER) cc_final: 0.6971 (tpp80) REVERT: E 134 LEU cc_start: 0.5380 (OUTLIER) cc_final: 0.5068 (tt) REVERT: E 162 LYS cc_start: 0.7199 (tptt) cc_final: 0.5373 (tmtt) REVERT: E 210 MET cc_start: 0.6917 (OUTLIER) cc_final: 0.6706 (tpt) REVERT: E 233 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8404 (mm) REVERT: E 312 CYS cc_start: 0.7849 (m) cc_final: 0.7402 (m) REVERT: E 329 ASP cc_start: 0.8335 (t0) cc_final: 0.7950 (t0) REVERT: F 106 VAL cc_start: 0.8673 (t) cc_final: 0.8313 (m) REVERT: F 166 PHE cc_start: 0.6707 (t80) cc_final: 0.6162 (t80) REVERT: F 188 LEU cc_start: 0.5455 (tp) cc_final: 0.4755 (mp) REVERT: F 201 MET cc_start: 0.8087 (tpp) cc_final: 0.7436 (tpp) REVERT: F 223 LYS cc_start: 0.8859 (tptm) cc_final: 0.8567 (tptp) REVERT: G 56 MET cc_start: 0.6336 (mmt) cc_final: 0.4873 (ptp) REVERT: G 64 MET cc_start: 0.7748 (ptm) cc_final: 0.7393 (ptm) REVERT: G 68 GLU cc_start: 0.8655 (pt0) cc_final: 0.8325 (pt0) REVERT: G 114 ASP cc_start: 0.7978 (t0) cc_final: 0.7688 (t0) REVERT: G 120 MET cc_start: 0.8615 (tpp) cc_final: 0.8346 (tpt) REVERT: G 164 GLN cc_start: 0.7893 (OUTLIER) cc_final: 0.7398 (mp10) REVERT: G 313 ARG cc_start: 0.7981 (mtp-110) cc_final: 0.7149 (mmt-90) REVERT: G 360 MET cc_start: 0.8431 (mtp) cc_final: 0.8161 (mtt) REVERT: H 144 TYR cc_start: 0.7509 (OUTLIER) cc_final: 0.6116 (m-80) REVERT: J 1 MET cc_start: 0.5633 (tpp) cc_final: 0.4810 (pmm) REVERT: J 73 ILE cc_start: 0.7266 (OUTLIER) cc_final: 0.6956 (mm) REVERT: J 77 MET cc_start: 0.7773 (OUTLIER) cc_final: 0.7563 (mpp) REVERT: J 95 ASP cc_start: 0.8296 (m-30) cc_final: 0.8066 (p0) REVERT: J 107 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7475 (tp) REVERT: J 120 MET cc_start: 0.8811 (OUTLIER) cc_final: 0.8378 (tmm) REVERT: J 208 TYR cc_start: 0.7416 (m-80) cc_final: 0.6223 (t80) REVERT: J 223 LYS cc_start: 0.8773 (tttt) cc_final: 0.8463 (ptpp) REVERT: J 301 SER cc_start: 0.9321 (t) cc_final: 0.9009 (m) REVERT: J 312 CYS cc_start: 0.8807 (t) cc_final: 0.8388 (m) REVERT: J 322 ASN cc_start: 0.8793 (t0) cc_final: 0.8222 (t0) REVERT: L 70 ARG cc_start: 0.8153 (ttp-170) cc_final: 0.7756 (ptm160) REVERT: L 77 MET cc_start: 0.8134 (pmm) cc_final: 0.7702 (ppp) REVERT: L 175 MET cc_start: 0.6455 (tmm) cc_final: 0.6068 (tmm) REVERT: L 184 GLN cc_start: 0.6228 (tm-30) cc_final: 0.5943 (pt0) REVERT: L 194 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.6790 (mt-10) REVERT: L 317 TRP cc_start: 0.8794 (m-10) cc_final: 0.8586 (m-10) outliers start: 188 outliers final: 155 residues processed: 624 average time/residue: 0.2024 time to fit residues: 213.2460 Evaluate side-chains 650 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 475 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 50 ILE Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 112 ILE Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 153 THR Chi-restraints excluded: chain K residue 199 PRO Chi-restraints excluded: chain K residue 215 PHE Chi-restraints excluded: chain K residue 245 CYS Chi-restraints excluded: chain K residue 290 THR Chi-restraints excluded: chain K residue 306 CYS Chi-restraints excluded: chain K residue 324 THR Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 167 VAL Chi-restraints excluded: chain I residue 176 TYR Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 193 ILE Chi-restraints excluded: chain I residue 199 PRO Chi-restraints excluded: chain I residue 221 GLN Chi-restraints excluded: chain I residue 229 MET Chi-restraints excluded: chain I residue 233 LEU Chi-restraints excluded: chain I residue 306 CYS Chi-restraints excluded: chain I residue 312 CYS Chi-restraints excluded: chain A residue 2 LEU Chi-restraints excluded: chain A residue 166 HIS Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 368 ARG Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 118 CYS Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 326 HIS Chi-restraints excluded: chain B residue 408 LYS Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 412 ARG Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 3 LYS Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 118 CYS Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 253 SER Chi-restraints excluded: chain D residue 265 TYR Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 304 ASN Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 15 ARG Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 79 HIS Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 176 TYR Chi-restraints excluded: chain E residue 199 PRO Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 266 CYS Chi-restraints excluded: chain E residue 286 ILE Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 153 THR Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 193 ILE Chi-restraints excluded: chain F residue 199 PRO Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 215 PHE Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 289 CYS Chi-restraints excluded: chain F residue 306 CYS Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 77 MET Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 164 GLN Chi-restraints excluded: chain G residue 193 ILE Chi-restraints excluded: chain G residue 197 VAL Chi-restraints excluded: chain G residue 215 PHE Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain G residue 257 ASP Chi-restraints excluded: chain G residue 328 GLU Chi-restraints excluded: chain G residue 353 VAL Chi-restraints excluded: chain G residue 359 ILE Chi-restraints excluded: chain H residue 35 LEU Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 79 HIS Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 126 HIS Chi-restraints excluded: chain H residue 144 TYR Chi-restraints excluded: chain H residue 153 THR Chi-restraints excluded: chain H residue 193 ILE Chi-restraints excluded: chain H residue 199 PRO Chi-restraints excluded: chain H residue 278 VAL Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain H residue 335 GLU Chi-restraints excluded: chain H residue 359 ILE Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 7 VAL Chi-restraints excluded: chain J residue 10 TYR Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 36 HIS Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 73 ILE Chi-restraints excluded: chain J residue 77 MET Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 120 MET Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 147 VAL Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 186 ILE Chi-restraints excluded: chain J residue 191 THR Chi-restraints excluded: chain J residue 199 PRO Chi-restraints excluded: chain J residue 230 CYS Chi-restraints excluded: chain J residue 278 VAL Chi-restraints excluded: chain J residue 304 GLU Chi-restraints excluded: chain J residue 324 THR Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain L residue 60 LEU Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 153 THR Chi-restraints excluded: chain L residue 176 TYR Chi-restraints excluded: chain L residue 191 THR Chi-restraints excluded: chain L residue 193 ILE Chi-restraints excluded: chain L residue 194 GLU Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain L residue 199 PRO Chi-restraints excluded: chain L residue 256 VAL Chi-restraints excluded: chain L residue 278 VAL Chi-restraints excluded: chain L residue 321 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 262 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 chunk 368 optimal weight: 0.9990 chunk 416 optimal weight: 40.0000 chunk 217 optimal weight: 6.9990 chunk 417 optimal weight: 10.0000 chunk 182 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 43 optimal weight: 6.9990 chunk 228 optimal weight: 0.2980 chunk 20 optimal weight: 0.4980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 HIS B 326 HIS C 38 GLN ** D 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 286 ASN ** E 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 126 HIS ** E 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 126 HIS ** G 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 265 ASN J 36 HIS J 108 ASN ** J 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 234 GLN L 265 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.158453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.111792 restraints weight = 55253.251| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.38 r_work: 0.3167 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3036 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3036 r_free = 0.3036 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3036 r_free = 0.3036 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3036 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 36254 Z= 0.113 Angle : 0.633 14.340 49301 Z= 0.315 Chirality : 0.049 0.228 5611 Planarity : 0.005 0.064 6325 Dihedral : 7.294 77.093 5581 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.78 % Favored : 95.19 % Rotamer: Outliers : 4.00 % Allowed : 25.61 % Favored : 70.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.44 (0.13), residues: 4473 helix: 0.83 (0.17), residues: 974 sheet: -0.52 (0.15), residues: 1301 loop : -0.55 (0.13), residues: 2198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 366 TYR 0.019 0.001 TYR G 10 PHE 0.042 0.002 PHE L 215 TRP 0.035 0.001 TRP E 216 HIS 0.010 0.001 HIS J 36 Details of bonding type rmsd covalent geometry : bond 0.00257 (36249) covalent geometry : angle 0.63275 (49293) SS BOND : bond 0.00445 ( 4) SS BOND : angle 1.84278 ( 8) hydrogen bonds : bond 0.03205 ( 969) hydrogen bonds : angle 5.19652 ( 2787) Misc. bond : bond 0.00160 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12725.13 seconds wall clock time: 217 minutes 19.89 seconds (13039.89 seconds total)