Starting phenix.real_space_refine on Mon Jun 8 00:00:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9urz_64462/06_2026/9urz_64462.cif Found real_map, /net/cci-nas-00/data/ceres_data/9urz_64462/06_2026/9urz_64462.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9urz_64462/06_2026/9urz_64462.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9urz_64462/06_2026/9urz_64462.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9urz_64462/06_2026/9urz_64462.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9urz_64462/06_2026/9urz_64462.map" } resolution = 3.2 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: 4 Type Number sf(0) Gaussians S 88 5.16 5 C 28303 2.51 5 N 8085 2.21 5 O 8360 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 97 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 44836 Number of models: 1 Model: "" Number of chains: 22 Chain: "B" Number of atoms: 2007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2007 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 9, 'TRANS': 246} Chain: "C" Number of atoms: 2007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2007 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 9, 'TRANS': 246} Chain: "D" Number of atoms: 2069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2069 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 7, 'TRANS': 256} Chain: "E" Number of atoms: 2069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2069 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 7, 'TRANS': 256} Chain: "F" Number of atoms: 2007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2007 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 9, 'TRANS': 246} Chain: "G" Number of atoms: 2007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2007 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 9, 'TRANS': 246} Chain: "H" Number of atoms: 2069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2069 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 7, 'TRANS': 256} Chain: "I" Number of atoms: 2069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2069 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 7, 'TRANS': 256} Chain: "J" Number of atoms: 2007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2007 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 9, 'TRANS': 246} Chain: "K" Number of atoms: 2007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2007 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 9, 'TRANS': 246} Chain: "L" Number of atoms: 2069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2069 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 7, 'TRANS': 256} Chain: "M" Number of atoms: 2069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2069 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 7, 'TRANS': 256} Chain: "N" Number of atoms: 2007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2007 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 9, 'TRANS': 246} Chain: "O" Number of atoms: 2007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2007 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 9, 'TRANS': 246} Chain: "P" Number of atoms: 2069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2069 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 7, 'TRANS': 256} Chain: "Q" Number of atoms: 2069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2069 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 7, 'TRANS': 256} Chain: "R" Number of atoms: 2007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2007 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 9, 'TRANS': 246} Chain: "S" Number of atoms: 2007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2007 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 9, 'TRANS': 246} Chain: "T" Number of atoms: 2069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2069 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 7, 'TRANS': 256} Chain: "U" Number of atoms: 2069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2069 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 7, 'TRANS': 256} Chain: "V" Number of atoms: 2007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2007 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 9, 'TRANS': 246} Chain: "W" Number of atoms: 2069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2069 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 7, 'TRANS': 256} Time building chain proxies: 10.47, per 1000 atoms: 0.23 Number of scatterers: 44836 At special positions: 0 Unit cell: (208.296, 209.348, 136.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 88 16.00 O 8360 8.00 N 8085 7.00 C 28303 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.85 Conformation dependent library (CDL) restraints added in 2.0 seconds 11352 Ramachandran restraints generated. 5676 Oldfield, 0 Emsley, 5676 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10780 Finding SS restraints... Secondary structure from input PDB file: 195 helices and 80 sheets defined 59.6% alpha, 19.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.66 Creating SS restraints... Processing helix chain 'B' and resid 8 through 26 Proline residue: B 15 - end of helix removed outlier: 3.772A pdb=" N GLY B 21 " --> pdb=" O ALA B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 101 No H-bonds generated for 'chain 'B' and resid 99 through 101' Processing helix chain 'B' and resid 102 through 110 Processing helix chain 'B' and resid 113 through 132 removed outlier: 3.683A pdb=" N ARG B 117 " --> pdb=" O ASP B 113 " (cutoff:3.500A) Proline residue: B 120 - end of helix removed outlier: 3.570A pdb=" N GLU B 125 " --> pdb=" O SER B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 141 removed outlier: 3.900A pdb=" N THR B 141 " --> pdb=" O ALA B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 161 removed outlier: 3.743A pdb=" N LYS B 156 " --> pdb=" O HIS B 152 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARG B 157 " --> pdb=" O ASP B 153 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU B 160 " --> pdb=" O LYS B 156 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE B 161 " --> pdb=" O ARG B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 232 removed outlier: 4.647A pdb=" N ARG B 197 " --> pdb=" O ALA B 193 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N PHE B 198 " --> pdb=" O GLU B 194 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE B 199 " --> pdb=" O ARG B 195 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLN B 208 " --> pdb=" O GLU B 204 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ALA B 209 " --> pdb=" O GLN B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 251 removed outlier: 3.859A pdb=" N ILE B 238 " --> pdb=" O GLY B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 254 No H-bonds generated for 'chain 'B' and resid 252 through 254' Processing helix chain 'C' and resid 9 through 26 Proline residue: C 15 - end of helix Processing helix chain 'C' and resid 99 through 101 No H-bonds generated for 'chain 'C' and resid 99 through 101' Processing helix chain 'C' and resid 102 through 111 Processing helix chain 'C' and resid 114 through 132 removed outlier: 3.617A pdb=" N LEU C 119 " --> pdb=" O ASP C 115 " (cutoff:3.500A) Proline residue: C 120 - end of helix removed outlier: 3.856A pdb=" N GLU C 125 " --> pdb=" O SER C 121 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS C 128 " --> pdb=" O ASN C 124 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA C 132 " --> pdb=" O LYS C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 141 removed outlier: 3.910A pdb=" N THR C 141 " --> pdb=" O ALA C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 161 removed outlier: 3.754A pdb=" N LYS C 156 " --> pdb=" O HIS C 152 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG C 157 " --> pdb=" O ASP C 153 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU C 160 " --> pdb=" O LYS C 156 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N PHE C 161 " --> pdb=" O ARG C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 232 removed outlier: 4.233A pdb=" N ARG C 197 " --> pdb=" O ALA C 193 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N PHE C 198 " --> pdb=" O GLU C 194 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE C 199 " --> pdb=" O ARG C 195 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLN C 208 " --> pdb=" O GLU C 204 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ALA C 209 " --> pdb=" O GLN C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 251 removed outlier: 4.321A pdb=" N GLN C 237 " --> pdb=" O ASP C 233 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE C 238 " --> pdb=" O GLY C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 254 No H-bonds generated for 'chain 'C' and resid 252 through 254' Processing helix chain 'D' and resid 44 through 58 removed outlier: 4.012A pdb=" N THR D 51 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 143 Processing helix chain 'D' and resid 145 through 166 removed outlier: 3.592A pdb=" N ARG D 149 " --> pdb=" O ASP D 145 " (cutoff:3.500A) Proline residue: D 152 - end of helix removed outlier: 3.967A pdb=" N GLN D 165 " --> pdb=" O ALA D 161 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N PHE D 166 " --> pdb=" O VAL D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 174 removed outlier: 3.703A pdb=" N LEU D 171 " --> pdb=" O ASN D 167 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE D 172 " --> pdb=" O ALA D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 191 removed outlier: 3.640A pdb=" N VAL D 178 " --> pdb=" O GLN D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 261 removed outlier: 3.859A pdb=" N PHE D 230 " --> pdb=" O GLN D 226 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ASP D 233 " --> pdb=" O ALA D 229 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN D 237 " --> pdb=" O ASP D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 283 Processing helix chain 'D' and resid 293 through 297 Processing helix chain 'D' and resid 302 through 306 removed outlier: 3.680A pdb=" N GLN D 305 " --> pdb=" O PHE D 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 58 removed outlier: 3.845A pdb=" N THR E 51 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 143 Processing helix chain 'E' and resid 145 through 166 removed outlier: 3.732A pdb=" N ARG E 149 " --> pdb=" O ASP E 145 " (cutoff:3.500A) Proline residue: E 152 - end of helix removed outlier: 3.564A pdb=" N ASN E 156 " --> pdb=" O PRO E 152 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU E 157 " --> pdb=" O SER E 153 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS E 160 " --> pdb=" O ASN E 156 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLN E 165 " --> pdb=" O ALA E 161 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N PHE E 166 " --> pdb=" O VAL E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 174 removed outlier: 3.756A pdb=" N LEU E 171 " --> pdb=" O ASN E 167 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ILE E 172 " --> pdb=" O ALA E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 191 removed outlier: 3.694A pdb=" N VAL E 178 " --> pdb=" O GLN E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 261 removed outlier: 3.569A pdb=" N ALA E 229 " --> pdb=" O ALA E 225 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N PHE E 230 " --> pdb=" O GLN E 226 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ASP E 233 " --> pdb=" O ALA E 229 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN E 237 " --> pdb=" O ASP E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 264 through 283 Processing helix chain 'E' and resid 293 through 297 Processing helix chain 'E' and resid 302 through 306 removed outlier: 3.648A pdb=" N GLN E 305 " --> pdb=" O PHE E 302 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 26 Proline residue: F 15 - end of helix Processing helix chain 'F' and resid 99 through 101 No H-bonds generated for 'chain 'F' and resid 99 through 101' Processing helix chain 'F' and resid 102 through 110 Processing helix chain 'F' and resid 114 through 132 removed outlier: 3.652A pdb=" N LEU F 119 " --> pdb=" O ASP F 115 " (cutoff:3.500A) Proline residue: F 120 - end of helix removed outlier: 3.865A pdb=" N GLU F 125 " --> pdb=" O SER F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 141 removed outlier: 3.925A pdb=" N THR F 141 " --> pdb=" O ALA F 137 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 161 removed outlier: 3.790A pdb=" N LYS F 156 " --> pdb=" O HIS F 152 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG F 157 " --> pdb=" O ASP F 153 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU F 160 " --> pdb=" O LYS F 156 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N PHE F 161 " --> pdb=" O ARG F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 232 removed outlier: 4.250A pdb=" N ARG F 197 " --> pdb=" O ALA F 193 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N PHE F 198 " --> pdb=" O GLU F 194 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE F 199 " --> pdb=" O ARG F 195 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN F 208 " --> pdb=" O GLU F 204 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ALA F 209 " --> pdb=" O GLN F 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 251 removed outlier: 3.615A pdb=" N ILE F 238 " --> pdb=" O GLY F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 254 No H-bonds generated for 'chain 'F' and resid 252 through 254' Processing helix chain 'G' and resid 9 through 26 Proline residue: G 15 - end of helix removed outlier: 3.504A pdb=" N GLY G 21 " --> pdb=" O ALA G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 101 No H-bonds generated for 'chain 'G' and resid 99 through 101' Processing helix chain 'G' and resid 102 through 110 Processing helix chain 'G' and resid 114 through 132 removed outlier: 3.704A pdb=" N LEU G 119 " --> pdb=" O ASP G 115 " (cutoff:3.500A) Proline residue: G 120 - end of helix removed outlier: 3.893A pdb=" N GLU G 125 " --> pdb=" O SER G 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 141 removed outlier: 3.886A pdb=" N THR G 141 " --> pdb=" O ALA G 137 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 160 removed outlier: 3.752A pdb=" N LYS G 156 " --> pdb=" O HIS G 152 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG G 157 " --> pdb=" O ASP G 153 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU G 160 " --> pdb=" O LYS G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 176 through 232 removed outlier: 4.237A pdb=" N ARG G 197 " --> pdb=" O ALA G 193 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N PHE G 198 " --> pdb=" O GLU G 194 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE G 199 " --> pdb=" O ARG G 195 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLN G 208 " --> pdb=" O GLU G 204 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ALA G 209 " --> pdb=" O GLN G 205 " (cutoff:3.500A) Processing helix chain 'G' and resid 234 through 251 removed outlier: 3.575A pdb=" N ILE G 238 " --> pdb=" O GLY G 234 " (cutoff:3.500A) Processing helix chain 'G' and resid 252 through 254 No H-bonds generated for 'chain 'G' and resid 252 through 254' Processing helix chain 'H' and resid 44 through 58 removed outlier: 4.045A pdb=" N THR H 51 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing helix chain 'H' and resid 134 through 143 Processing helix chain 'H' and resid 145 through 166 removed outlier: 3.669A pdb=" N ARG H 149 " --> pdb=" O ASP H 145 " (cutoff:3.500A) Proline residue: H 152 - end of helix removed outlier: 3.620A pdb=" N ASN H 156 " --> pdb=" O PRO H 152 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU H 157 " --> pdb=" O SER H 153 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL H 158 " --> pdb=" O ILE H 154 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS H 160 " --> pdb=" O ASN H 156 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLN H 165 " --> pdb=" O ALA H 161 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N PHE H 166 " --> pdb=" O VAL H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 167 through 174 removed outlier: 3.709A pdb=" N LEU H 171 " --> pdb=" O ASN H 167 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ILE H 172 " --> pdb=" O ALA H 168 " (cutoff:3.500A) Processing helix chain 'H' and resid 174 through 191 removed outlier: 3.677A pdb=" N VAL H 178 " --> pdb=" O GLN H 174 " (cutoff:3.500A) Processing helix chain 'H' and resid 208 through 261 removed outlier: 3.625A pdb=" N ALA H 229 " --> pdb=" O ALA H 225 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE H 230 " --> pdb=" O GLN H 226 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ASP H 233 " --> pdb=" O ALA H 229 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN H 237 " --> pdb=" O ASP H 233 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA H 259 " --> pdb=" O LEU H 255 " (cutoff:3.500A) Processing helix chain 'H' and resid 264 through 283 Processing helix chain 'H' and resid 293 through 297 Processing helix chain 'H' and resid 302 through 306 removed outlier: 3.681A pdb=" N GLN H 305 " --> pdb=" O PHE H 302 " (cutoff:3.500A) Processing helix chain 'I' and resid 44 through 58 removed outlier: 3.959A pdb=" N THR I 51 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing helix chain 'I' and resid 134 through 143 removed outlier: 3.506A pdb=" N TYR I 139 " --> pdb=" O LEU I 135 " (cutoff:3.500A) Processing helix chain 'I' and resid 145 through 166 removed outlier: 3.745A pdb=" N ARG I 149 " --> pdb=" O ASP I 145 " (cutoff:3.500A) Proline residue: I 152 - end of helix removed outlier: 3.567A pdb=" N ASN I 156 " --> pdb=" O PRO I 152 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU I 157 " --> pdb=" O SER I 153 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYS I 160 " --> pdb=" O ASN I 156 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLN I 165 " --> pdb=" O ALA I 161 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N PHE I 166 " --> pdb=" O VAL I 162 " (cutoff:3.500A) Processing helix chain 'I' and resid 167 through 174 removed outlier: 3.734A pdb=" N LEU I 171 " --> pdb=" O ASN I 167 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE I 172 " --> pdb=" O ALA I 168 " (cutoff:3.500A) Processing helix chain 'I' and resid 174 through 191 removed outlier: 3.706A pdb=" N VAL I 178 " --> pdb=" O GLN I 174 " (cutoff:3.500A) Processing helix chain 'I' and resid 208 through 261 removed outlier: 3.618A pdb=" N ALA I 229 " --> pdb=" O ALA I 225 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N PHE I 230 " --> pdb=" O GLN I 226 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ASP I 233 " --> pdb=" O ALA I 229 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN I 237 " --> pdb=" O ASP I 233 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA I 259 " --> pdb=" O LEU I 255 " (cutoff:3.500A) Processing helix chain 'I' and resid 264 through 283 Processing helix chain 'I' and resid 293 through 297 Processing helix chain 'I' and resid 302 through 306 removed outlier: 3.725A pdb=" N GLN I 305 " --> pdb=" O PHE I 302 " (cutoff:3.500A) Processing helix chain 'J' and resid 9 through 26 Proline residue: J 15 - end of helix Processing helix chain 'J' and resid 99 through 101 No H-bonds generated for 'chain 'J' and resid 99 through 101' Processing helix chain 'J' and resid 102 through 110 Processing helix chain 'J' and resid 114 through 132 removed outlier: 3.509A pdb=" N LEU J 119 " --> pdb=" O ASP J 115 " (cutoff:3.500A) Proline residue: J 120 - end of helix removed outlier: 3.944A pdb=" N GLU J 125 " --> pdb=" O SER J 121 " (cutoff:3.500A) Processing helix chain 'J' and resid 135 through 141 removed outlier: 3.917A pdb=" N THR J 141 " --> pdb=" O ALA J 137 " (cutoff:3.500A) Processing helix chain 'J' and resid 142 through 160 removed outlier: 3.757A pdb=" N LYS J 156 " --> pdb=" O HIS J 152 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG J 157 " --> pdb=" O ASP J 153 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU J 160 " --> pdb=" O LYS J 156 " (cutoff:3.500A) Processing helix chain 'J' and resid 176 through 232 removed outlier: 4.235A pdb=" N ARG J 197 " --> pdb=" O ALA J 193 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N PHE J 198 " --> pdb=" O GLU J 194 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE J 199 " --> pdb=" O ARG J 195 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLN J 208 " --> pdb=" O GLU J 204 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ALA J 209 " --> pdb=" O GLN J 205 " (cutoff:3.500A) Processing helix chain 'J' and resid 234 through 251 removed outlier: 3.609A pdb=" N ILE J 238 " --> pdb=" O GLY J 234 " (cutoff:3.500A) Processing helix chain 'J' and resid 252 through 254 No H-bonds generated for 'chain 'J' and resid 252 through 254' Processing helix chain 'K' and resid 9 through 26 Proline residue: K 15 - end of helix removed outlier: 3.507A pdb=" N GLY K 21 " --> pdb=" O ALA K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 99 through 101 No H-bonds generated for 'chain 'K' and resid 99 through 101' Processing helix chain 'K' and resid 102 through 110 Processing helix chain 'K' and resid 114 through 132 removed outlier: 3.573A pdb=" N LEU K 119 " --> pdb=" O ASP K 115 " (cutoff:3.500A) Proline residue: K 120 - end of helix removed outlier: 3.922A pdb=" N GLU K 125 " --> pdb=" O SER K 121 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS K 128 " --> pdb=" O ASN K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 135 through 141 removed outlier: 3.923A pdb=" N THR K 141 " --> pdb=" O ALA K 137 " (cutoff:3.500A) Processing helix chain 'K' and resid 142 through 161 removed outlier: 3.732A pdb=" N LYS K 156 " --> pdb=" O HIS K 152 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG K 157 " --> pdb=" O ASP K 153 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU K 160 " --> pdb=" O LYS K 156 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N PHE K 161 " --> pdb=" O ARG K 157 " (cutoff:3.500A) Processing helix chain 'K' and resid 176 through 232 removed outlier: 4.250A pdb=" N ARG K 197 " --> pdb=" O ALA K 193 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N PHE K 198 " --> pdb=" O GLU K 194 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE K 199 " --> pdb=" O ARG K 195 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLN K 208 " --> pdb=" O GLU K 204 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ALA K 209 " --> pdb=" O GLN K 205 " (cutoff:3.500A) Processing helix chain 'K' and resid 234 through 251 removed outlier: 3.583A pdb=" N ILE K 238 " --> pdb=" O GLY K 234 " (cutoff:3.500A) Processing helix chain 'K' and resid 252 through 254 No H-bonds generated for 'chain 'K' and resid 252 through 254' Processing helix chain 'L' and resid 44 through 58 removed outlier: 3.767A pdb=" N THR L 51 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing helix chain 'L' and resid 134 through 143 removed outlier: 3.500A pdb=" N TYR L 139 " --> pdb=" O LEU L 135 " (cutoff:3.500A) Processing helix chain 'L' and resid 145 through 166 removed outlier: 3.678A pdb=" N ARG L 149 " --> pdb=" O ASP L 145 " (cutoff:3.500A) Proline residue: L 152 - end of helix removed outlier: 3.556A pdb=" N ASN L 156 " --> pdb=" O PRO L 152 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU L 157 " --> pdb=" O SER L 153 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS L 160 " --> pdb=" O ASN L 156 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLN L 165 " --> pdb=" O ALA L 161 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N PHE L 166 " --> pdb=" O VAL L 162 " (cutoff:3.500A) Processing helix chain 'L' and resid 167 through 174 removed outlier: 3.762A pdb=" N LEU L 171 " --> pdb=" O ASN L 167 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ILE L 172 " --> pdb=" O ALA L 168 " (cutoff:3.500A) Processing helix chain 'L' and resid 174 through 191 removed outlier: 3.802A pdb=" N VAL L 178 " --> pdb=" O GLN L 174 " (cutoff:3.500A) Processing helix chain 'L' and resid 208 through 261 removed outlier: 3.545A pdb=" N ALA L 229 " --> pdb=" O ALA L 225 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE L 230 " --> pdb=" O GLN L 226 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ASP L 233 " --> pdb=" O ALA L 229 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN L 237 " --> pdb=" O ASP L 233 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA L 259 " --> pdb=" O LEU L 255 " (cutoff:3.500A) Processing helix chain 'L' and resid 264 through 283 Processing helix chain 'L' and resid 293 through 297 Processing helix chain 'M' and resid 44 through 58 removed outlier: 3.846A pdb=" N THR M 51 " --> pdb=" O LEU M 47 " (cutoff:3.500A) Processing helix chain 'M' and resid 134 through 142 Processing helix chain 'M' and resid 145 through 166 removed outlier: 3.704A pdb=" N ARG M 149 " --> pdb=" O ASP M 145 " (cutoff:3.500A) Proline residue: M 152 - end of helix removed outlier: 3.557A pdb=" N ASN M 156 " --> pdb=" O PRO M 152 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU M 157 " --> pdb=" O SER M 153 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL M 158 " --> pdb=" O ILE M 154 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LYS M 160 " --> pdb=" O ASN M 156 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLN M 165 " --> pdb=" O ALA M 161 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N PHE M 166 " --> pdb=" O VAL M 162 " (cutoff:3.500A) Processing helix chain 'M' and resid 167 through 174 removed outlier: 3.697A pdb=" N LEU M 171 " --> pdb=" O ASN M 167 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ILE M 172 " --> pdb=" O ALA M 168 " (cutoff:3.500A) Processing helix chain 'M' and resid 174 through 191 removed outlier: 3.735A pdb=" N VAL M 178 " --> pdb=" O GLN M 174 " (cutoff:3.500A) Processing helix chain 'M' and resid 208 through 261 removed outlier: 3.584A pdb=" N ALA M 213 " --> pdb=" O PRO M 209 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA M 229 " --> pdb=" O ALA M 225 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE M 230 " --> pdb=" O GLN M 226 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ASP M 233 " --> pdb=" O ALA M 229 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN M 237 " --> pdb=" O ASP M 233 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA M 259 " --> pdb=" O LEU M 255 " (cutoff:3.500A) Processing helix chain 'M' and resid 264 through 283 Processing helix chain 'M' and resid 295 through 297 No H-bonds generated for 'chain 'M' and resid 295 through 297' Processing helix chain 'M' and resid 302 through 306 removed outlier: 3.660A pdb=" N GLN M 305 " --> pdb=" O PHE M 302 " (cutoff:3.500A) Processing helix chain 'N' and resid 9 through 26 Proline residue: N 15 - end of helix Processing helix chain 'N' and resid 99 through 101 No H-bonds generated for 'chain 'N' and resid 99 through 101' Processing helix chain 'N' and resid 102 through 111 Processing helix chain 'N' and resid 114 through 132 Proline residue: N 120 - end of helix removed outlier: 3.918A pdb=" N GLU N 125 " --> pdb=" O SER N 121 " (cutoff:3.500A) Processing helix chain 'N' and resid 135 through 141 removed outlier: 3.891A pdb=" N THR N 141 " --> pdb=" O ALA N 137 " (cutoff:3.500A) Processing helix chain 'N' and resid 142 through 161 removed outlier: 3.727A pdb=" N LYS N 156 " --> pdb=" O HIS N 152 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG N 157 " --> pdb=" O ASP N 153 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU N 160 " --> pdb=" O LYS N 156 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N PHE N 161 " --> pdb=" O ARG N 157 " (cutoff:3.500A) Processing helix chain 'N' and resid 176 through 232 removed outlier: 4.306A pdb=" N ARG N 197 " --> pdb=" O ALA N 193 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N PHE N 198 " --> pdb=" O GLU N 194 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLN N 208 " --> pdb=" O GLU N 204 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ALA N 209 " --> pdb=" O GLN N 205 " (cutoff:3.500A) Processing helix chain 'N' and resid 234 through 251 removed outlier: 3.603A pdb=" N ILE N 238 " --> pdb=" O GLY N 234 " (cutoff:3.500A) Processing helix chain 'O' and resid 9 through 26 Proline residue: O 15 - end of helix removed outlier: 3.525A pdb=" N GLY O 21 " --> pdb=" O ALA O 17 " (cutoff:3.500A) Processing helix chain 'O' and resid 99 through 101 No H-bonds generated for 'chain 'O' and resid 99 through 101' Processing helix chain 'O' and resid 102 through 110 Processing helix chain 'O' and resid 114 through 132 removed outlier: 3.608A pdb=" N LEU O 119 " --> pdb=" O ASP O 115 " (cutoff:3.500A) Proline residue: O 120 - end of helix removed outlier: 3.957A pdb=" N GLU O 125 " --> pdb=" O SER O 121 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS O 128 " --> pdb=" O ASN O 124 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA O 132 " --> pdb=" O LYS O 128 " (cutoff:3.500A) Processing helix chain 'O' and resid 135 through 141 removed outlier: 3.934A pdb=" N THR O 141 " --> pdb=" O ALA O 137 " (cutoff:3.500A) Processing helix chain 'O' and resid 142 through 161 removed outlier: 3.750A pdb=" N LYS O 156 " --> pdb=" O HIS O 152 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG O 157 " --> pdb=" O ASP O 153 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU O 160 " --> pdb=" O LYS O 156 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N PHE O 161 " --> pdb=" O ARG O 157 " (cutoff:3.500A) Processing helix chain 'O' and resid 176 through 232 removed outlier: 4.250A pdb=" N ARG O 197 " --> pdb=" O ALA O 193 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N PHE O 198 " --> pdb=" O GLU O 194 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLN O 208 " --> pdb=" O GLU O 204 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ALA O 209 " --> pdb=" O GLN O 205 " (cutoff:3.500A) Processing helix chain 'O' and resid 233 through 251 removed outlier: 4.325A pdb=" N GLN O 237 " --> pdb=" O ASP O 233 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE O 238 " --> pdb=" O GLY O 234 " (cutoff:3.500A) Processing helix chain 'P' and resid 44 through 58 removed outlier: 3.866A pdb=" N THR P 51 " --> pdb=" O LEU P 47 " (cutoff:3.500A) Processing helix chain 'P' and resid 134 through 143 Processing helix chain 'P' and resid 145 through 166 removed outlier: 3.715A pdb=" N ARG P 149 " --> pdb=" O ASP P 145 " (cutoff:3.500A) Proline residue: P 152 - end of helix removed outlier: 3.660A pdb=" N ASN P 156 " --> pdb=" O PRO P 152 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU P 157 " --> pdb=" O SER P 153 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS P 160 " --> pdb=" O ASN P 156 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLN P 165 " --> pdb=" O ALA P 161 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N PHE P 166 " --> pdb=" O VAL P 162 " (cutoff:3.500A) Processing helix chain 'P' and resid 167 through 174 removed outlier: 3.753A pdb=" N LEU P 171 " --> pdb=" O ASN P 167 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ILE P 172 " --> pdb=" O ALA P 168 " (cutoff:3.500A) Processing helix chain 'P' and resid 174 through 191 removed outlier: 3.816A pdb=" N VAL P 178 " --> pdb=" O GLN P 174 " (cutoff:3.500A) Processing helix chain 'P' and resid 208 through 261 removed outlier: 3.575A pdb=" N ALA P 229 " --> pdb=" O ALA P 225 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N PHE P 230 " --> pdb=" O GLN P 226 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ASP P 233 " --> pdb=" O ALA P 229 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN P 237 " --> pdb=" O ASP P 233 " (cutoff:3.500A) Processing helix chain 'P' and resid 264 through 283 Processing helix chain 'P' and resid 293 through 297 Processing helix chain 'P' and resid 302 through 306 removed outlier: 3.730A pdb=" N GLN P 305 " --> pdb=" O PHE P 302 " (cutoff:3.500A) Processing helix chain 'Q' and resid 44 through 58 removed outlier: 3.941A pdb=" N THR Q 51 " --> pdb=" O LEU Q 47 " (cutoff:3.500A) Processing helix chain 'Q' and resid 134 through 143 Processing helix chain 'Q' and resid 145 through 166 removed outlier: 3.681A pdb=" N ARG Q 149 " --> pdb=" O ASP Q 145 " (cutoff:3.500A) Proline residue: Q 152 - end of helix removed outlier: 3.585A pdb=" N ASN Q 156 " --> pdb=" O PRO Q 152 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU Q 157 " --> pdb=" O SER Q 153 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS Q 160 " --> pdb=" O ASN Q 156 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLN Q 165 " --> pdb=" O ALA Q 161 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N PHE Q 166 " --> pdb=" O VAL Q 162 " (cutoff:3.500A) Processing helix chain 'Q' and resid 167 through 174 removed outlier: 3.771A pdb=" N LEU Q 171 " --> pdb=" O ASN Q 167 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ILE Q 172 " --> pdb=" O ALA Q 168 " (cutoff:3.500A) Processing helix chain 'Q' and resid 174 through 191 removed outlier: 3.745A pdb=" N VAL Q 178 " --> pdb=" O GLN Q 174 " (cutoff:3.500A) Processing helix chain 'Q' and resid 208 through 261 removed outlier: 3.593A pdb=" N ALA Q 229 " --> pdb=" O ALA Q 225 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N PHE Q 230 " --> pdb=" O GLN Q 226 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ASP Q 233 " --> pdb=" O ALA Q 229 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN Q 237 " --> pdb=" O ASP Q 233 " (cutoff:3.500A) Processing helix chain 'Q' and resid 264 through 283 Processing helix chain 'Q' and resid 295 through 297 No H-bonds generated for 'chain 'Q' and resid 295 through 297' Processing helix chain 'Q' and resid 302 through 306 removed outlier: 3.697A pdb=" N GLN Q 305 " --> pdb=" O PHE Q 302 " (cutoff:3.500A) Processing helix chain 'R' and resid 9 through 26 Proline residue: R 15 - end of helix Processing helix chain 'R' and resid 99 through 101 No H-bonds generated for 'chain 'R' and resid 99 through 101' Processing helix chain 'R' and resid 102 through 111 Processing helix chain 'R' and resid 114 through 132 removed outlier: 3.716A pdb=" N LEU R 119 " --> pdb=" O ASP R 115 " (cutoff:3.500A) Proline residue: R 120 - end of helix removed outlier: 3.887A pdb=" N GLU R 125 " --> pdb=" O SER R 121 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS R 128 " --> pdb=" O ASN R 124 " (cutoff:3.500A) Processing helix chain 'R' and resid 135 through 141 removed outlier: 3.968A pdb=" N THR R 141 " --> pdb=" O ALA R 137 " (cutoff:3.500A) Processing helix chain 'R' and resid 142 through 160 removed outlier: 3.733A pdb=" N LYS R 156 " --> pdb=" O HIS R 152 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG R 157 " --> pdb=" O ASP R 153 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU R 160 " --> pdb=" O LYS R 156 " (cutoff:3.500A) Processing helix chain 'R' and resid 176 through 232 removed outlier: 4.305A pdb=" N ARG R 197 " --> pdb=" O ALA R 193 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N PHE R 198 " --> pdb=" O GLU R 194 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLN R 208 " --> pdb=" O GLU R 204 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ALA R 209 " --> pdb=" O GLN R 205 " (cutoff:3.500A) Processing helix chain 'R' and resid 234 through 251 removed outlier: 3.584A pdb=" N ILE R 238 " --> pdb=" O GLY R 234 " (cutoff:3.500A) Processing helix chain 'R' and resid 252 through 254 No H-bonds generated for 'chain 'R' and resid 252 through 254' Processing helix chain 'S' and resid 9 through 26 Proline residue: S 15 - end of helix Processing helix chain 'S' and resid 99 through 101 No H-bonds generated for 'chain 'S' and resid 99 through 101' Processing helix chain 'S' and resid 102 through 110 Processing helix chain 'S' and resid 114 through 132 removed outlier: 3.638A pdb=" N LEU S 119 " --> pdb=" O ASP S 115 " (cutoff:3.500A) Proline residue: S 120 - end of helix removed outlier: 3.884A pdb=" N GLU S 125 " --> pdb=" O SER S 121 " (cutoff:3.500A) Processing helix chain 'S' and resid 135 through 141 removed outlier: 3.933A pdb=" N THR S 141 " --> pdb=" O ALA S 137 " (cutoff:3.500A) Processing helix chain 'S' and resid 142 through 161 removed outlier: 3.799A pdb=" N LYS S 156 " --> pdb=" O HIS S 152 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG S 157 " --> pdb=" O ASP S 153 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU S 160 " --> pdb=" O LYS S 156 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N PHE S 161 " --> pdb=" O ARG S 157 " (cutoff:3.500A) Processing helix chain 'S' and resid 176 through 232 removed outlier: 4.280A pdb=" N ARG S 197 " --> pdb=" O ALA S 193 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N PHE S 198 " --> pdb=" O GLU S 194 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE S 199 " --> pdb=" O ARG S 195 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN S 208 " --> pdb=" O GLU S 204 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ALA S 209 " --> pdb=" O GLN S 205 " (cutoff:3.500A) Processing helix chain 'S' and resid 234 through 251 removed outlier: 3.605A pdb=" N ILE S 238 " --> pdb=" O GLY S 234 " (cutoff:3.500A) Processing helix chain 'S' and resid 252 through 254 No H-bonds generated for 'chain 'S' and resid 252 through 254' Processing helix chain 'T' and resid 44 through 58 removed outlier: 3.798A pdb=" N THR T 51 " --> pdb=" O LEU T 47 " (cutoff:3.500A) Processing helix chain 'T' and resid 134 through 143 Processing helix chain 'T' and resid 145 through 166 removed outlier: 3.677A pdb=" N ARG T 149 " --> pdb=" O ASP T 145 " (cutoff:3.500A) Proline residue: T 152 - end of helix removed outlier: 3.628A pdb=" N ASN T 156 " --> pdb=" O PRO T 152 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU T 157 " --> pdb=" O SER T 153 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS T 160 " --> pdb=" O ASN T 156 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLN T 165 " --> pdb=" O ALA T 161 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N PHE T 166 " --> pdb=" O VAL T 162 " (cutoff:3.500A) Processing helix chain 'T' and resid 167 through 174 removed outlier: 3.793A pdb=" N LEU T 171 " --> pdb=" O ASN T 167 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ILE T 172 " --> pdb=" O ALA T 168 " (cutoff:3.500A) Processing helix chain 'T' and resid 174 through 191 removed outlier: 3.827A pdb=" N VAL T 178 " --> pdb=" O GLN T 174 " (cutoff:3.500A) Processing helix chain 'T' and resid 208 through 261 removed outlier: 3.618A pdb=" N ALA T 229 " --> pdb=" O ALA T 225 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N PHE T 230 " --> pdb=" O GLN T 226 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ASP T 233 " --> pdb=" O ALA T 229 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN T 237 " --> pdb=" O ASP T 233 " (cutoff:3.500A) Processing helix chain 'T' and resid 264 through 283 Processing helix chain 'T' and resid 295 through 297 No H-bonds generated for 'chain 'T' and resid 295 through 297' Processing helix chain 'T' and resid 302 through 306 removed outlier: 3.668A pdb=" N GLN T 305 " --> pdb=" O PHE T 302 " (cutoff:3.500A) Processing helix chain 'U' and resid 44 through 58 removed outlier: 3.796A pdb=" N THR U 51 " --> pdb=" O LEU U 47 " (cutoff:3.500A) Processing helix chain 'U' and resid 134 through 143 Processing helix chain 'U' and resid 145 through 166 removed outlier: 3.724A pdb=" N ARG U 149 " --> pdb=" O ASP U 145 " (cutoff:3.500A) Proline residue: U 152 - end of helix removed outlier: 3.607A pdb=" N ASN U 156 " --> pdb=" O PRO U 152 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU U 157 " --> pdb=" O SER U 153 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LYS U 160 " --> pdb=" O ASN U 156 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLN U 165 " --> pdb=" O ALA U 161 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N PHE U 166 " --> pdb=" O VAL U 162 " (cutoff:3.500A) Processing helix chain 'U' and resid 167 through 174 removed outlier: 3.743A pdb=" N LEU U 171 " --> pdb=" O ASN U 167 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ILE U 172 " --> pdb=" O ALA U 168 " (cutoff:3.500A) Processing helix chain 'U' and resid 174 through 191 removed outlier: 3.739A pdb=" N VAL U 178 " --> pdb=" O GLN U 174 " (cutoff:3.500A) Processing helix chain 'U' and resid 208 through 261 removed outlier: 3.577A pdb=" N ALA U 229 " --> pdb=" O ALA U 225 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE U 230 " --> pdb=" O GLN U 226 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ASP U 233 " --> pdb=" O ALA U 229 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN U 237 " --> pdb=" O ASP U 233 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA U 259 " --> pdb=" O LEU U 255 " (cutoff:3.500A) Processing helix chain 'U' and resid 264 through 283 Processing helix chain 'U' and resid 293 through 297 Processing helix chain 'U' and resid 302 through 306 removed outlier: 3.646A pdb=" N GLN U 305 " --> pdb=" O PHE U 302 " (cutoff:3.500A) Processing helix chain 'V' and resid 9 through 26 Proline residue: V 15 - end of helix Processing helix chain 'V' and resid 99 through 101 No H-bonds generated for 'chain 'V' and resid 99 through 101' Processing helix chain 'V' and resid 102 through 110 Processing helix chain 'V' and resid 114 through 132 removed outlier: 3.655A pdb=" N LEU V 119 " --> pdb=" O ASP V 115 " (cutoff:3.500A) Proline residue: V 120 - end of helix removed outlier: 3.838A pdb=" N GLU V 125 " --> pdb=" O SER V 121 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS V 128 " --> pdb=" O ASN V 124 " (cutoff:3.500A) Processing helix chain 'V' and resid 135 through 141 removed outlier: 3.968A pdb=" N THR V 141 " --> pdb=" O ALA V 137 " (cutoff:3.500A) Processing helix chain 'V' and resid 142 through 161 removed outlier: 3.819A pdb=" N LYS V 156 " --> pdb=" O HIS V 152 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG V 157 " --> pdb=" O ASP V 153 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU V 160 " --> pdb=" O LYS V 156 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N PHE V 161 " --> pdb=" O ARG V 157 " (cutoff:3.500A) Processing helix chain 'V' and resid 176 through 232 removed outlier: 4.234A pdb=" N ARG V 197 " --> pdb=" O ALA V 193 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N PHE V 198 " --> pdb=" O GLU V 194 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE V 199 " --> pdb=" O ARG V 195 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN V 208 " --> pdb=" O GLU V 204 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ALA V 209 " --> pdb=" O GLN V 205 " (cutoff:3.500A) Processing helix chain 'V' and resid 233 through 251 removed outlier: 4.305A pdb=" N GLN V 237 " --> pdb=" O ASP V 233 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE V 238 " --> pdb=" O GLY V 234 " (cutoff:3.500A) Processing helix chain 'V' and resid 252 through 254 No H-bonds generated for 'chain 'V' and resid 252 through 254' Processing helix chain 'W' and resid 44 through 58 removed outlier: 3.822A pdb=" N THR W 51 " --> pdb=" O LEU W 47 " (cutoff:3.500A) Processing helix chain 'W' and resid 134 through 143 Processing helix chain 'W' and resid 145 through 166 removed outlier: 3.629A pdb=" N ARG W 149 " --> pdb=" O ASP W 145 " (cutoff:3.500A) Proline residue: W 152 - end of helix removed outlier: 3.595A pdb=" N ASN W 156 " --> pdb=" O PRO W 152 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU W 157 " --> pdb=" O SER W 153 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYS W 160 " --> pdb=" O ASN W 156 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLN W 165 " --> pdb=" O ALA W 161 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N PHE W 166 " --> pdb=" O VAL W 162 " (cutoff:3.500A) Processing helix chain 'W' and resid 167 through 174 removed outlier: 3.743A pdb=" N LEU W 171 " --> pdb=" O ASN W 167 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ILE W 172 " --> pdb=" O ALA W 168 " (cutoff:3.500A) Processing helix chain 'W' and resid 174 through 191 removed outlier: 3.641A pdb=" N VAL W 178 " --> pdb=" O GLN W 174 " (cutoff:3.500A) Processing helix chain 'W' and resid 208 through 261 removed outlier: 3.522A pdb=" N ALA W 229 " --> pdb=" O ALA W 225 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N PHE W 230 " --> pdb=" O GLN W 226 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ASP W 233 " --> pdb=" O ALA W 229 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN W 237 " --> pdb=" O ASP W 233 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA W 259 " --> pdb=" O LEU W 255 " (cutoff:3.500A) Processing helix chain 'W' and resid 264 through 283 Processing helix chain 'W' and resid 293 through 297 Processing helix chain 'W' and resid 302 through 306 removed outlier: 3.671A pdb=" N GLN W 305 " --> pdb=" O PHE W 302 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.544A pdb=" N GLY B 53 " --> pdb=" O VAL B 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 44 through 45 Processing sheet with id=AA3, first strand: chain 'B' and resid 72 through 75 Processing sheet with id=AA4, first strand: chain 'B' and resid 72 through 75 removed outlier: 6.771A pdb=" N ARG B 93 " --> pdb=" O ILE B 170 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N ILE B 170 " --> pdb=" O ARG B 93 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N LEU B 95 " --> pdb=" O VAL B 168 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N VAL B 168 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 8.878A pdb=" N ARG B 97 " --> pdb=" O GLU B 166 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N GLU B 166 " --> pdb=" O ARG B 97 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.569A pdb=" N GLY C 53 " --> pdb=" O VAL C 30 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 44 through 50 removed outlier: 5.354A pdb=" N ILE C 38 " --> pdb=" O LYS C 46 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N GLN C 48 " --> pdb=" O ALA C 36 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N ALA C 36 " --> pdb=" O GLN C 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 72 through 75 removed outlier: 3.513A pdb=" N HIS C 96 " --> pdb=" O LYS C 72 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 72 through 75 removed outlier: 3.513A pdb=" N HIS C 96 " --> pdb=" O LYS C 72 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N HIS C 172 " --> pdb=" O THR C 91 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ARG C 93 " --> pdb=" O ILE C 170 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N ILE C 170 " --> pdb=" O ARG C 93 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N LEU C 95 " --> pdb=" O VAL C 168 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N VAL C 168 " --> pdb=" O LEU C 95 " (cutoff:3.500A) removed outlier: 8.917A pdb=" N ARG C 97 " --> pdb=" O GLU C 166 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N GLU C 166 " --> pdb=" O ARG C 97 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 59 through 62 removed outlier: 3.711A pdb=" N PHE D 60 " --> pdb=" O HIS D 87 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N HIS D 87 " --> pdb=" O PHE D 60 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY D 85 " --> pdb=" O VAL D 62 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 68 through 72 Processing sheet with id=AB2, first strand: chain 'D' and resid 104 through 111 removed outlier: 3.579A pdb=" N VAL D 108 " --> pdb=" O CYS D 124 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE D 122 " --> pdb=" O SER D 110 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N HIS D 204 " --> pdb=" O THR D 123 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ARG D 125 " --> pdb=" O LEU D 202 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N LEU D 202 " --> pdb=" O ARG D 125 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N LEU D 127 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL D 200 " --> pdb=" O LEU D 127 " (cutoff:3.500A) removed outlier: 9.034A pdb=" N ARG D 129 " --> pdb=" O ASP D 198 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ASP D 198 " --> pdb=" O ARG D 129 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 59 through 62 removed outlier: 3.773A pdb=" N PHE E 60 " --> pdb=" O HIS E 87 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N HIS E 87 " --> pdb=" O PHE E 60 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY E 85 " --> pdb=" O VAL E 62 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 68 through 72 Processing sheet with id=AB5, first strand: chain 'E' and resid 104 through 111 removed outlier: 3.614A pdb=" N VAL E 108 " --> pdb=" O CYS E 124 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE E 122 " --> pdb=" O SER E 110 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ASN E 121 " --> pdb=" O HIS E 204 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N HIS E 204 " --> pdb=" O ASN E 121 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N THR E 123 " --> pdb=" O LEU E 202 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N LEU E 202 " --> pdb=" O THR E 123 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ARG E 125 " --> pdb=" O VAL E 200 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N VAL E 200 " --> pdb=" O ARG E 125 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU E 127 " --> pdb=" O ASP E 198 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 27 through 30 removed outlier: 3.606A pdb=" N GLY F 53 " --> pdb=" O VAL F 30 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 44 through 50 removed outlier: 5.414A pdb=" N ILE F 38 " --> pdb=" O LYS F 46 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N GLN F 48 " --> pdb=" O ALA F 36 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ALA F 36 " --> pdb=" O GLN F 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 72 through 75 Processing sheet with id=AB9, first strand: chain 'F' and resid 72 through 75 removed outlier: 8.592A pdb=" N MET F 87 " --> pdb=" O PHE F 175 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N PHE F 175 " --> pdb=" O MET F 87 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N SER F 89 " --> pdb=" O LEU F 173 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LEU F 173 " --> pdb=" O SER F 89 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N THR F 91 " --> pdb=" O THR F 171 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASP F 167 " --> pdb=" O LEU F 95 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ARG F 97 " --> pdb=" O LEU F 165 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N LEU F 165 " --> pdb=" O ARG F 97 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 27 through 30 removed outlier: 3.660A pdb=" N GLY G 53 " --> pdb=" O VAL G 30 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 44 through 45 Processing sheet with id=AC3, first strand: chain 'G' and resid 72 through 75 removed outlier: 3.519A pdb=" N HIS G 96 " --> pdb=" O LYS G 72 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 72 through 75 removed outlier: 3.519A pdb=" N HIS G 96 " --> pdb=" O LYS G 72 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N MET G 87 " --> pdb=" O PHE G 175 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N PHE G 175 " --> pdb=" O MET G 87 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N SER G 89 " --> pdb=" O LEU G 173 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU G 173 " --> pdb=" O SER G 89 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N THR G 91 " --> pdb=" O THR G 171 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASP G 167 " --> pdb=" O LEU G 95 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ARG G 97 " --> pdb=" O LEU G 165 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU G 165 " --> pdb=" O ARG G 97 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 59 through 62 removed outlier: 3.773A pdb=" N PHE H 60 " --> pdb=" O HIS H 87 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N HIS H 87 " --> pdb=" O PHE H 60 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY H 85 " --> pdb=" O VAL H 62 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 68 through 72 Processing sheet with id=AC7, first strand: chain 'H' and resid 104 through 111 removed outlier: 3.567A pdb=" N VAL H 108 " --> pdb=" O CYS H 124 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE H 122 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ASN H 121 " --> pdb=" O HIS H 204 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N HIS H 204 " --> pdb=" O ASN H 121 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N THR H 123 " --> pdb=" O LEU H 202 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N LEU H 202 " --> pdb=" O THR H 123 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ARG H 125 " --> pdb=" O VAL H 200 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N VAL H 200 " --> pdb=" O ARG H 125 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU H 127 " --> pdb=" O ASP H 198 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 59 through 62 removed outlier: 3.755A pdb=" N PHE I 60 " --> pdb=" O HIS I 87 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N HIS I 87 " --> pdb=" O PHE I 60 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY I 85 " --> pdb=" O VAL I 62 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 68 through 72 Processing sheet with id=AD1, first strand: chain 'I' and resid 104 through 111 removed outlier: 3.578A pdb=" N VAL I 108 " --> pdb=" O CYS I 124 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ARG I 125 " --> pdb=" O LEU I 202 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N LEU I 202 " --> pdb=" O ARG I 125 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N LEU I 127 " --> pdb=" O VAL I 200 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL I 200 " --> pdb=" O LEU I 127 " (cutoff:3.500A) removed outlier: 9.066A pdb=" N ARG I 129 " --> pdb=" O ASP I 198 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ASP I 198 " --> pdb=" O ARG I 129 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 27 through 30 removed outlier: 3.612A pdb=" N GLY J 53 " --> pdb=" O VAL J 30 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 44 through 45 Processing sheet with id=AD4, first strand: chain 'J' and resid 72 through 75 removed outlier: 3.514A pdb=" N HIS J 96 " --> pdb=" O LYS J 72 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 72 through 75 removed outlier: 3.514A pdb=" N HIS J 96 " --> pdb=" O LYS J 72 " (cutoff:3.500A) removed outlier: 8.509A pdb=" N MET J 87 " --> pdb=" O PHE J 175 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N PHE J 175 " --> pdb=" O MET J 87 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N SER J 89 " --> pdb=" O LEU J 173 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU J 173 " --> pdb=" O SER J 89 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N THR J 91 " --> pdb=" O THR J 171 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASP J 167 " --> pdb=" O LEU J 95 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ARG J 97 " --> pdb=" O LEU J 165 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N LEU J 165 " --> pdb=" O ARG J 97 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 258 through 259 Processing sheet with id=AD7, first strand: chain 'K' and resid 27 through 30 removed outlier: 3.577A pdb=" N GLY K 53 " --> pdb=" O VAL K 30 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 44 through 45 Processing sheet with id=AD9, first strand: chain 'K' and resid 72 through 75 removed outlier: 3.537A pdb=" N HIS K 96 " --> pdb=" O LYS K 72 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 72 through 75 removed outlier: 3.537A pdb=" N HIS K 96 " --> pdb=" O LYS K 72 " (cutoff:3.500A) removed outlier: 8.507A pdb=" N MET K 87 " --> pdb=" O PHE K 175 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N PHE K 175 " --> pdb=" O MET K 87 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N SER K 89 " --> pdb=" O LEU K 173 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LEU K 173 " --> pdb=" O SER K 89 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N THR K 91 " --> pdb=" O THR K 171 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASP K 167 " --> pdb=" O LEU K 95 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ARG K 97 " --> pdb=" O LEU K 165 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N LEU K 165 " --> pdb=" O ARG K 97 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 59 through 62 removed outlier: 3.679A pdb=" N PHE L 60 " --> pdb=" O HIS L 87 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N HIS L 87 " --> pdb=" O PHE L 60 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY L 85 " --> pdb=" O VAL L 62 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'L' and resid 68 through 72 Processing sheet with id=AE4, first strand: chain 'L' and resid 104 through 111 removed outlier: 3.585A pdb=" N VAL L 108 " --> pdb=" O CYS L 124 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE L 122 " --> pdb=" O SER L 110 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ASN L 121 " --> pdb=" O HIS L 204 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N HIS L 204 " --> pdb=" O ASN L 121 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N THR L 123 " --> pdb=" O LEU L 202 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N LEU L 202 " --> pdb=" O THR L 123 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ARG L 125 " --> pdb=" O VAL L 200 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VAL L 200 " --> pdb=" O ARG L 125 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N LEU L 127 " --> pdb=" O ASP L 198 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'M' and resid 59 through 62 removed outlier: 3.782A pdb=" N PHE M 60 " --> pdb=" O HIS M 87 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N HIS M 87 " --> pdb=" O PHE M 60 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY M 85 " --> pdb=" O VAL M 62 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'M' and resid 68 through 72 Processing sheet with id=AE7, first strand: chain 'M' and resid 104 through 111 removed outlier: 3.589A pdb=" N VAL M 108 " --> pdb=" O CYS M 124 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ASN M 121 " --> pdb=" O HIS M 204 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N HIS M 204 " --> pdb=" O ASN M 121 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N THR M 123 " --> pdb=" O LEU M 202 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N LEU M 202 " --> pdb=" O THR M 123 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ARG M 125 " --> pdb=" O VAL M 200 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N VAL M 200 " --> pdb=" O ARG M 125 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU M 127 " --> pdb=" O ASP M 198 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'N' and resid 27 through 30 removed outlier: 3.607A pdb=" N GLY N 53 " --> pdb=" O VAL N 30 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'N' and resid 44 through 45 Processing sheet with id=AF1, first strand: chain 'N' and resid 72 through 75 Processing sheet with id=AF2, first strand: chain 'N' and resid 72 through 75 removed outlier: 8.163A pdb=" N MET N 87 " --> pdb=" O THR N 174 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N THR N 174 " --> pdb=" O MET N 87 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N SER N 89 " --> pdb=" O HIS N 172 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N HIS N 172 " --> pdb=" O SER N 89 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N THR N 91 " --> pdb=" O ILE N 170 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ILE N 170 " --> pdb=" O THR N 91 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ARG N 93 " --> pdb=" O VAL N 168 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N VAL N 168 " --> pdb=" O ARG N 93 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LEU N 95 " --> pdb=" O GLU N 166 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'O' and resid 27 through 30 removed outlier: 3.563A pdb=" N GLY O 53 " --> pdb=" O VAL O 30 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'O' and resid 44 through 45 Processing sheet with id=AF5, first strand: chain 'O' and resid 72 through 75 Processing sheet with id=AF6, first strand: chain 'O' and resid 72 through 75 removed outlier: 8.229A pdb=" N MET O 87 " --> pdb=" O THR O 174 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N THR O 174 " --> pdb=" O MET O 87 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N SER O 89 " --> pdb=" O HIS O 172 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N HIS O 172 " --> pdb=" O SER O 89 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N THR O 91 " --> pdb=" O ILE O 170 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N ILE O 170 " --> pdb=" O THR O 91 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ARG O 93 " --> pdb=" O VAL O 168 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N VAL O 168 " --> pdb=" O ARG O 93 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LEU O 95 " --> pdb=" O GLU O 166 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'O' and resid 258 through 260 Processing sheet with id=AF8, first strand: chain 'P' and resid 59 through 62 removed outlier: 3.689A pdb=" N PHE P 60 " --> pdb=" O HIS P 87 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N HIS P 87 " --> pdb=" O PHE P 60 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'P' and resid 68 through 72 Processing sheet with id=AG1, first strand: chain 'P' and resid 104 through 111 removed outlier: 3.614A pdb=" N VAL P 108 " --> pdb=" O CYS P 124 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE P 122 " --> pdb=" O SER P 110 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ASN P 121 " --> pdb=" O HIS P 204 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N HIS P 204 " --> pdb=" O ASN P 121 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N THR P 123 " --> pdb=" O LEU P 202 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N LEU P 202 " --> pdb=" O THR P 123 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ARG P 125 " --> pdb=" O VAL P 200 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VAL P 200 " --> pdb=" O ARG P 125 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LEU P 127 " --> pdb=" O ASP P 198 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'Q' and resid 59 through 62 removed outlier: 3.777A pdb=" N PHE Q 60 " --> pdb=" O HIS Q 87 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N HIS Q 87 " --> pdb=" O PHE Q 60 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY Q 85 " --> pdb=" O VAL Q 62 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'Q' and resid 68 through 72 Processing sheet with id=AG4, first strand: chain 'Q' and resid 104 through 111 removed outlier: 3.588A pdb=" N VAL Q 108 " --> pdb=" O CYS Q 124 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE Q 122 " --> pdb=" O SER Q 110 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ASN Q 121 " --> pdb=" O HIS Q 204 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N HIS Q 204 " --> pdb=" O ASN Q 121 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N THR Q 123 " --> pdb=" O LEU Q 202 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N LEU Q 202 " --> pdb=" O THR Q 123 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ARG Q 125 " --> pdb=" O VAL Q 200 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL Q 200 " --> pdb=" O ARG Q 125 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LEU Q 127 " --> pdb=" O ASP Q 198 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'R' and resid 27 through 30 removed outlier: 3.526A pdb=" N GLY R 53 " --> pdb=" O VAL R 30 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'R' and resid 44 through 45 Processing sheet with id=AG7, first strand: chain 'R' and resid 72 through 75 Processing sheet with id=AG8, first strand: chain 'R' and resid 72 through 75 removed outlier: 8.534A pdb=" N MET R 87 " --> pdb=" O PHE R 175 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N PHE R 175 " --> pdb=" O MET R 87 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N SER R 89 " --> pdb=" O LEU R 173 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU R 173 " --> pdb=" O SER R 89 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N THR R 91 " --> pdb=" O THR R 171 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASP R 167 " --> pdb=" O LEU R 95 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ARG R 97 " --> pdb=" O LEU R 165 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N LEU R 165 " --> pdb=" O ARG R 97 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'R' and resid 258 through 260 removed outlier: 6.810A pdb=" N VAL R 258 " --> pdb=" O LEU T 292 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG9 Processing sheet with id=AH1, first strand: chain 'S' and resid 27 through 30 removed outlier: 3.611A pdb=" N GLY S 53 " --> pdb=" O VAL S 30 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'S' and resid 44 through 50 removed outlier: 5.354A pdb=" N ILE S 38 " --> pdb=" O LYS S 46 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N GLN S 48 " --> pdb=" O ALA S 36 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N ALA S 36 " --> pdb=" O GLN S 48 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'S' and resid 72 through 75 Processing sheet with id=AH4, first strand: chain 'S' and resid 72 through 75 removed outlier: 6.754A pdb=" N ARG S 93 " --> pdb=" O ILE S 170 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N ILE S 170 " --> pdb=" O ARG S 93 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N LEU S 95 " --> pdb=" O VAL S 168 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N VAL S 168 " --> pdb=" O LEU S 95 " (cutoff:3.500A) removed outlier: 8.913A pdb=" N ARG S 97 " --> pdb=" O GLU S 166 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N GLU S 166 " --> pdb=" O ARG S 97 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'T' and resid 59 through 62 removed outlier: 3.702A pdb=" N PHE T 60 " --> pdb=" O HIS T 87 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N HIS T 87 " --> pdb=" O PHE T 60 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY T 85 " --> pdb=" O VAL T 62 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'T' and resid 68 through 72 Processing sheet with id=AH7, first strand: chain 'T' and resid 104 through 111 removed outlier: 3.575A pdb=" N VAL T 108 " --> pdb=" O CYS T 124 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ASN T 121 " --> pdb=" O HIS T 204 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N HIS T 204 " --> pdb=" O ASN T 121 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N THR T 123 " --> pdb=" O LEU T 202 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N LEU T 202 " --> pdb=" O THR T 123 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ARG T 125 " --> pdb=" O VAL T 200 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N VAL T 200 " --> pdb=" O ARG T 125 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LEU T 127 " --> pdb=" O ASP T 198 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'U' and resid 59 through 62 removed outlier: 3.762A pdb=" N PHE U 60 " --> pdb=" O HIS U 87 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N HIS U 87 " --> pdb=" O PHE U 60 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY U 85 " --> pdb=" O VAL U 62 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'U' and resid 68 through 72 Processing sheet with id=AI1, first strand: chain 'U' and resid 104 through 111 removed outlier: 3.653A pdb=" N VAL U 108 " --> pdb=" O CYS U 124 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER U 110 " --> pdb=" O ILE U 122 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE U 122 " --> pdb=" O SER U 110 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ARG U 125 " --> pdb=" O LEU U 202 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N LEU U 202 " --> pdb=" O ARG U 125 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N LEU U 127 " --> pdb=" O VAL U 200 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N VAL U 200 " --> pdb=" O LEU U 127 " (cutoff:3.500A) removed outlier: 9.078A pdb=" N ARG U 129 " --> pdb=" O ASP U 198 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ASP U 198 " --> pdb=" O ARG U 129 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'V' and resid 27 through 30 removed outlier: 3.597A pdb=" N GLY V 53 " --> pdb=" O VAL V 30 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'V' and resid 44 through 50 removed outlier: 6.543A pdb=" N LYS V 46 " --> pdb=" O ASP V 40 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N ASP V 40 " --> pdb=" O LYS V 46 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N GLN V 48 " --> pdb=" O ILE V 38 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ILE V 38 " --> pdb=" O GLN V 48 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA V 36 " --> pdb=" O VAL V 50 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'V' and resid 72 through 75 removed outlier: 3.537A pdb=" N HIS V 96 " --> pdb=" O LYS V 72 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'V' and resid 72 through 75 removed outlier: 3.537A pdb=" N HIS V 96 " --> pdb=" O LYS V 72 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N MET V 87 " --> pdb=" O THR V 174 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N THR V 174 " --> pdb=" O MET V 87 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N SER V 89 " --> pdb=" O HIS V 172 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N HIS V 172 " --> pdb=" O SER V 89 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N THR V 91 " --> pdb=" O ILE V 170 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N ILE V 170 " --> pdb=" O THR V 91 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ARG V 93 " --> pdb=" O VAL V 168 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N VAL V 168 " --> pdb=" O ARG V 93 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LEU V 95 " --> pdb=" O GLU V 166 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'W' and resid 59 through 62 removed outlier: 3.698A pdb=" N PHE W 60 " --> pdb=" O HIS W 87 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N HIS W 87 " --> pdb=" O PHE W 60 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY W 85 " --> pdb=" O VAL W 62 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'W' and resid 68 through 72 removed outlier: 3.577A pdb=" N ILE W 97 " --> pdb=" O ILE W 69 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR W 71 " --> pdb=" O THR W 95 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'W' and resid 104 through 111 removed outlier: 3.577A pdb=" N VAL W 108 " --> pdb=" O CYS W 124 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ASN W 121 " --> pdb=" O HIS W 204 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N HIS W 204 " --> pdb=" O ASN W 121 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N THR W 123 " --> pdb=" O LEU W 202 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N LEU W 202 " --> pdb=" O THR W 123 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ARG W 125 " --> pdb=" O VAL W 200 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N VAL W 200 " --> pdb=" O ARG W 125 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N LEU W 127 " --> pdb=" O ASP W 198 " (cutoff:3.500A) 2699 hydrogen bonds defined for protein. 7800 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: 14.12 Time building geometry restraints manager: 5.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 15111 1.34 - 1.45: 4242 1.45 - 1.57: 25942 1.57 - 1.69: 3 1.69 - 1.81: 154 Bond restraints: 45452 Sorted by residual: bond pdb=" N VAL W 101 " pdb=" CA VAL W 101 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.25e-02 6.40e+03 6.65e+00 bond pdb=" N VAL Q 101 " pdb=" CA VAL Q 101 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.25e-02 6.40e+03 6.62e+00 bond pdb=" N VAL E 101 " pdb=" CA VAL E 101 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.25e-02 6.40e+03 6.62e+00 bond pdb=" N VAL U 101 " pdb=" CA VAL U 101 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.25e-02 6.40e+03 6.58e+00 bond pdb=" N VAL M 101 " pdb=" CA VAL M 101 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.25e-02 6.40e+03 6.54e+00 ... (remaining 45447 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 60874 2.30 - 4.60: 418 4.60 - 6.91: 129 6.91 - 9.21: 10 9.21 - 11.51: 4 Bond angle restraints: 61435 Sorted by residual: angle pdb=" CB MET L 119 " pdb=" CG MET L 119 " pdb=" SD MET L 119 " ideal model delta sigma weight residual 112.70 124.21 -11.51 3.00e+00 1.11e-01 1.47e+01 angle pdb=" CA GLN M 137 " pdb=" CB GLN M 137 " pdb=" CG GLN M 137 " ideal model delta sigma weight residual 114.10 121.51 -7.41 2.00e+00 2.50e-01 1.37e+01 angle pdb=" CA GLN D 137 " pdb=" CB GLN D 137 " pdb=" CG GLN D 137 " ideal model delta sigma weight residual 114.10 121.51 -7.41 2.00e+00 2.50e-01 1.37e+01 angle pdb=" CA PRO D 96 " pdb=" N PRO D 96 " pdb=" CD PRO D 96 " ideal model delta sigma weight residual 112.00 106.85 5.15 1.40e+00 5.10e-01 1.35e+01 angle pdb=" CA GLN E 137 " pdb=" CB GLN E 137 " pdb=" CG GLN E 137 " ideal model delta sigma weight residual 114.10 121.44 -7.34 2.00e+00 2.50e-01 1.35e+01 ... (remaining 61430 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 23194 17.84 - 35.67: 3526 35.67 - 53.51: 1031 53.51 - 71.34: 164 71.34 - 89.18: 69 Dihedral angle restraints: 27984 sinusoidal: 11374 harmonic: 16610 Sorted by residual: dihedral pdb=" CA ILE Q 69 " pdb=" C ILE Q 69 " pdb=" N LYS Q 70 " pdb=" CA LYS Q 70 " ideal model delta harmonic sigma weight residual -180.00 -162.89 -17.11 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA VAL D 150 " pdb=" C VAL D 150 " pdb=" N LEU D 151 " pdb=" CA LEU D 151 " ideal model delta harmonic sigma weight residual -180.00 -163.15 -16.85 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA ASP Q 304 " pdb=" CB ASP Q 304 " pdb=" CG ASP Q 304 " pdb=" OD1 ASP Q 304 " ideal model delta sinusoidal sigma weight residual -30.00 -87.34 57.34 1 2.00e+01 2.50e-03 1.10e+01 ... (remaining 27981 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 5517 0.039 - 0.079: 1134 0.079 - 0.118: 428 0.118 - 0.157: 76 0.157 - 0.197: 6 Chirality restraints: 7161 Sorted by residual: chirality pdb=" CA VAL M 101 " pdb=" N VAL M 101 " pdb=" C VAL M 101 " pdb=" CB VAL M 101 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 9.66e-01 chirality pdb=" CA VAL Q 101 " pdb=" N VAL Q 101 " pdb=" C VAL Q 101 " pdb=" CB VAL Q 101 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 9.55e-01 chirality pdb=" CA VAL E 101 " pdb=" N VAL E 101 " pdb=" C VAL E 101 " pdb=" CB VAL E 101 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.21e-01 ... (remaining 7158 not shown) Planarity restraints: 8030 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU M 273 " 0.011 2.00e-02 2.50e+03 2.15e-02 4.64e+00 pdb=" CD GLU M 273 " -0.037 2.00e-02 2.50e+03 pdb=" OE1 GLU M 273 " 0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU M 273 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU E 273 " -0.010 2.00e-02 2.50e+03 2.14e-02 4.56e+00 pdb=" CD GLU E 273 " 0.037 2.00e-02 2.50e+03 pdb=" OE1 GLU E 273 " -0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU E 273 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU O 219 " 0.010 2.00e-02 2.50e+03 2.09e-02 4.36e+00 pdb=" CD GLU O 219 " -0.036 2.00e-02 2.50e+03 pdb=" OE1 GLU O 219 " 0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU O 219 " 0.013 2.00e-02 2.50e+03 ... (remaining 8027 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 784 2.70 - 3.25: 44605 3.25 - 3.80: 67395 3.80 - 4.35: 83350 4.35 - 4.90: 143814 Nonbonded interactions: 339948 Sorted by model distance: nonbonded pdb=" NZ LYS I 70 " pdb=" OE1 GLU I 94 " model vdw 2.149 3.120 nonbonded pdb=" OE2 GLU B 217 " pdb=" OH TYR D 266 " model vdw 2.180 3.040 nonbonded pdb=" NZ LYS Q 70 " pdb=" OE2 GLU Q 94 " model vdw 2.192 3.120 nonbonded pdb=" OE2 GLU C 217 " pdb=" OH TYR E 266 " model vdw 2.215 3.040 nonbonded pdb=" OE2 GLU F 217 " pdb=" OH TYR H 266 " model vdw 2.229 3.040 ... (remaining 339943 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: 0.01 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'F' selection = chain 'G' selection = chain 'J' selection = chain 'K' selection = chain 'N' selection = chain 'O' selection = chain 'R' selection = chain 'S' selection = chain 'V' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'H' selection = chain 'I' selection = chain 'L' selection = chain 'M' selection = chain 'P' selection = chain 'Q' selection = chain 'T' selection = chain 'U' selection = chain 'W' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 0.810 Check model and map are aligned: 0.150 Set scattering table: 0.160 Process input model: 46.240 Find NCS groups from input model: 1.290 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 52.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 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 : 0.003 0.114 45452 Z= 0.115 Angle : 0.536 11.510 61435 Z= 0.280 Chirality : 0.039 0.197 7161 Planarity : 0.003 0.040 8030 Dihedral : 18.645 89.176 17204 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.32 % Allowed : 33.11 % Favored : 66.58 % 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: 0.03 (0.11), residues: 5676 helix: 0.76 (0.09), residues: 2970 sheet: -0.23 (0.18), residues: 880 loop : -0.92 (0.15), residues: 1826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG U 289 TYR 0.013 0.001 TYR Q 139 PHE 0.007 0.001 PHE B 67 TRP 0.007 0.001 TRP W 92 HIS 0.003 0.000 HIS B 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (45452) covalent geometry : angle 0.53627 / 0.28 (61435) hydrogen bonds : bond 0.24568 / 16.58 ( 2660) hydrogen bonds : angle 7.99711 / 5.73 ( 7800) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11352 Ramachandran restraints generated. 5676 Oldfield, 0 Emsley, 5676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11352 Ramachandran restraints generated. 5676 Oldfield, 0 Emsley, 5676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 4730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 586 time to evaluate : 1.852 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 271 LYS cc_start: 0.7030 (tttt) cc_final: 0.6735 (ttmt) REVERT: G 242 GLU cc_start: 0.7125 (tt0) cc_final: 0.6750 (tp30) REVERT: I 80 ASP cc_start: 0.7615 (p0) cc_final: 0.7335 (p0) REVERT: I 192 ARG cc_start: 0.7663 (ttp-110) cc_final: 0.7342 (mtm110) REVERT: I 240 GLN cc_start: 0.7320 (tt0) cc_final: 0.6978 (mt0) REVERT: I 273 GLU cc_start: 0.7574 (tm-30) cc_final: 0.7046 (tm-30) REVERT: L 271 LYS cc_start: 0.6962 (tttt) cc_final: 0.6677 (ttmt) REVERT: M 89 MET cc_start: 0.5795 (ttp) cc_final: 0.5583 (tmm) REVERT: M 154 ILE cc_start: 0.7701 (tt) cc_final: 0.7493 (tt) REVERT: M 273 GLU cc_start: 0.7612 (tm-30) cc_final: 0.7082 (tm-30) REVERT: R 51 ASN cc_start: 0.8354 (m-40) cc_final: 0.8132 (m-40) REVERT: R 67 PHE cc_start: 0.6760 (OUTLIER) cc_final: 0.6398 (m-10) REVERT: R 219 GLU cc_start: 0.7989 (tp30) cc_final: 0.7363 (tp30) REVERT: S 70 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.8002 (ptp-170) REVERT: U 46 MET cc_start: 0.4458 (mmm) cc_final: 0.4217 (mmp) REVERT: V 72 LYS cc_start: 0.8111 (mttt) cc_final: 0.7809 (mttp) REVERT: V 113 ASP cc_start: 0.7745 (p0) cc_final: 0.7438 (p0) outliers start: 15 outliers final: 4 residues processed: 597 average time/residue: 0.2636 time to fit residues: 262.4523 Evaluate side-chains 553 residues out of total 4730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 547 time to evaluate : 1.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain N residue 48 GLN Chi-restraints excluded: chain O residue 106 ILE Chi-restraints excluded: chain R residue 67 PHE Chi-restraints excluded: chain S residue 70 ARG Chi-restraints excluded: chain W residue 208 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 561 random chunks: chunk 394 optimal weight: 6.9990 chunk 430 optimal weight: 0.5980 chunk 41 optimal weight: 3.9990 chunk 265 optimal weight: 6.9990 chunk 523 optimal weight: 0.7980 chunk 497 optimal weight: 4.9990 chunk 414 optimal weight: 3.9990 chunk 310 optimal weight: 9.9990 chunk 488 optimal weight: 4.9990 chunk 366 optimal weight: 6.9990 chunk 223 optimal weight: 0.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 ASN ** G 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 137 GLN ** N 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 194 ASN ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 194 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.121367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.097929 restraints weight = 67519.113| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 3.33 r_work: 0.3147 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6570 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 45452 Z= 0.159 Angle : 0.556 8.818 61435 Z= 0.293 Chirality : 0.041 0.146 7161 Planarity : 0.004 0.023 8030 Dihedral : 4.128 39.553 6272 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.91 % Allowed : 31.71 % Favored : 64.38 % 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 (0.11), residues: 5676 helix: 1.39 (0.10), residues: 2904 sheet: -0.30 (0.17), residues: 968 loop : -0.95 (0.15), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 140 TYR 0.018 0.001 TYR Q 139 PHE 0.013 0.001 PHE F 198 TRP 0.004 0.000 TRP I 92 HIS 0.002 0.000 HIS J 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 (45452) covalent geometry : angle 0.55649 / 0.29 (61435) hydrogen bonds : bond 0.05921 / 4.03 ( 2660) hydrogen bonds : angle 5.40731 / 3.91 ( 7800) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11352 Ramachandran restraints generated. 5676 Oldfield, 0 Emsley, 5676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11352 Ramachandran restraints generated. 5676 Oldfield, 0 Emsley, 5676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 798 residues out of total 4730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 613 time to evaluate : 1.825 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 178 GLU cc_start: 0.7197 (tp30) cc_final: 0.6962 (tp30) REVERT: C 125 GLU cc_start: 0.8077 (tm-30) cc_final: 0.7585 (tm-30) REVERT: C 134 TYR cc_start: 0.7202 (m-80) cc_final: 0.6993 (m-80) REVERT: D 70 LYS cc_start: 0.7678 (mtpt) cc_final: 0.7435 (mtpt) REVERT: D 249 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7218 (tp30) REVERT: D 269 LEU cc_start: 0.6566 (OUTLIER) cc_final: 0.6297 (tt) REVERT: D 271 LYS cc_start: 0.6792 (tttt) cc_final: 0.6505 (ttmt) REVERT: E 137 GLN cc_start: 0.6786 (tm-30) cc_final: 0.6537 (tm-30) REVERT: E 148 GLU cc_start: 0.8433 (mm-30) cc_final: 0.7801 (tt0) REVERT: E 231 ILE cc_start: 0.6320 (OUTLIER) cc_final: 0.5989 (tp) REVERT: F 113 ASP cc_start: 0.7141 (p0) cc_final: 0.6913 (p0) REVERT: G 219 GLU cc_start: 0.6931 (tp30) cc_final: 0.6655 (tp30) REVERT: H 137 GLN cc_start: 0.7105 (tm-30) cc_final: 0.6789 (tm-30) REVERT: I 70 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7762 (mtpt) REVERT: I 119 MET cc_start: 0.7634 (ttp) cc_final: 0.7258 (ttp) REVERT: I 137 GLN cc_start: 0.6621 (tm-30) cc_final: 0.6290 (tm-30) REVERT: I 273 GLU cc_start: 0.7134 (tm-30) cc_final: 0.6577 (tm-30) REVERT: K 173 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7415 (tt) REVERT: L 119 MET cc_start: 0.7128 (tmm) cc_final: 0.6502 (tmm) REVERT: M 137 GLN cc_start: 0.6944 (tm-30) cc_final: 0.6669 (tm-30) REVERT: M 144 LEU cc_start: 0.6385 (OUTLIER) cc_final: 0.6165 (mp) REVERT: M 148 GLU cc_start: 0.8647 (mm-30) cc_final: 0.8357 (mm-30) REVERT: M 154 ILE cc_start: 0.7439 (tt) cc_final: 0.7197 (tt) REVERT: M 273 GLU cc_start: 0.7144 (tm-30) cc_final: 0.6646 (tm-30) REVERT: P 133 GLN cc_start: 0.9008 (mm-40) cc_final: 0.8729 (mm-40) REVERT: P 137 GLN cc_start: 0.7316 (tp-100) cc_final: 0.6938 (tm-30) REVERT: Q 231 ILE cc_start: 0.6291 (OUTLIER) cc_final: 0.6063 (tp) REVERT: R 24 GLN cc_start: 0.6358 (mm110) cc_final: 0.5852 (mt0) REVERT: R 51 ASN cc_start: 0.8224 (m-40) cc_final: 0.8001 (m-40) REVERT: S 217 GLU cc_start: 0.8135 (tp30) cc_final: 0.7907 (tp30) REVERT: T 288 ASN cc_start: 0.7448 (m-40) cc_final: 0.7248 (m-40) REVERT: U 119 MET cc_start: 0.7807 (ttp) cc_final: 0.7008 (tmm) REVERT: V 113 ASP cc_start: 0.7303 (p0) cc_final: 0.7084 (p0) outliers start: 185 outliers final: 84 residues processed: 763 average time/residue: 0.2430 time to fit residues: 318.1666 Evaluate side-chains 667 residues out of total 4730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 576 time to evaluate : 1.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 249 GLU Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 305 GLN Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 231 ILE Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 206 GLU Chi-restraints excluded: chain F residue 250 THR Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 211 VAL Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain H residue 208 SER Chi-restraints excluded: chain I residue 70 LYS Chi-restraints excluded: chain I residue 81 ILE Chi-restraints excluded: chain I residue 135 LEU Chi-restraints excluded: chain I residue 208 SER Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 243 VAL Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 250 THR Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 141 THR Chi-restraints excluded: chain L residue 153 SER Chi-restraints excluded: chain L residue 208 SER Chi-restraints excluded: chain M residue 144 LEU Chi-restraints excluded: chain M residue 153 SER Chi-restraints excluded: chain M residue 269 LEU Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 88 VAL Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 163 ILE Chi-restraints excluded: chain O residue 88 VAL Chi-restraints excluded: chain O residue 91 THR Chi-restraints excluded: chain O residue 153 ASP Chi-restraints excluded: chain P residue 141 THR Chi-restraints excluded: chain P residue 153 SER Chi-restraints excluded: chain P residue 208 SER Chi-restraints excluded: chain P residue 215 VAL Chi-restraints excluded: chain Q residue 108 VAL Chi-restraints excluded: chain Q residue 184 GLU Chi-restraints excluded: chain Q residue 208 SER Chi-restraints excluded: chain Q residue 231 ILE Chi-restraints excluded: chain R residue 76 ILE Chi-restraints excluded: chain R residue 91 THR Chi-restraints excluded: chain R residue 169 SER Chi-restraints excluded: chain S residue 22 LEU Chi-restraints excluded: chain S residue 23 LEU Chi-restraints excluded: chain S residue 88 VAL Chi-restraints excluded: chain S residue 100 VAL Chi-restraints excluded: chain S residue 106 ILE Chi-restraints excluded: chain T residue 135 LEU Chi-restraints excluded: chain T residue 153 SER Chi-restraints excluded: chain T residue 208 SER Chi-restraints excluded: chain T residue 305 GLN Chi-restraints excluded: chain U residue 135 LEU Chi-restraints excluded: chain U residue 208 SER Chi-restraints excluded: chain U residue 242 THR Chi-restraints excluded: chain U residue 269 LEU Chi-restraints excluded: chain V residue 23 LEU Chi-restraints excluded: chain V residue 37 VAL Chi-restraints excluded: chain V residue 88 VAL Chi-restraints excluded: chain V residue 91 THR Chi-restraints excluded: chain V residue 153 ASP Chi-restraints excluded: chain V residue 206 GLU Chi-restraints excluded: chain V residue 211 VAL Chi-restraints excluded: chain W residue 81 ILE Chi-restraints excluded: chain W residue 153 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 561 random chunks: chunk 452 optimal weight: 0.9980 chunk 291 optimal weight: 3.9990 chunk 170 optimal weight: 8.9990 chunk 114 optimal weight: 4.9990 chunk 343 optimal weight: 1.9990 chunk 263 optimal weight: 0.7980 chunk 209 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 176 optimal weight: 3.9990 chunk 405 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 109 ASN H 300 ASN ** J 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 249 GLN W 194 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.152826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.129834 restraints weight = 68000.686| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 3.20 r_work: 0.3472 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6768 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 45452 Z= 0.151 Angle : 0.526 9.006 61435 Z= 0.273 Chirality : 0.041 0.166 7161 Planarity : 0.003 0.022 8030 Dihedral : 4.088 45.665 6260 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 4.21 % Allowed : 32.43 % Favored : 63.36 % 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 (0.11), residues: 5676 helix: 1.52 (0.10), residues: 2838 sheet: -0.39 (0.17), residues: 968 loop : -1.03 (0.15), residues: 1870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 159 TYR 0.017 0.001 TYR T 139 PHE 0.011 0.001 PHE B 198 TRP 0.005 0.000 TRP W 92 HIS 0.002 0.000 HIS V 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (45452) covalent geometry : angle 0.52626 / 0.27 (61435) hydrogen bonds : bond 0.05397 / 3.68 ( 2660) hydrogen bonds : angle 4.99076 / 3.60 ( 7800) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11352 Ramachandran restraints generated. 5676 Oldfield, 0 Emsley, 5676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11352 Ramachandran restraints generated. 5676 Oldfield, 0 Emsley, 5676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 821 residues out of total 4730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 199 poor density : 622 time to evaluate : 1.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 87 MET cc_start: 0.7742 (ptt) cc_final: 0.7193 (ttm) REVERT: C 113 ASP cc_start: 0.7421 (p0) cc_final: 0.7215 (p0) REVERT: C 125 GLU cc_start: 0.8220 (tm-30) cc_final: 0.7726 (tm-30) REVERT: D 269 LEU cc_start: 0.6741 (OUTLIER) cc_final: 0.6456 (tt) REVERT: D 271 LYS cc_start: 0.6992 (tttt) cc_final: 0.6691 (ttmt) REVERT: E 137 GLN cc_start: 0.7038 (tm-30) cc_final: 0.6702 (tm-30) REVERT: E 148 GLU cc_start: 0.8446 (mm-30) cc_final: 0.7894 (tt0) REVERT: F 113 ASP cc_start: 0.7415 (p0) cc_final: 0.7213 (p0) REVERT: F 134 TYR cc_start: 0.7529 (m-80) cc_final: 0.7317 (m-80) REVERT: G 219 GLU cc_start: 0.7121 (tp30) cc_final: 0.6773 (tp30) REVERT: H 137 GLN cc_start: 0.7299 (tm-30) cc_final: 0.6952 (tm-30) REVERT: I 80 ASP cc_start: 0.7415 (p0) cc_final: 0.7108 (p0) REVERT: I 92 TRP cc_start: 0.7835 (t60) cc_final: 0.7425 (t60) REVERT: I 137 GLN cc_start: 0.6849 (tm-30) cc_final: 0.6492 (tm-30) REVERT: I 144 LEU cc_start: 0.6752 (OUTLIER) cc_final: 0.6544 (mp) REVERT: I 186 LEU cc_start: 0.7472 (OUTLIER) cc_final: 0.7048 (tt) REVERT: K 173 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7632 (tt) REVERT: K 199 ILE cc_start: 0.6747 (OUTLIER) cc_final: 0.6513 (tp) REVERT: L 70 LYS cc_start: 0.7619 (mtpt) cc_final: 0.7312 (mtpt) REVERT: L 119 MET cc_start: 0.7340 (tmm) cc_final: 0.6679 (tmm) REVERT: L 133 GLN cc_start: 0.8428 (tp40) cc_final: 0.8000 (mp10) REVERT: L 144 LEU cc_start: 0.6429 (OUTLIER) cc_final: 0.6198 (mp) REVERT: M 137 GLN cc_start: 0.7191 (tm-30) cc_final: 0.6816 (tm-30) REVERT: M 148 GLU cc_start: 0.8657 (mm-30) cc_final: 0.8323 (mm-30) REVERT: M 154 ILE cc_start: 0.7562 (tt) cc_final: 0.7240 (tt) REVERT: N 113 ASP cc_start: 0.7746 (p0) cc_final: 0.7462 (p0) REVERT: N 199 ILE cc_start: 0.6473 (OUTLIER) cc_final: 0.6236 (tp) REVERT: P 133 GLN cc_start: 0.8977 (mm-40) cc_final: 0.8712 (mm-40) REVERT: P 137 GLN cc_start: 0.7522 (tp-100) cc_final: 0.7142 (tm-30) REVERT: P 163 VAL cc_start: 0.6957 (OUTLIER) cc_final: 0.6733 (p) REVERT: Q 46 MET cc_start: 0.2253 (tmt) cc_final: 0.2025 (mmp) REVERT: Q 70 LYS cc_start: 0.7716 (tttp) cc_final: 0.7507 (mtpp) REVERT: Q 163 VAL cc_start: 0.7021 (OUTLIER) cc_final: 0.6766 (p) REVERT: Q 231 ILE cc_start: 0.6469 (OUTLIER) cc_final: 0.6220 (tp) REVERT: R 24 GLN cc_start: 0.6503 (mm110) cc_final: 0.6007 (mt0) REVERT: R 67 PHE cc_start: 0.6095 (OUTLIER) cc_final: 0.5672 (m-10) REVERT: S 70 ARG cc_start: 0.7951 (mtt180) cc_final: 0.7679 (ptp-170) REVERT: S 125 GLU cc_start: 0.7782 (tm-30) cc_final: 0.7062 (tm-30) REVERT: S 217 GLU cc_start: 0.8257 (tp30) cc_final: 0.7968 (tp30) REVERT: T 288 ASN cc_start: 0.7818 (m-40) cc_final: 0.7537 (m-40) REVERT: U 46 MET cc_start: 0.4000 (mmp) cc_final: 0.3791 (mmm) REVERT: U 119 MET cc_start: 0.7783 (ttp) cc_final: 0.7000 (tmm) REVERT: V 113 ASP cc_start: 0.7541 (p0) cc_final: 0.7250 (p0) outliers start: 199 outliers final: 110 residues processed: 798 average time/residue: 0.2428 time to fit residues: 331.2553 Evaluate side-chains 712 residues out of total 4730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 591 time to evaluate : 1.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 305 GLN Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 206 GLU Chi-restraints excluded: chain F residue 250 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 76 ILE Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 211 VAL Chi-restraints excluded: chain H residue 89 MET Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain H residue 208 SER Chi-restraints excluded: chain H residue 243 VAL Chi-restraints excluded: chain H residue 281 LEU Chi-restraints excluded: chain H residue 305 GLN Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 89 MET Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain I residue 208 SER Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 243 VAL Chi-restraints excluded: chain I residue 256 ILE Chi-restraints excluded: chain I residue 281 LEU Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain J residue 88 VAL Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 106 ILE Chi-restraints excluded: chain J residue 250 THR Chi-restraints excluded: chain K residue 23 LEU Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 126 VAL Chi-restraints excluded: chain K residue 163 ILE Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain K residue 199 ILE Chi-restraints excluded: chain K residue 242 GLU Chi-restraints excluded: chain K residue 250 THR Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 153 SER Chi-restraints excluded: chain L residue 186 LEU Chi-restraints excluded: chain L residue 208 SER Chi-restraints excluded: chain L residue 256 ILE Chi-restraints excluded: chain L residue 281 LEU Chi-restraints excluded: chain M residue 153 SER Chi-restraints excluded: chain M residue 256 ILE Chi-restraints excluded: chain N residue 88 VAL Chi-restraints excluded: chain N residue 100 VAL Chi-restraints excluded: chain N residue 163 ILE Chi-restraints excluded: chain N residue 169 SER Chi-restraints excluded: chain N residue 173 LEU Chi-restraints excluded: chain N residue 199 ILE Chi-restraints excluded: chain N residue 211 VAL Chi-restraints excluded: chain O residue 67 PHE Chi-restraints excluded: chain O residue 88 VAL Chi-restraints excluded: chain O residue 91 THR Chi-restraints excluded: chain O residue 153 ASP Chi-restraints excluded: chain O residue 163 ILE Chi-restraints excluded: chain P residue 135 LEU Chi-restraints excluded: chain P residue 153 SER Chi-restraints excluded: chain P residue 163 VAL Chi-restraints excluded: chain P residue 208 SER Chi-restraints excluded: chain P residue 215 VAL Chi-restraints excluded: chain Q residue 108 VAL Chi-restraints excluded: chain Q residue 135 LEU Chi-restraints excluded: chain Q residue 141 THR Chi-restraints excluded: chain Q residue 163 VAL Chi-restraints excluded: chain Q residue 208 SER Chi-restraints excluded: chain Q residue 231 ILE Chi-restraints excluded: chain R residue 23 LEU Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 67 PHE Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 91 THR Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 169 SER Chi-restraints excluded: chain S residue 22 LEU Chi-restraints excluded: chain S residue 88 VAL Chi-restraints excluded: chain S residue 100 VAL Chi-restraints excluded: chain T residue 153 SER Chi-restraints excluded: chain T residue 208 SER Chi-restraints excluded: chain T residue 243 VAL Chi-restraints excluded: chain T residue 269 LEU Chi-restraints excluded: chain T residue 305 GLN Chi-restraints excluded: chain U residue 135 LEU Chi-restraints excluded: chain U residue 208 SER Chi-restraints excluded: chain U residue 243 VAL Chi-restraints excluded: chain U residue 269 LEU Chi-restraints excluded: chain V residue 37 VAL Chi-restraints excluded: chain V residue 76 ILE Chi-restraints excluded: chain V residue 88 VAL Chi-restraints excluded: chain V residue 91 THR Chi-restraints excluded: chain V residue 153 ASP Chi-restraints excluded: chain V residue 163 ILE Chi-restraints excluded: chain V residue 206 GLU Chi-restraints excluded: chain V residue 211 VAL Chi-restraints excluded: chain W residue 153 SER Chi-restraints excluded: chain W residue 256 ILE Chi-restraints excluded: chain W residue 305 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 561 random chunks: chunk 210 optimal weight: 0.0470 chunk 5 optimal weight: 6.9990 chunk 273 optimal weight: 3.9990 chunk 261 optimal weight: 7.9990 chunk 145 optimal weight: 0.6980 chunk 58 optimal weight: 10.0000 chunk 28 optimal weight: 0.3980 chunk 120 optimal weight: 0.8980 chunk 538 optimal weight: 9.9990 chunk 68 optimal weight: 7.9990 chunk 167 optimal weight: 10.0000 overall best weight: 1.2080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 109 ASN ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 109 ASN ** J 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 137 GLN ** N 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 109 ASN S 162 ASN ** V 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 194 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.128619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.106269 restraints weight = 67056.095| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 3.02 r_work: 0.3278 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 45452 Z= 0.119 Angle : 0.495 9.304 61435 Z= 0.255 Chirality : 0.040 0.145 7161 Planarity : 0.003 0.019 8030 Dihedral : 3.998 48.218 6260 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.68 % Allowed : 33.26 % Favored : 63.07 % 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 (0.11), residues: 5676 helix: 1.55 (0.10), residues: 2871 sheet: -0.44 (0.17), residues: 968 loop : -1.08 (0.14), residues: 1837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 159 TYR 0.013 0.001 TYR T 139 PHE 0.007 0.001 PHE B 198 TRP 0.009 0.000 TRP W 92 HIS 0.002 0.000 HIS V 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 (45452) covalent geometry : angle 0.49513 / 0.26 (61435) hydrogen bonds : bond 0.04764 / 3.24 ( 2660) hydrogen bonds : angle 4.74103 / 3.42 ( 7800) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11352 Ramachandran restraints generated. 5676 Oldfield, 0 Emsley, 5676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11352 Ramachandran restraints generated. 5676 Oldfield, 0 Emsley, 5676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 809 residues out of total 4730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 635 time to evaluate : 1.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 87 MET cc_start: 0.7720 (ptt) cc_final: 0.7152 (ttm) REVERT: C 113 ASP cc_start: 0.7462 (p0) cc_final: 0.7211 (p0) REVERT: C 125 GLU cc_start: 0.8309 (tm-30) cc_final: 0.7850 (tm-30) REVERT: D 140 ARG cc_start: 0.7676 (mtm-85) cc_final: 0.7453 (mtm-85) REVERT: D 269 LEU cc_start: 0.6800 (OUTLIER) cc_final: 0.6511 (tt) REVERT: D 271 LYS cc_start: 0.7044 (tttt) cc_final: 0.6697 (ttmt) REVERT: E 119 MET cc_start: 0.7693 (ttt) cc_final: 0.7152 (tmm) REVERT: E 137 GLN cc_start: 0.7164 (tm-30) cc_final: 0.6795 (tm-30) REVERT: E 148 GLU cc_start: 0.8405 (mm-30) cc_final: 0.7938 (tt0) REVERT: F 134 TYR cc_start: 0.7546 (m-80) cc_final: 0.7325 (m-80) REVERT: G 217 GLU cc_start: 0.8037 (tp30) cc_final: 0.7726 (tp30) REVERT: G 219 GLU cc_start: 0.7003 (tp30) cc_final: 0.6630 (tp30) REVERT: H 70 LYS cc_start: 0.7849 (mtpt) cc_final: 0.7581 (mtpp) REVERT: H 137 GLN cc_start: 0.7406 (tm-30) cc_final: 0.6912 (tm-30) REVERT: H 231 ILE cc_start: 0.6414 (OUTLIER) cc_final: 0.6071 (tp) REVERT: I 80 ASP cc_start: 0.7338 (p0) cc_final: 0.7081 (p0) REVERT: I 119 MET cc_start: 0.7777 (ttp) cc_final: 0.7320 (tmm) REVERT: I 137 GLN cc_start: 0.6974 (tm-30) cc_final: 0.6541 (tm-30) REVERT: I 144 LEU cc_start: 0.6722 (OUTLIER) cc_final: 0.6443 (mp) REVERT: J 113 ASP cc_start: 0.7433 (p0) cc_final: 0.7222 (p0) REVERT: K 173 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7683 (tt) REVERT: K 199 ILE cc_start: 0.6931 (OUTLIER) cc_final: 0.6702 (tp) REVERT: L 70 LYS cc_start: 0.7547 (mtpt) cc_final: 0.7147 (mtpt) REVERT: L 119 MET cc_start: 0.7469 (OUTLIER) cc_final: 0.6645 (tmm) REVERT: M 137 GLN cc_start: 0.7333 (tm-30) cc_final: 0.6902 (tm-30) REVERT: M 148 GLU cc_start: 0.8651 (mm-30) cc_final: 0.8298 (mm-30) REVERT: M 154 ILE cc_start: 0.7602 (tt) cc_final: 0.7305 (tt) REVERT: N 48 GLN cc_start: 0.7487 (pt0) cc_final: 0.7287 (pt0) REVERT: N 113 ASP cc_start: 0.7581 (p0) cc_final: 0.7324 (p0) REVERT: O 125 GLU cc_start: 0.8376 (tm-30) cc_final: 0.8052 (tm-30) REVERT: O 199 ILE cc_start: 0.6388 (OUTLIER) cc_final: 0.6185 (tp) REVERT: P 133 GLN cc_start: 0.8993 (mm-40) cc_final: 0.8757 (mm-40) REVERT: P 137 GLN cc_start: 0.7632 (tp-100) cc_final: 0.7184 (tm-30) REVERT: P 163 VAL cc_start: 0.6958 (OUTLIER) cc_final: 0.6735 (p) REVERT: Q 70 LYS cc_start: 0.7868 (tttp) cc_final: 0.7633 (mtpp) REVERT: Q 163 VAL cc_start: 0.6996 (OUTLIER) cc_final: 0.6721 (p) REVERT: R 24 GLN cc_start: 0.6580 (mm110) cc_final: 0.6101 (mt0) REVERT: R 67 PHE cc_start: 0.6127 (OUTLIER) cc_final: 0.5676 (m-10) REVERT: R 219 GLU cc_start: 0.7548 (tp30) cc_final: 0.6932 (tm-30) REVERT: S 70 ARG cc_start: 0.7933 (mtt180) cc_final: 0.7680 (ptp-170) REVERT: S 125 GLU cc_start: 0.7715 (tm-30) cc_final: 0.7050 (tm-30) REVERT: S 217 GLU cc_start: 0.8243 (tp30) cc_final: 0.7938 (tp30) REVERT: T 137 GLN cc_start: 0.7210 (tm-30) cc_final: 0.6972 (tm-30) REVERT: T 186 LEU cc_start: 0.7190 (OUTLIER) cc_final: 0.6693 (tt) REVERT: T 276 ARG cc_start: 0.7177 (mtp180) cc_final: 0.6862 (mtp180) REVERT: T 288 ASN cc_start: 0.7685 (m-40) cc_final: 0.7358 (m-40) REVERT: U 70 LYS cc_start: 0.7772 (mtpt) cc_final: 0.7516 (mtpt) REVERT: U 119 MET cc_start: 0.7824 (ttp) cc_final: 0.7009 (tmm) REVERT: U 137 GLN cc_start: 0.6891 (tm-30) cc_final: 0.6624 (tm-30) REVERT: V 113 ASP cc_start: 0.7585 (p0) cc_final: 0.7251 (p0) REVERT: W 70 LYS cc_start: 0.7258 (mtpt) cc_final: 0.6880 (mtpp) REVERT: W 119 MET cc_start: 0.7988 (ttp) cc_final: 0.7517 (tmm) outliers start: 174 outliers final: 93 residues processed: 794 average time/residue: 0.2427 time to fit residues: 329.2147 Evaluate side-chains 704 residues out of total 4730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 600 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 76 ILE Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 242 GLU Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain H residue 208 SER Chi-restraints excluded: chain H residue 231 ILE Chi-restraints excluded: chain H residue 281 LEU Chi-restraints excluded: chain I residue 89 MET Chi-restraints excluded: chain I residue 135 LEU Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain I residue 208 SER Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 269 LEU Chi-restraints excluded: chain I residue 281 LEU Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain J residue 88 VAL Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 106 ILE Chi-restraints excluded: chain J residue 250 THR Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 126 VAL Chi-restraints excluded: chain K residue 163 ILE Chi-restraints excluded: chain K residue 165 LEU Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain K residue 199 ILE Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 119 MET Chi-restraints excluded: chain L residue 153 SER Chi-restraints excluded: chain L residue 208 SER Chi-restraints excluded: chain L residue 281 LEU Chi-restraints excluded: chain M residue 117 LEU Chi-restraints excluded: chain M residue 135 LEU Chi-restraints excluded: chain M residue 153 SER Chi-restraints excluded: chain M residue 269 LEU Chi-restraints excluded: chain M residue 281 LEU Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 76 ILE Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 163 ILE Chi-restraints excluded: chain N residue 173 LEU Chi-restraints excluded: chain O residue 23 LEU Chi-restraints excluded: chain O residue 67 PHE Chi-restraints excluded: chain O residue 88 VAL Chi-restraints excluded: chain O residue 91 THR Chi-restraints excluded: chain O residue 153 ASP Chi-restraints excluded: chain O residue 199 ILE Chi-restraints excluded: chain P residue 118 GLN Chi-restraints excluded: chain P residue 135 LEU Chi-restraints excluded: chain P residue 153 SER Chi-restraints excluded: chain P residue 163 VAL Chi-restraints excluded: chain P residue 208 SER Chi-restraints excluded: chain Q residue 108 VAL Chi-restraints excluded: chain Q residue 135 LEU Chi-restraints excluded: chain Q residue 163 VAL Chi-restraints excluded: chain Q residue 208 SER Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 67 PHE Chi-restraints excluded: chain R residue 91 THR Chi-restraints excluded: chain R residue 109 ASN Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 169 SER Chi-restraints excluded: chain S residue 22 LEU Chi-restraints excluded: chain S residue 100 VAL Chi-restraints excluded: chain S residue 251 LEU Chi-restraints excluded: chain T residue 135 LEU Chi-restraints excluded: chain T residue 153 SER Chi-restraints excluded: chain T residue 186 LEU Chi-restraints excluded: chain T residue 208 SER Chi-restraints excluded: chain U residue 118 GLN Chi-restraints excluded: chain U residue 186 LEU Chi-restraints excluded: chain U residue 208 SER Chi-restraints excluded: chain U residue 269 LEU Chi-restraints excluded: chain U residue 281 LEU Chi-restraints excluded: chain V residue 76 ILE Chi-restraints excluded: chain V residue 91 THR Chi-restraints excluded: chain V residue 153 ASP Chi-restraints excluded: chain V residue 163 ILE Chi-restraints excluded: chain V residue 206 GLU Chi-restraints excluded: chain W residue 153 SER Chi-restraints excluded: chain W residue 281 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 561 random chunks: chunk 223 optimal weight: 0.9990 chunk 334 optimal weight: 9.9990 chunk 333 optimal weight: 5.9990 chunk 527 optimal weight: 1.9990 chunk 554 optimal weight: 4.9990 chunk 417 optimal weight: 4.9990 chunk 447 optimal weight: 7.9990 chunk 408 optimal weight: 30.0000 chunk 250 optimal weight: 10.0000 chunk 295 optimal weight: 7.9990 chunk 338 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 223 GLN ** G 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 137 GLN ** N 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 249 GLN ** O 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 174 GLN ** V 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 194 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.123774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.101602 restraints weight = 68732.698| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 3.05 r_work: 0.3221 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6788 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 45452 Z= 0.200 Angle : 0.573 8.773 61435 Z= 0.295 Chirality : 0.043 0.158 7161 Planarity : 0.003 0.023 8030 Dihedral : 4.238 54.165 6260 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 4.97 % Allowed : 32.85 % Favored : 62.18 % 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: 0.38 (0.11), residues: 5676 helix: 1.28 (0.10), residues: 2992 sheet: -0.51 (0.17), residues: 968 loop : -1.01 (0.15), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 159 TYR 0.015 0.002 TYR D 266 PHE 0.016 0.001 PHE B 198 TRP 0.005 0.001 TRP U 92 HIS 0.002 0.001 HIS J 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.20 (45452) covalent geometry : angle 0.57325 / 0.30 (61435) hydrogen bonds : bond 0.05272 / 3.59 ( 2660) hydrogen bonds : angle 4.85695 / 3.50 ( 7800) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11352 Ramachandran restraints generated. 5676 Oldfield, 0 Emsley, 5676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11352 Ramachandran restraints generated. 5676 Oldfield, 0 Emsley, 5676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 844 residues out of total 4730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 235 poor density : 609 time to evaluate : 1.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 199 ILE cc_start: 0.6893 (OUTLIER) cc_final: 0.6649 (tp) REVERT: C 87 MET cc_start: 0.7791 (ptt) cc_final: 0.7217 (ttm) REVERT: C 125 GLU cc_start: 0.8241 (tm-30) cc_final: 0.7738 (tm-30) REVERT: C 217 GLU cc_start: 0.8126 (tp30) cc_final: 0.7863 (tp30) REVERT: D 249 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7475 (tp30) REVERT: D 269 LEU cc_start: 0.6713 (OUTLIER) cc_final: 0.6391 (tt) REVERT: E 94 GLU cc_start: 0.7323 (pt0) cc_final: 0.7074 (pt0) REVERT: E 119 MET cc_start: 0.7711 (ttt) cc_final: 0.7127 (tmm) REVERT: E 137 GLN cc_start: 0.7240 (tm-30) cc_final: 0.6841 (tm-30) REVERT: E 148 GLU cc_start: 0.8429 (mm-30) cc_final: 0.7878 (tt0) REVERT: F 134 TYR cc_start: 0.7529 (m-80) cc_final: 0.7245 (m-80) REVERT: G 217 GLU cc_start: 0.8019 (tp30) cc_final: 0.7343 (tp30) REVERT: H 70 LYS cc_start: 0.7940 (mtpt) cc_final: 0.7595 (mtpt) REVERT: H 118 GLN cc_start: 0.7781 (OUTLIER) cc_final: 0.7159 (tp40) REVERT: H 137 GLN cc_start: 0.7412 (tm-30) cc_final: 0.7060 (tm-30) REVERT: H 154 ILE cc_start: 0.7479 (tt) cc_final: 0.7274 (tt) REVERT: I 70 LYS cc_start: 0.7787 (mtpt) cc_final: 0.7559 (tttm) REVERT: I 80 ASP cc_start: 0.7462 (p0) cc_final: 0.7148 (p0) REVERT: I 92 TRP cc_start: 0.7902 (t60) cc_final: 0.6924 (t60) REVERT: I 119 MET cc_start: 0.7780 (ttp) cc_final: 0.7262 (tmm) REVERT: I 137 GLN cc_start: 0.7021 (tm-30) cc_final: 0.6588 (tm-30) REVERT: I 144 LEU cc_start: 0.6631 (OUTLIER) cc_final: 0.6379 (mp) REVERT: I 186 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.6994 (tt) REVERT: J 113 ASP cc_start: 0.7541 (p0) cc_final: 0.7278 (p0) REVERT: J 199 ILE cc_start: 0.6935 (OUTLIER) cc_final: 0.6660 (tp) REVERT: K 173 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7593 (tt) REVERT: K 199 ILE cc_start: 0.6790 (OUTLIER) cc_final: 0.6538 (tp) REVERT: L 70 LYS cc_start: 0.7638 (mtpt) cc_final: 0.7310 (mtpt) REVERT: L 118 GLN cc_start: 0.7610 (OUTLIER) cc_final: 0.7273 (mt0) REVERT: L 119 MET cc_start: 0.7556 (OUTLIER) cc_final: 0.6836 (tmm) REVERT: L 144 LEU cc_start: 0.6499 (OUTLIER) cc_final: 0.6241 (mp) REVERT: M 137 GLN cc_start: 0.7262 (tm-30) cc_final: 0.6789 (tm-30) REVERT: M 144 LEU cc_start: 0.6605 (OUTLIER) cc_final: 0.6329 (mp) REVERT: M 148 GLU cc_start: 0.8656 (mm-30) cc_final: 0.8318 (mm-30) REVERT: M 154 ILE cc_start: 0.7531 (tt) cc_final: 0.7308 (tt) REVERT: M 273 GLU cc_start: 0.7294 (tm-30) cc_final: 0.6749 (tm-30) REVERT: N 113 ASP cc_start: 0.7870 (p0) cc_final: 0.7577 (p0) REVERT: N 199 ILE cc_start: 0.6601 (OUTLIER) cc_final: 0.6371 (tp) REVERT: O 125 GLU cc_start: 0.8124 (tm-30) cc_final: 0.7725 (tm-30) REVERT: O 199 ILE cc_start: 0.6340 (OUTLIER) cc_final: 0.6089 (tp) REVERT: P 137 GLN cc_start: 0.7632 (tp-100) cc_final: 0.7186 (tm-30) REVERT: P 144 LEU cc_start: 0.6718 (OUTLIER) cc_final: 0.6406 (mp) REVERT: P 163 VAL cc_start: 0.6952 (OUTLIER) cc_final: 0.6729 (p) REVERT: Q 70 LYS cc_start: 0.8089 (tttp) cc_final: 0.7883 (mtpt) REVERT: Q 163 VAL cc_start: 0.7036 (OUTLIER) cc_final: 0.6783 (p) REVERT: R 24 GLN cc_start: 0.6543 (mm110) cc_final: 0.6081 (mt0) REVERT: R 67 PHE cc_start: 0.6070 (OUTLIER) cc_final: 0.5596 (m-10) REVERT: R 100 VAL cc_start: 0.8399 (OUTLIER) cc_final: 0.8183 (p) REVERT: R 199 ILE cc_start: 0.6723 (OUTLIER) cc_final: 0.6462 (tp) REVERT: S 68 ASP cc_start: 0.7612 (t0) cc_final: 0.6977 (t0) REVERT: S 70 ARG cc_start: 0.7960 (mtt180) cc_final: 0.7246 (ptp-170) REVERT: S 125 GLU cc_start: 0.7820 (tm-30) cc_final: 0.7112 (tm-30) REVERT: S 217 GLU cc_start: 0.8292 (tp30) cc_final: 0.7918 (tp30) REVERT: T 79 LYS cc_start: 0.8584 (mmtt) cc_final: 0.8253 (mtmt) REVERT: T 186 LEU cc_start: 0.7210 (OUTLIER) cc_final: 0.6794 (tt) REVERT: T 273 GLU cc_start: 0.7393 (tm-30) cc_final: 0.7155 (tm-30) REVERT: T 276 ARG cc_start: 0.7232 (mtp180) cc_final: 0.6912 (mtp180) REVERT: T 288 ASN cc_start: 0.8052 (m-40) cc_final: 0.7649 (m-40) REVERT: U 119 MET cc_start: 0.7820 (ttp) cc_final: 0.6990 (tmm) REVERT: V 113 ASP cc_start: 0.7720 (p0) cc_final: 0.7373 (p0) REVERT: W 119 MET cc_start: 0.8020 (ttp) cc_final: 0.7506 (tmm) outliers start: 235 outliers final: 150 residues processed: 812 average time/residue: 0.2220 time to fit residues: 308.7553 Evaluate side-chains 760 residues out of total 4730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 588 time to evaluate : 1.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 249 GLU Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 305 GLN Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 250 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 76 ILE Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 211 VAL Chi-restraints excluded: chain G residue 242 GLU Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 89 MET Chi-restraints excluded: chain H residue 118 GLN Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain H residue 208 SER Chi-restraints excluded: chain H residue 243 VAL Chi-restraints excluded: chain H residue 256 ILE Chi-restraints excluded: chain H residue 281 LEU Chi-restraints excluded: chain I residue 89 MET Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain I residue 118 GLN Chi-restraints excluded: chain I residue 135 LEU Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain I residue 153 SER Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain I residue 208 SER Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 242 THR Chi-restraints excluded: chain I residue 243 VAL Chi-restraints excluded: chain I residue 256 ILE Chi-restraints excluded: chain I residue 269 LEU Chi-restraints excluded: chain I residue 281 LEU Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain J residue 88 VAL Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 106 ILE Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain J residue 199 ILE Chi-restraints excluded: chain J residue 206 GLU Chi-restraints excluded: chain J residue 211 VAL Chi-restraints excluded: chain J residue 250 THR Chi-restraints excluded: chain K residue 23 LEU Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 126 VAL Chi-restraints excluded: chain K residue 163 ILE Chi-restraints excluded: chain K residue 165 LEU Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain K residue 199 ILE Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 118 GLN Chi-restraints excluded: chain L residue 119 MET Chi-restraints excluded: chain L residue 133 GLN Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 153 SER Chi-restraints excluded: chain L residue 186 LEU Chi-restraints excluded: chain L residue 208 SER Chi-restraints excluded: chain L residue 256 ILE Chi-restraints excluded: chain L residue 281 LEU Chi-restraints excluded: chain M residue 135 LEU Chi-restraints excluded: chain M residue 144 LEU Chi-restraints excluded: chain M residue 153 SER Chi-restraints excluded: chain M residue 256 ILE Chi-restraints excluded: chain M residue 269 LEU Chi-restraints excluded: chain M residue 278 ILE Chi-restraints excluded: chain M residue 281 LEU Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 88 VAL Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 169 SER Chi-restraints excluded: chain N residue 199 ILE Chi-restraints excluded: chain N residue 211 VAL Chi-restraints excluded: chain O residue 67 PHE Chi-restraints excluded: chain O residue 88 VAL Chi-restraints excluded: chain O residue 91 THR Chi-restraints excluded: chain O residue 153 ASP Chi-restraints excluded: chain O residue 163 ILE Chi-restraints excluded: chain O residue 199 ILE Chi-restraints excluded: chain O residue 211 VAL Chi-restraints excluded: chain O residue 242 GLU Chi-restraints excluded: chain P residue 118 GLN Chi-restraints excluded: chain P residue 135 LEU Chi-restraints excluded: chain P residue 144 LEU Chi-restraints excluded: chain P residue 153 SER Chi-restraints excluded: chain P residue 163 VAL Chi-restraints excluded: chain P residue 186 LEU Chi-restraints excluded: chain P residue 208 SER Chi-restraints excluded: chain P residue 215 VAL Chi-restraints excluded: chain Q residue 108 VAL Chi-restraints excluded: chain Q residue 135 LEU Chi-restraints excluded: chain Q residue 163 VAL Chi-restraints excluded: chain Q residue 208 SER Chi-restraints excluded: chain R residue 23 LEU Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 67 PHE Chi-restraints excluded: chain R residue 91 THR Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 106 ILE Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 169 SER Chi-restraints excluded: chain R residue 199 ILE Chi-restraints excluded: chain R residue 211 VAL Chi-restraints excluded: chain S residue 22 LEU Chi-restraints excluded: chain S residue 23 LEU Chi-restraints excluded: chain S residue 88 VAL Chi-restraints excluded: chain S residue 165 LEU Chi-restraints excluded: chain S residue 200 VAL Chi-restraints excluded: chain S residue 211 VAL Chi-restraints excluded: chain S residue 251 LEU Chi-restraints excluded: chain T residue 135 LEU Chi-restraints excluded: chain T residue 153 SER Chi-restraints excluded: chain T residue 186 LEU Chi-restraints excluded: chain T residue 208 SER Chi-restraints excluded: chain T residue 305 GLN Chi-restraints excluded: chain U residue 118 GLN Chi-restraints excluded: chain U residue 135 LEU Chi-restraints excluded: chain U residue 186 LEU Chi-restraints excluded: chain U residue 208 SER Chi-restraints excluded: chain U residue 243 VAL Chi-restraints excluded: chain U residue 269 LEU Chi-restraints excluded: chain U residue 281 LEU Chi-restraints excluded: chain V residue 76 ILE Chi-restraints excluded: chain V residue 88 VAL Chi-restraints excluded: chain V residue 91 THR Chi-restraints excluded: chain V residue 106 ILE Chi-restraints excluded: chain V residue 153 ASP Chi-restraints excluded: chain V residue 163 ILE Chi-restraints excluded: chain V residue 206 GLU Chi-restraints excluded: chain V residue 211 VAL Chi-restraints excluded: chain W residue 153 SER Chi-restraints excluded: chain W residue 243 VAL Chi-restraints excluded: chain W residue 281 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 561 random chunks: chunk 509 optimal weight: 2.9990 chunk 360 optimal weight: 8.9990 chunk 219 optimal weight: 2.9990 chunk 473 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 436 optimal weight: 2.9990 chunk 143 optimal weight: 5.9990 chunk 240 optimal weight: 5.9990 chunk 482 optimal weight: 8.9990 chunk 284 optimal weight: 5.9990 chunk 161 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 137 GLN ** N 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 109 ASN S 162 ASN T 174 GLN T 288 ASN ** V 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 194 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.124552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.102438 restraints weight = 68494.620| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 3.03 r_work: 0.3217 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 45452 Z= 0.173 Angle : 0.547 9.109 61435 Z= 0.281 Chirality : 0.042 0.149 7161 Planarity : 0.003 0.032 8030 Dihedral : 4.230 59.552 6260 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 4.61 % Allowed : 33.81 % Favored : 61.59 % 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: 0.40 (0.11), residues: 5676 helix: 1.36 (0.10), residues: 2926 sheet: -0.55 (0.17), residues: 968 loop : -1.02 (0.15), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 140 TYR 0.016 0.002 TYR V 107 PHE 0.013 0.001 PHE S 198 TRP 0.003 0.000 TRP U 92 HIS 0.003 0.000 HIS J 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 (45452) covalent geometry : angle 0.54652 / 0.28 (61435) hydrogen bonds : bond 0.05080 / 3.46 ( 2660) hydrogen bonds : angle 4.77435 / 3.44 ( 7800) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11352 Ramachandran restraints generated. 5676 Oldfield, 0 Emsley, 5676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11352 Ramachandran restraints generated. 5676 Oldfield, 0 Emsley, 5676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 830 residues out of total 4730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 218 poor density : 612 time to evaluate : 1.828 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 87 MET cc_start: 0.7812 (ptt) cc_final: 0.7232 (ttm) REVERT: C 125 GLU cc_start: 0.8268 (tm-30) cc_final: 0.7796 (tm-30) REVERT: C 162 ASN cc_start: 0.8175 (m-40) cc_final: 0.7713 (t0) REVERT: C 217 GLU cc_start: 0.8201 (tp30) cc_final: 0.7936 (tp30) REVERT: D 269 LEU cc_start: 0.6750 (OUTLIER) cc_final: 0.6423 (tt) REVERT: E 70 LYS cc_start: 0.7953 (mtpt) cc_final: 0.7743 (tttm) REVERT: E 94 GLU cc_start: 0.7351 (pt0) cc_final: 0.7011 (pt0) REVERT: E 102 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7845 (ptp-170) REVERT: E 119 MET cc_start: 0.7720 (ttt) cc_final: 0.7165 (tmm) REVERT: E 137 GLN cc_start: 0.7301 (tm-30) cc_final: 0.6851 (tm-30) REVERT: F 134 TYR cc_start: 0.7607 (m-80) cc_final: 0.7158 (m-10) REVERT: G 217 GLU cc_start: 0.8034 (tp30) cc_final: 0.7368 (tp30) REVERT: H 70 LYS cc_start: 0.8062 (mtpt) cc_final: 0.7820 (mtpt) REVERT: H 137 GLN cc_start: 0.7443 (tm-30) cc_final: 0.7060 (tm-30) REVERT: H 186 LEU cc_start: 0.7388 (OUTLIER) cc_final: 0.6947 (tt) REVERT: I 70 LYS cc_start: 0.7901 (mtpt) cc_final: 0.7678 (mtpt) REVERT: I 80 ASP cc_start: 0.7524 (p0) cc_final: 0.7210 (p0) REVERT: I 92 TRP cc_start: 0.7966 (t60) cc_final: 0.7050 (t60) REVERT: I 119 MET cc_start: 0.7776 (ttp) cc_final: 0.7296 (tmm) REVERT: I 137 GLN cc_start: 0.7109 (tm-30) cc_final: 0.6652 (tm-30) REVERT: I 144 LEU cc_start: 0.6787 (OUTLIER) cc_final: 0.6488 (mp) REVERT: I 186 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.7096 (tt) REVERT: J 113 ASP cc_start: 0.7627 (p0) cc_final: 0.7386 (p0) REVERT: J 199 ILE cc_start: 0.7049 (OUTLIER) cc_final: 0.6780 (tp) REVERT: K 173 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7687 (tt) REVERT: K 199 ILE cc_start: 0.6867 (OUTLIER) cc_final: 0.6615 (tp) REVERT: L 46 MET cc_start: 0.3308 (mmp) cc_final: 0.3074 (mmm) REVERT: L 70 LYS cc_start: 0.7708 (mtpt) cc_final: 0.7425 (mtpt) REVERT: L 118 GLN cc_start: 0.7544 (OUTLIER) cc_final: 0.7214 (mt0) REVERT: L 119 MET cc_start: 0.7607 (OUTLIER) cc_final: 0.6954 (tmm) REVERT: L 144 LEU cc_start: 0.6585 (OUTLIER) cc_final: 0.6357 (mp) REVERT: M 137 GLN cc_start: 0.7344 (tm-30) cc_final: 0.6854 (tm-30) REVERT: M 144 LEU cc_start: 0.6674 (OUTLIER) cc_final: 0.6397 (mp) REVERT: M 148 GLU cc_start: 0.8679 (mm-30) cc_final: 0.8327 (mm-30) REVERT: M 154 ILE cc_start: 0.7675 (tt) cc_final: 0.7353 (tt) REVERT: M 273 GLU cc_start: 0.7387 (tm-30) cc_final: 0.6817 (tm-30) REVERT: N 113 ASP cc_start: 0.7941 (p0) cc_final: 0.7665 (p0) REVERT: N 162 ASN cc_start: 0.7487 (OUTLIER) cc_final: 0.6954 (t0) REVERT: N 199 ILE cc_start: 0.6620 (OUTLIER) cc_final: 0.6396 (tp) REVERT: O 125 GLU cc_start: 0.8119 (tm-30) cc_final: 0.7709 (tm-30) REVERT: O 199 ILE cc_start: 0.6444 (OUTLIER) cc_final: 0.6197 (tp) REVERT: P 137 GLN cc_start: 0.7687 (tp-100) cc_final: 0.7234 (tm-30) REVERT: P 163 VAL cc_start: 0.7005 (OUTLIER) cc_final: 0.6765 (p) REVERT: P 269 LEU cc_start: 0.7235 (OUTLIER) cc_final: 0.6970 (tt) REVERT: Q 163 VAL cc_start: 0.7134 (OUTLIER) cc_final: 0.6887 (p) REVERT: R 24 GLN cc_start: 0.6487 (mm110) cc_final: 0.6027 (mt0) REVERT: R 67 PHE cc_start: 0.6152 (OUTLIER) cc_final: 0.5651 (m-10) REVERT: R 199 ILE cc_start: 0.6757 (OUTLIER) cc_final: 0.6482 (tp) REVERT: S 68 ASP cc_start: 0.7645 (t0) cc_final: 0.7150 (t0) REVERT: S 70 ARG cc_start: 0.8038 (mtt180) cc_final: 0.7537 (ptp-170) REVERT: S 125 GLU cc_start: 0.7860 (tm-30) cc_final: 0.7191 (tm-30) REVERT: S 217 GLU cc_start: 0.8314 (tp30) cc_final: 0.7964 (tp30) REVERT: T 79 LYS cc_start: 0.8651 (mmtt) cc_final: 0.8286 (mtmt) REVERT: T 186 LEU cc_start: 0.7298 (OUTLIER) cc_final: 0.6872 (tt) REVERT: T 273 GLU cc_start: 0.7466 (tm-30) cc_final: 0.7171 (tm-30) REVERT: T 276 ARG cc_start: 0.7280 (mtp180) cc_final: 0.6944 (mtp180) REVERT: T 288 ASN cc_start: 0.8087 (m-40) cc_final: 0.7555 (m-40) REVERT: U 95 THR cc_start: 0.7937 (p) cc_final: 0.7736 (p) REVERT: U 119 MET cc_start: 0.7877 (ttp) cc_final: 0.7060 (tmm) REVERT: V 113 ASP cc_start: 0.7823 (p0) cc_final: 0.7485 (p0) REVERT: W 119 MET cc_start: 0.8040 (ttp) cc_final: 0.7572 (tmm) outliers start: 218 outliers final: 149 residues processed: 802 average time/residue: 0.2130 time to fit residues: 292.1805 Evaluate side-chains 762 residues out of total 4730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 592 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain E residue 102 ARG Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 250 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 76 ILE Chi-restraints excluded: chain G residue 87 MET Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 242 GLU Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 118 GLN Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 208 SER Chi-restraints excluded: chain H residue 256 ILE Chi-restraints excluded: chain H residue 281 LEU Chi-restraints excluded: chain I residue 89 MET Chi-restraints excluded: chain I residue 118 GLN Chi-restraints excluded: chain I residue 135 LEU Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain I residue 153 SER Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain I residue 205 LEU Chi-restraints excluded: chain I residue 208 SER Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 243 VAL Chi-restraints excluded: chain I residue 256 ILE Chi-restraints excluded: chain I residue 269 LEU Chi-restraints excluded: chain I residue 281 LEU Chi-restraints excluded: chain J residue 23 LEU Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain J residue 87 MET Chi-restraints excluded: chain J residue 88 VAL Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 106 ILE Chi-restraints excluded: chain J residue 199 ILE Chi-restraints excluded: chain J residue 250 THR Chi-restraints excluded: chain K residue 23 LEU Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 126 VAL Chi-restraints excluded: chain K residue 163 ILE Chi-restraints excluded: chain K residue 165 LEU Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain K residue 199 ILE Chi-restraints excluded: chain K residue 200 VAL Chi-restraints excluded: chain K residue 242 GLU Chi-restraints excluded: chain K residue 250 THR Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 118 GLN Chi-restraints excluded: chain L residue 119 MET Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 133 GLN Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 153 SER Chi-restraints excluded: chain L residue 186 LEU Chi-restraints excluded: chain L residue 208 SER Chi-restraints excluded: chain L residue 256 ILE Chi-restraints excluded: chain L residue 281 LEU Chi-restraints excluded: chain M residue 135 LEU Chi-restraints excluded: chain M residue 144 LEU Chi-restraints excluded: chain M residue 153 SER Chi-restraints excluded: chain M residue 208 SER Chi-restraints excluded: chain M residue 256 ILE Chi-restraints excluded: chain M residue 269 LEU Chi-restraints excluded: chain M residue 281 LEU Chi-restraints excluded: chain M residue 305 GLN Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 88 VAL Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 162 ASN Chi-restraints excluded: chain N residue 169 SER Chi-restraints excluded: chain N residue 199 ILE Chi-restraints excluded: chain O residue 23 LEU Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 88 VAL Chi-restraints excluded: chain O residue 91 THR Chi-restraints excluded: chain O residue 153 ASP Chi-restraints excluded: chain O residue 163 ILE Chi-restraints excluded: chain O residue 199 ILE Chi-restraints excluded: chain O residue 242 GLU Chi-restraints excluded: chain P residue 112 THR Chi-restraints excluded: chain P residue 118 GLN Chi-restraints excluded: chain P residue 135 LEU Chi-restraints excluded: chain P residue 153 SER Chi-restraints excluded: chain P residue 163 VAL Chi-restraints excluded: chain P residue 186 LEU Chi-restraints excluded: chain P residue 208 SER Chi-restraints excluded: chain P residue 215 VAL Chi-restraints excluded: chain P residue 269 LEU Chi-restraints excluded: chain Q residue 108 VAL Chi-restraints excluded: chain Q residue 135 LEU Chi-restraints excluded: chain Q residue 163 VAL Chi-restraints excluded: chain Q residue 208 SER Chi-restraints excluded: chain Q residue 281 LEU Chi-restraints excluded: chain R residue 23 LEU Chi-restraints excluded: chain R residue 26 SER Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 67 PHE Chi-restraints excluded: chain R residue 91 THR Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 199 ILE Chi-restraints excluded: chain S residue 22 LEU Chi-restraints excluded: chain S residue 23 LEU Chi-restraints excluded: chain S residue 88 VAL Chi-restraints excluded: chain S residue 165 LEU Chi-restraints excluded: chain S residue 251 LEU Chi-restraints excluded: chain T residue 135 LEU Chi-restraints excluded: chain T residue 153 SER Chi-restraints excluded: chain T residue 186 LEU Chi-restraints excluded: chain T residue 208 SER Chi-restraints excluded: chain T residue 243 VAL Chi-restraints excluded: chain T residue 269 LEU Chi-restraints excluded: chain U residue 118 GLN Chi-restraints excluded: chain U residue 135 LEU Chi-restraints excluded: chain U residue 186 LEU Chi-restraints excluded: chain U residue 208 SER Chi-restraints excluded: chain U residue 242 THR Chi-restraints excluded: chain U residue 269 LEU Chi-restraints excluded: chain U residue 281 LEU Chi-restraints excluded: chain V residue 76 ILE Chi-restraints excluded: chain V residue 88 VAL Chi-restraints excluded: chain V residue 91 THR Chi-restraints excluded: chain V residue 106 ILE Chi-restraints excluded: chain V residue 153 ASP Chi-restraints excluded: chain V residue 163 ILE Chi-restraints excluded: chain V residue 200 VAL Chi-restraints excluded: chain V residue 206 GLU Chi-restraints excluded: chain W residue 153 SER Chi-restraints excluded: chain W residue 256 ILE Chi-restraints excluded: chain W residue 281 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 561 random chunks: chunk 19 optimal weight: 0.7980 chunk 31 optimal weight: 7.9990 chunk 250 optimal weight: 7.9990 chunk 183 optimal weight: 5.9990 chunk 353 optimal weight: 7.9990 chunk 243 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 315 optimal weight: 5.9990 chunk 366 optimal weight: 5.9990 chunk 556 optimal weight: 7.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 109 ASN ** V 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 194 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.124776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.102632 restraints weight = 67927.353| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 3.02 r_work: 0.3234 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6782 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 45452 Z= 0.164 Angle : 0.542 9.232 61435 Z= 0.277 Chirality : 0.042 0.150 7161 Planarity : 0.003 0.034 8030 Dihedral : 4.212 51.078 6260 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 4.93 % Allowed : 33.42 % Favored : 61.65 % 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: 0.40 (0.11), residues: 5676 helix: 1.38 (0.10), residues: 2926 sheet: -0.59 (0.17), residues: 968 loop : -1.04 (0.15), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 140 TYR 0.013 0.002 TYR W 139 PHE 0.013 0.001 PHE S 198 TRP 0.006 0.000 TRP W 92 HIS 0.003 0.000 HIS J 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 (45452) covalent geometry : angle 0.54239 / 0.28 (61435) hydrogen bonds : bond 0.04995 / 3.40 ( 2660) hydrogen bonds : angle 4.72063 / 3.40 ( 7800) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11352 Ramachandran restraints generated. 5676 Oldfield, 0 Emsley, 5676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11352 Ramachandran restraints generated. 5676 Oldfield, 0 Emsley, 5676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 833 residues out of total 4730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 233 poor density : 600 time to evaluate : 1.231 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 199 ILE cc_start: 0.6897 (OUTLIER) cc_final: 0.6656 (tp) REVERT: C 87 MET cc_start: 0.7768 (ptt) cc_final: 0.7173 (ttm) REVERT: C 125 GLU cc_start: 0.8256 (tm-30) cc_final: 0.7769 (tm-30) REVERT: C 217 GLU cc_start: 0.8162 (tp30) cc_final: 0.7878 (tp30) REVERT: D 269 LEU cc_start: 0.6654 (OUTLIER) cc_final: 0.6336 (tt) REVERT: E 70 LYS cc_start: 0.7937 (mtpt) cc_final: 0.7709 (tttm) REVERT: E 102 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7779 (ptp-170) REVERT: E 119 MET cc_start: 0.7756 (ttt) cc_final: 0.7177 (tmm) REVERT: E 137 GLN cc_start: 0.7261 (tm-30) cc_final: 0.6842 (tm-30) REVERT: F 134 TYR cc_start: 0.7527 (m-80) cc_final: 0.7061 (m-10) REVERT: G 199 ILE cc_start: 0.6774 (OUTLIER) cc_final: 0.6534 (tp) REVERT: G 217 GLU cc_start: 0.8011 (tp30) cc_final: 0.7341 (tp30) REVERT: G 219 GLU cc_start: 0.7028 (tp30) cc_final: 0.6652 (tp30) REVERT: H 137 GLN cc_start: 0.7371 (tm-30) cc_final: 0.6993 (tm-30) REVERT: H 186 LEU cc_start: 0.7320 (OUTLIER) cc_final: 0.6932 (tt) REVERT: H 231 ILE cc_start: 0.6296 (OUTLIER) cc_final: 0.5923 (tp) REVERT: I 80 ASP cc_start: 0.7504 (p0) cc_final: 0.7146 (p0) REVERT: I 92 TRP cc_start: 0.7848 (t60) cc_final: 0.6905 (t60) REVERT: I 119 MET cc_start: 0.7899 (ttp) cc_final: 0.7405 (tmm) REVERT: I 137 GLN cc_start: 0.7032 (tm-30) cc_final: 0.6593 (tm-30) REVERT: I 144 LEU cc_start: 0.6674 (OUTLIER) cc_final: 0.6434 (mp) REVERT: I 186 LEU cc_start: 0.7427 (OUTLIER) cc_final: 0.7021 (tt) REVERT: J 113 ASP cc_start: 0.7523 (p0) cc_final: 0.7291 (p0) REVERT: J 199 ILE cc_start: 0.6949 (OUTLIER) cc_final: 0.6680 (tp) REVERT: K 173 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7651 (tt) REVERT: K 199 ILE cc_start: 0.6773 (OUTLIER) cc_final: 0.6534 (tp) REVERT: L 70 LYS cc_start: 0.7659 (mtpt) cc_final: 0.7249 (mtpt) REVERT: L 118 GLN cc_start: 0.7500 (OUTLIER) cc_final: 0.7170 (mt0) REVERT: L 119 MET cc_start: 0.7574 (OUTLIER) cc_final: 0.6900 (tmm) REVERT: M 137 GLN cc_start: 0.7268 (tm-30) cc_final: 0.6771 (tm-30) REVERT: M 144 LEU cc_start: 0.6479 (OUTLIER) cc_final: 0.6203 (mp) REVERT: M 148 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8311 (mm-30) REVERT: M 154 ILE cc_start: 0.7627 (tt) cc_final: 0.7310 (tt) REVERT: N 113 ASP cc_start: 0.7712 (p0) cc_final: 0.7437 (p0) REVERT: N 162 ASN cc_start: 0.7490 (OUTLIER) cc_final: 0.6943 (t0) REVERT: N 199 ILE cc_start: 0.6560 (OUTLIER) cc_final: 0.6346 (tp) REVERT: O 113 ASP cc_start: 0.7344 (p0) cc_final: 0.7028 (p0) REVERT: O 125 GLU cc_start: 0.8041 (tm-30) cc_final: 0.7635 (tm-30) REVERT: O 199 ILE cc_start: 0.6363 (OUTLIER) cc_final: 0.6126 (tp) REVERT: P 46 MET cc_start: 0.2747 (mmt) cc_final: 0.2506 (mmm) REVERT: P 137 GLN cc_start: 0.7665 (tp-100) cc_final: 0.7191 (tm-30) REVERT: P 144 LEU cc_start: 0.6653 (OUTLIER) cc_final: 0.6341 (mp) REVERT: P 163 VAL cc_start: 0.6882 (OUTLIER) cc_final: 0.6651 (p) REVERT: P 269 LEU cc_start: 0.7151 (OUTLIER) cc_final: 0.6896 (tt) REVERT: Q 46 MET cc_start: 0.4379 (mmm) cc_final: 0.4022 (mmp) REVERT: Q 163 VAL cc_start: 0.7005 (OUTLIER) cc_final: 0.6772 (p) REVERT: Q 269 LEU cc_start: 0.6980 (OUTLIER) cc_final: 0.6769 (tt) REVERT: R 24 GLN cc_start: 0.6476 (mm110) cc_final: 0.6028 (mt0) REVERT: R 67 PHE cc_start: 0.6000 (OUTLIER) cc_final: 0.5511 (m-10) REVERT: R 199 ILE cc_start: 0.6701 (OUTLIER) cc_final: 0.6453 (tp) REVERT: S 68 ASP cc_start: 0.7601 (t0) cc_final: 0.7093 (t0) REVERT: S 70 ARG cc_start: 0.7965 (mtt180) cc_final: 0.7450 (ptp-170) REVERT: S 125 GLU cc_start: 0.7800 (tm-30) cc_final: 0.7123 (tm-30) REVERT: S 217 GLU cc_start: 0.8280 (tp30) cc_final: 0.7904 (tp30) REVERT: T 79 LYS cc_start: 0.8621 (mmtt) cc_final: 0.8272 (mtmt) REVERT: T 144 LEU cc_start: 0.6330 (OUTLIER) cc_final: 0.6071 (mp) REVERT: T 186 LEU cc_start: 0.7217 (OUTLIER) cc_final: 0.6802 (tt) REVERT: T 273 GLU cc_start: 0.7407 (tm-30) cc_final: 0.7093 (tm-30) REVERT: T 276 ARG cc_start: 0.7217 (mtp180) cc_final: 0.6885 (mtp180) REVERT: T 288 ASN cc_start: 0.8123 (m-40) cc_final: 0.7588 (m-40) REVERT: U 119 MET cc_start: 0.7804 (ttp) cc_final: 0.6971 (tmm) REVERT: V 113 ASP cc_start: 0.7804 (p0) cc_final: 0.7460 (p0) REVERT: W 119 MET cc_start: 0.8043 (ttp) cc_final: 0.7560 (tmm) outliers start: 233 outliers final: 168 residues processed: 801 average time/residue: 0.1942 time to fit residues: 268.2836 Evaluate side-chains 778 residues out of total 4730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 194 poor density : 584 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain E residue 102 ARG Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 250 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 76 ILE Chi-restraints excluded: chain G residue 87 MET Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 242 GLU Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 89 MET Chi-restraints excluded: chain H residue 118 GLN Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 208 SER Chi-restraints excluded: chain H residue 231 ILE Chi-restraints excluded: chain H residue 256 ILE Chi-restraints excluded: chain H residue 281 LEU Chi-restraints excluded: chain I residue 89 MET Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain I residue 118 GLN Chi-restraints excluded: chain I residue 135 LEU Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain I residue 153 SER Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain I residue 205 LEU Chi-restraints excluded: chain I residue 208 SER Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 243 VAL Chi-restraints excluded: chain I residue 256 ILE Chi-restraints excluded: chain I residue 269 LEU Chi-restraints excluded: chain I residue 281 LEU Chi-restraints excluded: chain J residue 23 LEU Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain J residue 87 MET Chi-restraints excluded: chain J residue 88 VAL Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 106 ILE Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain J residue 199 ILE Chi-restraints excluded: chain J residue 211 VAL Chi-restraints excluded: chain J residue 250 THR Chi-restraints excluded: chain K residue 23 LEU Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 126 VAL Chi-restraints excluded: chain K residue 163 ILE Chi-restraints excluded: chain K residue 165 LEU Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain K residue 199 ILE Chi-restraints excluded: chain K residue 200 VAL Chi-restraints excluded: chain K residue 242 GLU Chi-restraints excluded: chain K residue 250 THR Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 118 GLN Chi-restraints excluded: chain L residue 119 MET Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 133 GLN Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 153 SER Chi-restraints excluded: chain L residue 186 LEU Chi-restraints excluded: chain L residue 208 SER Chi-restraints excluded: chain L residue 256 ILE Chi-restraints excluded: chain L residue 281 LEU Chi-restraints excluded: chain M residue 89 MET Chi-restraints excluded: chain M residue 135 LEU Chi-restraints excluded: chain M residue 144 LEU Chi-restraints excluded: chain M residue 153 SER Chi-restraints excluded: chain M residue 208 SER Chi-restraints excluded: chain M residue 269 LEU Chi-restraints excluded: chain M residue 278 ILE Chi-restraints excluded: chain M residue 281 LEU Chi-restraints excluded: chain M residue 305 GLN Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 88 VAL Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 154 LEU Chi-restraints excluded: chain N residue 162 ASN Chi-restraints excluded: chain N residue 163 ILE Chi-restraints excluded: chain N residue 169 SER Chi-restraints excluded: chain N residue 199 ILE Chi-restraints excluded: chain N residue 211 VAL Chi-restraints excluded: chain O residue 23 LEU Chi-restraints excluded: chain O residue 88 VAL Chi-restraints excluded: chain O residue 91 THR Chi-restraints excluded: chain O residue 153 ASP Chi-restraints excluded: chain O residue 163 ILE Chi-restraints excluded: chain O residue 199 ILE Chi-restraints excluded: chain O residue 242 GLU Chi-restraints excluded: chain P residue 118 GLN Chi-restraints excluded: chain P residue 135 LEU Chi-restraints excluded: chain P residue 144 LEU Chi-restraints excluded: chain P residue 153 SER Chi-restraints excluded: chain P residue 163 VAL Chi-restraints excluded: chain P residue 186 LEU Chi-restraints excluded: chain P residue 208 SER Chi-restraints excluded: chain P residue 215 VAL Chi-restraints excluded: chain P residue 243 VAL Chi-restraints excluded: chain P residue 269 LEU Chi-restraints excluded: chain Q residue 108 VAL Chi-restraints excluded: chain Q residue 135 LEU Chi-restraints excluded: chain Q residue 163 VAL Chi-restraints excluded: chain Q residue 208 SER Chi-restraints excluded: chain Q residue 269 LEU Chi-restraints excluded: chain Q residue 281 LEU Chi-restraints excluded: chain R residue 23 LEU Chi-restraints excluded: chain R residue 26 SER Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 67 PHE Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 91 THR Chi-restraints excluded: chain R residue 109 ASN Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 169 SER Chi-restraints excluded: chain R residue 199 ILE Chi-restraints excluded: chain S residue 22 LEU Chi-restraints excluded: chain S residue 23 LEU Chi-restraints excluded: chain S residue 88 VAL Chi-restraints excluded: chain S residue 127 LEU Chi-restraints excluded: chain S residue 165 LEU Chi-restraints excluded: chain S residue 200 VAL Chi-restraints excluded: chain S residue 251 LEU Chi-restraints excluded: chain T residue 135 LEU Chi-restraints excluded: chain T residue 144 LEU Chi-restraints excluded: chain T residue 153 SER Chi-restraints excluded: chain T residue 186 LEU Chi-restraints excluded: chain T residue 205 LEU Chi-restraints excluded: chain T residue 208 SER Chi-restraints excluded: chain T residue 243 VAL Chi-restraints excluded: chain T residue 269 LEU Chi-restraints excluded: chain U residue 118 GLN Chi-restraints excluded: chain U residue 135 LEU Chi-restraints excluded: chain U residue 186 LEU Chi-restraints excluded: chain U residue 208 SER Chi-restraints excluded: chain U residue 242 THR Chi-restraints excluded: chain U residue 243 VAL Chi-restraints excluded: chain U residue 269 LEU Chi-restraints excluded: chain U residue 281 LEU Chi-restraints excluded: chain V residue 23 LEU Chi-restraints excluded: chain V residue 76 ILE Chi-restraints excluded: chain V residue 88 VAL Chi-restraints excluded: chain V residue 91 THR Chi-restraints excluded: chain V residue 153 ASP Chi-restraints excluded: chain V residue 163 ILE Chi-restraints excluded: chain V residue 200 VAL Chi-restraints excluded: chain V residue 206 GLU Chi-restraints excluded: chain W residue 118 GLN Chi-restraints excluded: chain W residue 153 SER Chi-restraints excluded: chain W residue 243 VAL Chi-restraints excluded: chain W residue 256 ILE Chi-restraints excluded: chain W residue 281 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 561 random chunks: chunk 319 optimal weight: 2.9990 chunk 486 optimal weight: 6.9990 chunk 42 optimal weight: 0.9990 chunk 427 optimal weight: 2.9990 chunk 528 optimal weight: 0.9980 chunk 445 optimal weight: 5.9990 chunk 202 optimal weight: 0.9980 chunk 404 optimal weight: 0.7980 chunk 509 optimal weight: 7.9990 chunk 254 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 ASN ** G 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 109 ASN S 162 ASN ** V 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 194 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.127479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.105227 restraints weight = 67526.519| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 3.03 r_work: 0.3258 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6820 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 45452 Z= 0.123 Angle : 0.516 9.986 61435 Z= 0.262 Chirality : 0.041 0.149 7161 Planarity : 0.003 0.030 8030 Dihedral : 4.095 43.566 6260 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.95 % Allowed : 34.59 % Favored : 61.46 % 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: 5676 helix: 1.58 (0.10), residues: 2860 sheet: -0.61 (0.17), residues: 968 loop : -1.00 (0.15), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 159 TYR 0.013 0.001 TYR W 139 PHE 0.008 0.001 PHE F 198 TRP 0.009 0.001 TRP Q 92 HIS 0.003 0.000 HIS J 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (45452) covalent geometry : angle 0.51635 / 0.26 (61435) hydrogen bonds : bond 0.04646 / 3.16 ( 2660) hydrogen bonds : angle 4.59731 / 3.32 ( 7800) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11352 Ramachandran restraints generated. 5676 Oldfield, 0 Emsley, 5676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11352 Ramachandran restraints generated. 5676 Oldfield, 0 Emsley, 5676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 814 residues out of total 4730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 187 poor density : 627 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 199 ILE cc_start: 0.6984 (OUTLIER) cc_final: 0.6738 (tp) REVERT: C 87 MET cc_start: 0.7770 (ptt) cc_final: 0.7196 (ttm) REVERT: C 113 ASP cc_start: 0.7198 (p0) cc_final: 0.6983 (p0) REVERT: C 162 ASN cc_start: 0.8046 (m-40) cc_final: 0.7606 (t0) REVERT: C 217 GLU cc_start: 0.8100 (tp30) cc_final: 0.7835 (tp30) REVERT: D 70 LYS cc_start: 0.7679 (mtpt) cc_final: 0.7445 (mtpt) REVERT: D 119 MET cc_start: 0.7801 (ttp) cc_final: 0.7429 (tmm) REVERT: D 269 LEU cc_start: 0.6719 (OUTLIER) cc_final: 0.6407 (tt) REVERT: E 70 LYS cc_start: 0.7955 (mtpt) cc_final: 0.7746 (tttm) REVERT: E 102 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7749 (ptp-170) REVERT: E 119 MET cc_start: 0.7746 (ttt) cc_final: 0.7178 (tmm) REVERT: E 137 GLN cc_start: 0.7335 (tm-30) cc_final: 0.6891 (tm-30) REVERT: E 148 GLU cc_start: 0.8411 (mm-30) cc_final: 0.7888 (tt0) REVERT: F 134 TYR cc_start: 0.7541 (m-80) cc_final: 0.7077 (m-10) REVERT: G 217 GLU cc_start: 0.8031 (tp30) cc_final: 0.7580 (tp30) REVERT: G 219 GLU cc_start: 0.7021 (tp30) cc_final: 0.6628 (tp30) REVERT: H 137 GLN cc_start: 0.7405 (tm-30) cc_final: 0.6877 (tm-30) REVERT: H 186 LEU cc_start: 0.7340 (OUTLIER) cc_final: 0.6909 (tt) REVERT: H 231 ILE cc_start: 0.6388 (OUTLIER) cc_final: 0.6006 (tp) REVERT: I 74 ILE cc_start: 0.9010 (mm) cc_final: 0.8803 (mp) REVERT: I 80 ASP cc_start: 0.7539 (p0) cc_final: 0.7207 (p0) REVERT: I 92 TRP cc_start: 0.7817 (t60) cc_final: 0.6921 (t60) REVERT: I 119 MET cc_start: 0.7937 (ttp) cc_final: 0.7445 (tmm) REVERT: I 137 GLN cc_start: 0.7077 (tm-30) cc_final: 0.6628 (tm-30) REVERT: I 144 LEU cc_start: 0.6750 (OUTLIER) cc_final: 0.6483 (mp) REVERT: J 113 ASP cc_start: 0.7458 (p0) cc_final: 0.7208 (p0) REVERT: J 199 ILE cc_start: 0.7049 (OUTLIER) cc_final: 0.6785 (tp) REVERT: K 173 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7671 (tt) REVERT: K 199 ILE cc_start: 0.6913 (OUTLIER) cc_final: 0.6664 (tp) REVERT: L 70 LYS cc_start: 0.7527 (mtpt) cc_final: 0.7195 (mtpt) REVERT: L 118 GLN cc_start: 0.7560 (OUTLIER) cc_final: 0.7179 (mt0) REVERT: L 119 MET cc_start: 0.7610 (OUTLIER) cc_final: 0.6934 (tmm) REVERT: M 137 GLN cc_start: 0.7314 (tm-30) cc_final: 0.6812 (tm-30) REVERT: M 144 LEU cc_start: 0.6540 (OUTLIER) cc_final: 0.6300 (mp) REVERT: M 148 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8310 (mm-30) REVERT: M 154 ILE cc_start: 0.7624 (tt) cc_final: 0.7275 (tt) REVERT: N 113 ASP cc_start: 0.7633 (p0) cc_final: 0.7417 (p0) REVERT: N 162 ASN cc_start: 0.7308 (OUTLIER) cc_final: 0.6839 (t0) REVERT: N 199 ILE cc_start: 0.6526 (OUTLIER) cc_final: 0.6315 (tp) REVERT: O 113 ASP cc_start: 0.7434 (p0) cc_final: 0.7133 (p0) REVERT: O 125 GLU cc_start: 0.8194 (tm-30) cc_final: 0.7800 (tm-30) REVERT: O 199 ILE cc_start: 0.6423 (OUTLIER) cc_final: 0.6200 (tp) REVERT: P 46 MET cc_start: 0.2732 (mmt) cc_final: 0.2494 (mmm) REVERT: P 133 GLN cc_start: 0.8971 (mm-40) cc_final: 0.8700 (mm-40) REVERT: P 137 GLN cc_start: 0.7587 (tp-100) cc_final: 0.7108 (tm-30) REVERT: P 163 VAL cc_start: 0.6960 (OUTLIER) cc_final: 0.6735 (p) REVERT: P 269 LEU cc_start: 0.7217 (OUTLIER) cc_final: 0.6961 (tt) REVERT: Q 46 MET cc_start: 0.4366 (mmm) cc_final: 0.4008 (mmp) REVERT: Q 70 LYS cc_start: 0.7790 (mtpt) cc_final: 0.7422 (tttp) REVERT: Q 163 VAL cc_start: 0.7064 (OUTLIER) cc_final: 0.6788 (p) REVERT: Q 269 LEU cc_start: 0.6963 (OUTLIER) cc_final: 0.6744 (tt) REVERT: R 24 GLN cc_start: 0.6485 (mm110) cc_final: 0.6046 (mt0) REVERT: R 67 PHE cc_start: 0.6047 (OUTLIER) cc_final: 0.5694 (m-10) REVERT: R 199 ILE cc_start: 0.6749 (OUTLIER) cc_final: 0.6532 (tp) REVERT: S 70 ARG cc_start: 0.7975 (mtt180) cc_final: 0.7686 (ptp-170) REVERT: S 125 GLU cc_start: 0.7680 (tm-30) cc_final: 0.7018 (tm-30) REVERT: S 217 GLU cc_start: 0.8170 (tp30) cc_final: 0.7809 (tp30) REVERT: T 79 LYS cc_start: 0.8689 (mmtt) cc_final: 0.8326 (mtmt) REVERT: T 137 GLN cc_start: 0.7243 (tm-30) cc_final: 0.6969 (tm-30) REVERT: T 186 LEU cc_start: 0.7234 (OUTLIER) cc_final: 0.6777 (tt) REVERT: T 273 GLU cc_start: 0.7454 (tm-30) cc_final: 0.7251 (tm-30) REVERT: T 276 ARG cc_start: 0.7216 (mtp180) cc_final: 0.6901 (mtp180) REVERT: T 288 ASN cc_start: 0.8034 (m-40) cc_final: 0.7575 (m-40) REVERT: U 89 MET cc_start: 0.6151 (ttp) cc_final: 0.5809 (tmm) REVERT: U 119 MET cc_start: 0.7805 (ttp) cc_final: 0.6971 (tmm) REVERT: V 113 ASP cc_start: 0.7829 (p0) cc_final: 0.7493 (p0) REVERT: V 217 GLU cc_start: 0.8197 (tp30) cc_final: 0.7912 (tp30) REVERT: W 119 MET cc_start: 0.8017 (ttp) cc_final: 0.7565 (tmm) outliers start: 187 outliers final: 136 residues processed: 789 average time/residue: 0.1840 time to fit residues: 249.5561 Evaluate side-chains 753 residues out of total 4730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 595 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 109 ASN Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain E residue 102 ARG Chi-restraints excluded: chain E residue 118 GLN Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 250 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 76 ILE Chi-restraints excluded: chain G residue 87 MET Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 242 GLU Chi-restraints excluded: chain H residue 118 GLN Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 208 SER Chi-restraints excluded: chain H residue 231 ILE Chi-restraints excluded: chain H residue 281 LEU Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain I residue 118 GLN Chi-restraints excluded: chain I residue 135 LEU Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain I residue 153 SER Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain I residue 208 SER Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 269 LEU Chi-restraints excluded: chain I residue 281 LEU Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain J residue 87 MET Chi-restraints excluded: chain J residue 88 VAL Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 106 ILE Chi-restraints excluded: chain J residue 199 ILE Chi-restraints excluded: chain J residue 200 VAL Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 126 VAL Chi-restraints excluded: chain K residue 163 ILE Chi-restraints excluded: chain K residue 165 LEU Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain K residue 199 ILE Chi-restraints excluded: chain K residue 200 VAL Chi-restraints excluded: chain K residue 242 GLU Chi-restraints excluded: chain K residue 250 THR Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 118 GLN Chi-restraints excluded: chain L residue 119 MET Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 153 SER Chi-restraints excluded: chain L residue 186 LEU Chi-restraints excluded: chain L residue 208 SER Chi-restraints excluded: chain L residue 281 LEU Chi-restraints excluded: chain M residue 89 MET Chi-restraints excluded: chain M residue 117 LEU Chi-restraints excluded: chain M residue 144 LEU Chi-restraints excluded: chain M residue 153 SER Chi-restraints excluded: chain M residue 208 SER Chi-restraints excluded: chain M residue 269 LEU Chi-restraints excluded: chain M residue 281 LEU Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 88 VAL Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 154 LEU Chi-restraints excluded: chain N residue 162 ASN Chi-restraints excluded: chain N residue 163 ILE Chi-restraints excluded: chain N residue 169 SER Chi-restraints excluded: chain N residue 199 ILE Chi-restraints excluded: chain O residue 23 LEU Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 88 VAL Chi-restraints excluded: chain O residue 91 THR Chi-restraints excluded: chain O residue 153 ASP Chi-restraints excluded: chain O residue 163 ILE Chi-restraints excluded: chain O residue 199 ILE Chi-restraints excluded: chain O residue 200 VAL Chi-restraints excluded: chain O residue 242 GLU Chi-restraints excluded: chain P residue 118 GLN Chi-restraints excluded: chain P residue 135 LEU Chi-restraints excluded: chain P residue 153 SER Chi-restraints excluded: chain P residue 163 VAL Chi-restraints excluded: chain P residue 208 SER Chi-restraints excluded: chain P residue 231 ILE Chi-restraints excluded: chain P residue 269 LEU Chi-restraints excluded: chain P residue 281 LEU Chi-restraints excluded: chain Q residue 108 VAL Chi-restraints excluded: chain Q residue 135 LEU Chi-restraints excluded: chain Q residue 153 SER Chi-restraints excluded: chain Q residue 163 VAL Chi-restraints excluded: chain Q residue 208 SER Chi-restraints excluded: chain Q residue 269 LEU Chi-restraints excluded: chain Q residue 281 LEU Chi-restraints excluded: chain R residue 23 LEU Chi-restraints excluded: chain R residue 26 SER Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 67 PHE Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 91 THR Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 169 SER Chi-restraints excluded: chain R residue 199 ILE Chi-restraints excluded: chain S residue 22 LEU Chi-restraints excluded: chain S residue 88 VAL Chi-restraints excluded: chain S residue 127 LEU Chi-restraints excluded: chain S residue 200 VAL Chi-restraints excluded: chain S residue 251 LEU Chi-restraints excluded: chain T residue 135 LEU Chi-restraints excluded: chain T residue 153 SER Chi-restraints excluded: chain T residue 186 LEU Chi-restraints excluded: chain T residue 208 SER Chi-restraints excluded: chain T residue 269 LEU Chi-restraints excluded: chain U residue 118 GLN Chi-restraints excluded: chain U residue 135 LEU Chi-restraints excluded: chain U residue 186 LEU Chi-restraints excluded: chain U residue 208 SER Chi-restraints excluded: chain U residue 269 LEU Chi-restraints excluded: chain U residue 281 LEU Chi-restraints excluded: chain V residue 76 ILE Chi-restraints excluded: chain V residue 88 VAL Chi-restraints excluded: chain V residue 91 THR Chi-restraints excluded: chain V residue 153 ASP Chi-restraints excluded: chain V residue 163 ILE Chi-restraints excluded: chain V residue 200 VAL Chi-restraints excluded: chain W residue 118 GLN Chi-restraints excluded: chain W residue 281 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 561 random chunks: chunk 197 optimal weight: 8.9990 chunk 518 optimal weight: 0.9990 chunk 439 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 123 optimal weight: 5.9990 chunk 384 optimal weight: 10.0000 chunk 91 optimal weight: 9.9990 chunk 166 optimal weight: 6.9990 chunk 287 optimal weight: 0.0670 chunk 492 optimal weight: 5.9990 chunk 408 optimal weight: 30.0000 overall best weight: 3.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 137 GLN L 174 GLN ** N 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 174 GLN R 108 GLN R 109 ASN U 194 ASN ** V 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 194 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.122858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.100757 restraints weight = 68923.531| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 3.01 r_work: 0.3202 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6922 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 45452 Z= 0.210 Angle : 0.596 9.152 61435 Z= 0.305 Chirality : 0.043 0.153 7161 Planarity : 0.003 0.033 8030 Dihedral : 4.316 43.133 6260 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 4.04 % Allowed : 34.76 % Favored : 61.21 % 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: 0.32 (0.11), residues: 5676 helix: 1.35 (0.10), residues: 2926 sheet: -0.65 (0.17), residues: 968 loop : -1.11 (0.15), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG N 159 TYR 0.017 0.002 TYR Q 266 PHE 0.016 0.001 PHE K 198 TRP 0.006 0.001 TRP W 92 HIS 0.003 0.001 HIS J 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.21 (45452) covalent geometry : angle 0.59582 / 0.30 (61435) hydrogen bonds : bond 0.05181 / 3.53 ( 2660) hydrogen bonds : angle 4.78386 / 3.45 ( 7800) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11352 Ramachandran restraints generated. 5676 Oldfield, 0 Emsley, 5676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11352 Ramachandran restraints generated. 5676 Oldfield, 0 Emsley, 5676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 783 residues out of total 4730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 592 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 199 ILE cc_start: 0.7032 (OUTLIER) cc_final: 0.6775 (tp) REVERT: C 87 MET cc_start: 0.7828 (ptt) cc_final: 0.7260 (ttm) REVERT: C 125 GLU cc_start: 0.8261 (tm-30) cc_final: 0.7785 (tm-30) REVERT: C 162 ASN cc_start: 0.8208 (m-40) cc_final: 0.7741 (t0) REVERT: C 217 GLU cc_start: 0.8184 (tp30) cc_final: 0.7886 (tp30) REVERT: D 269 LEU cc_start: 0.6849 (OUTLIER) cc_final: 0.6471 (tt) REVERT: E 70 LYS cc_start: 0.8052 (mtpt) cc_final: 0.7729 (tttm) REVERT: E 102 ARG cc_start: 0.8138 (OUTLIER) cc_final: 0.7884 (ptp-170) REVERT: E 119 MET cc_start: 0.7925 (ttt) cc_final: 0.7288 (tmm) REVERT: E 137 GLN cc_start: 0.7324 (tm-30) cc_final: 0.6870 (tm-30) REVERT: E 148 GLU cc_start: 0.8459 (mm-30) cc_final: 0.7917 (tt0) REVERT: F 134 TYR cc_start: 0.7653 (m-80) cc_final: 0.7159 (m-10) REVERT: G 199 ILE cc_start: 0.6931 (OUTLIER) cc_final: 0.6685 (tp) REVERT: G 217 GLU cc_start: 0.8086 (tp30) cc_final: 0.7410 (tp30) REVERT: H 118 GLN cc_start: 0.7876 (OUTLIER) cc_final: 0.7234 (tp40) REVERT: H 137 GLN cc_start: 0.7513 (tm-30) cc_final: 0.7129 (tm-30) REVERT: H 186 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.7013 (tt) REVERT: I 80 ASP cc_start: 0.7588 (p0) cc_final: 0.7192 (p0) REVERT: I 92 TRP cc_start: 0.7991 (t60) cc_final: 0.7071 (t60) REVERT: I 119 MET cc_start: 0.7947 (ttp) cc_final: 0.7423 (tmm) REVERT: I 137 GLN cc_start: 0.7114 (tm-30) cc_final: 0.6646 (tm-30) REVERT: I 144 LEU cc_start: 0.6755 (OUTLIER) cc_final: 0.6424 (mp) REVERT: I 186 LEU cc_start: 0.7548 (OUTLIER) cc_final: 0.7119 (tt) REVERT: J 68 ASP cc_start: 0.7999 (t0) cc_final: 0.7530 (t0) REVERT: J 113 ASP cc_start: 0.7650 (p0) cc_final: 0.7395 (p0) REVERT: J 199 ILE cc_start: 0.7071 (OUTLIER) cc_final: 0.6782 (tp) REVERT: K 173 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7680 (tt) REVERT: K 199 ILE cc_start: 0.6925 (OUTLIER) cc_final: 0.6670 (tp) REVERT: L 70 LYS cc_start: 0.7644 (mtpt) cc_final: 0.7219 (mtpt) REVERT: L 118 GLN cc_start: 0.7704 (OUTLIER) cc_final: 0.7360 (mt0) REVERT: L 119 MET cc_start: 0.7711 (OUTLIER) cc_final: 0.7116 (tmm) REVERT: M 137 GLN cc_start: 0.7399 (tm-30) cc_final: 0.6770 (tm-30) REVERT: M 148 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8348 (mm-30) REVERT: M 154 ILE cc_start: 0.7757 (tt) cc_final: 0.7427 (tt) REVERT: N 113 ASP cc_start: 0.7990 (p0) cc_final: 0.7738 (p0) REVERT: N 162 ASN cc_start: 0.7598 (OUTLIER) cc_final: 0.7049 (t0) REVERT: N 199 ILE cc_start: 0.6726 (OUTLIER) cc_final: 0.6481 (tp) REVERT: O 125 GLU cc_start: 0.8086 (tm-30) cc_final: 0.7680 (tm-30) REVERT: O 199 ILE cc_start: 0.6433 (OUTLIER) cc_final: 0.6181 (tp) REVERT: P 46 MET cc_start: 0.2740 (mmt) cc_final: 0.2506 (mmm) REVERT: P 137 GLN cc_start: 0.7759 (tp-100) cc_final: 0.7254 (tm-30) REVERT: P 144 LEU cc_start: 0.6823 (OUTLIER) cc_final: 0.6516 (mp) REVERT: P 163 VAL cc_start: 0.7138 (OUTLIER) cc_final: 0.6921 (p) REVERT: P 269 LEU cc_start: 0.7300 (OUTLIER) cc_final: 0.7023 (tt) REVERT: Q 46 MET cc_start: 0.4372 (mmm) cc_final: 0.4013 (mmp) REVERT: Q 89 MET cc_start: 0.5842 (ttp) cc_final: 0.5257 (tmm) REVERT: Q 163 VAL cc_start: 0.7217 (OUTLIER) cc_final: 0.6967 (p) REVERT: Q 218 LYS cc_start: 0.6179 (OUTLIER) cc_final: 0.5878 (ttmt) REVERT: Q 269 LEU cc_start: 0.7159 (OUTLIER) cc_final: 0.6914 (tt) REVERT: R 24 GLN cc_start: 0.6517 (mm110) cc_final: 0.6073 (mt0) REVERT: R 67 PHE cc_start: 0.6204 (OUTLIER) cc_final: 0.5698 (m-10) REVERT: R 199 ILE cc_start: 0.6912 (OUTLIER) cc_final: 0.6619 (tp) REVERT: R 206 GLU cc_start: 0.7710 (tm-30) cc_final: 0.7407 (tm-30) REVERT: S 68 ASP cc_start: 0.7670 (t0) cc_final: 0.7167 (t0) REVERT: S 70 ARG cc_start: 0.8101 (mtt180) cc_final: 0.7584 (ptp-170) REVERT: S 125 GLU cc_start: 0.7868 (tm-30) cc_final: 0.7211 (tm-30) REVERT: S 217 GLU cc_start: 0.8267 (tp30) cc_final: 0.7877 (tp30) REVERT: T 79 LYS cc_start: 0.8659 (mmtt) cc_final: 0.8314 (mtmt) REVERT: T 186 LEU cc_start: 0.7357 (OUTLIER) cc_final: 0.6931 (tt) REVERT: T 273 GLU cc_start: 0.7494 (tm-30) cc_final: 0.7276 (tm-30) REVERT: T 276 ARG cc_start: 0.7337 (mtp180) cc_final: 0.6998 (mtp180) REVERT: T 288 ASN cc_start: 0.8287 (m-40) cc_final: 0.7758 (m-40) REVERT: U 119 MET cc_start: 0.7911 (ttp) cc_final: 0.7082 (tmm) REVERT: V 113 ASP cc_start: 0.7943 (p0) cc_final: 0.7590 (p0) REVERT: V 206 GLU cc_start: 0.7815 (tt0) cc_final: 0.7533 (tt0) REVERT: W 119 MET cc_start: 0.8095 (ttp) cc_final: 0.7607 (tmm) outliers start: 191 outliers final: 141 residues processed: 760 average time/residue: 0.1615 time to fit residues: 210.9843 Evaluate side-chains 744 residues out of total 4730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 578 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain E residue 102 ARG Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 250 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 76 ILE Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 242 GLU Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 118 GLN Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 208 SER Chi-restraints excluded: chain H residue 231 ILE Chi-restraints excluded: chain H residue 281 LEU Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain I residue 118 GLN Chi-restraints excluded: chain I residue 135 LEU Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain I residue 153 SER Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain I residue 205 LEU Chi-restraints excluded: chain I residue 208 SER Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 269 LEU Chi-restraints excluded: chain I residue 281 LEU Chi-restraints excluded: chain J residue 23 LEU Chi-restraints excluded: chain J residue 87 MET Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 106 ILE Chi-restraints excluded: chain J residue 199 ILE Chi-restraints excluded: chain J residue 200 VAL Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 126 VAL Chi-restraints excluded: chain K residue 163 ILE Chi-restraints excluded: chain K residue 165 LEU Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain K residue 199 ILE Chi-restraints excluded: chain K residue 200 VAL Chi-restraints excluded: chain K residue 242 GLU Chi-restraints excluded: chain K residue 250 THR Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 118 GLN Chi-restraints excluded: chain L residue 119 MET Chi-restraints excluded: chain L residue 133 GLN Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 153 SER Chi-restraints excluded: chain L residue 186 LEU Chi-restraints excluded: chain L residue 208 SER Chi-restraints excluded: chain L residue 281 LEU Chi-restraints excluded: chain M residue 89 MET Chi-restraints excluded: chain M residue 135 LEU Chi-restraints excluded: chain M residue 144 LEU Chi-restraints excluded: chain M residue 153 SER Chi-restraints excluded: chain M residue 208 SER Chi-restraints excluded: chain M residue 256 ILE Chi-restraints excluded: chain M residue 269 LEU Chi-restraints excluded: chain M residue 281 LEU Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 88 VAL Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 154 LEU Chi-restraints excluded: chain N residue 162 ASN Chi-restraints excluded: chain N residue 163 ILE Chi-restraints excluded: chain N residue 169 SER Chi-restraints excluded: chain N residue 199 ILE Chi-restraints excluded: chain O residue 23 LEU Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 88 VAL Chi-restraints excluded: chain O residue 91 THR Chi-restraints excluded: chain O residue 153 ASP Chi-restraints excluded: chain O residue 163 ILE Chi-restraints excluded: chain O residue 199 ILE Chi-restraints excluded: chain O residue 200 VAL Chi-restraints excluded: chain O residue 211 VAL Chi-restraints excluded: chain O residue 242 GLU Chi-restraints excluded: chain P residue 118 GLN Chi-restraints excluded: chain P residue 135 LEU Chi-restraints excluded: chain P residue 144 LEU Chi-restraints excluded: chain P residue 153 SER Chi-restraints excluded: chain P residue 163 VAL Chi-restraints excluded: chain P residue 186 LEU Chi-restraints excluded: chain P residue 208 SER Chi-restraints excluded: chain P residue 231 ILE Chi-restraints excluded: chain P residue 269 LEU Chi-restraints excluded: chain P residue 281 LEU Chi-restraints excluded: chain Q residue 94 GLU Chi-restraints excluded: chain Q residue 108 VAL Chi-restraints excluded: chain Q residue 135 LEU Chi-restraints excluded: chain Q residue 153 SER Chi-restraints excluded: chain Q residue 163 VAL Chi-restraints excluded: chain Q residue 208 SER Chi-restraints excluded: chain Q residue 218 LYS Chi-restraints excluded: chain Q residue 269 LEU Chi-restraints excluded: chain Q residue 281 LEU Chi-restraints excluded: chain R residue 23 LEU Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 67 PHE Chi-restraints excluded: chain R residue 91 THR Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 169 SER Chi-restraints excluded: chain R residue 199 ILE Chi-restraints excluded: chain S residue 22 LEU Chi-restraints excluded: chain S residue 88 VAL Chi-restraints excluded: chain S residue 200 VAL Chi-restraints excluded: chain S residue 251 LEU Chi-restraints excluded: chain T residue 135 LEU Chi-restraints excluded: chain T residue 153 SER Chi-restraints excluded: chain T residue 186 LEU Chi-restraints excluded: chain T residue 208 SER Chi-restraints excluded: chain T residue 269 LEU Chi-restraints excluded: chain U residue 118 GLN Chi-restraints excluded: chain U residue 135 LEU Chi-restraints excluded: chain U residue 153 SER Chi-restraints excluded: chain U residue 186 LEU Chi-restraints excluded: chain U residue 208 SER Chi-restraints excluded: chain U residue 243 VAL Chi-restraints excluded: chain U residue 269 LEU Chi-restraints excluded: chain U residue 281 LEU Chi-restraints excluded: chain V residue 23 LEU Chi-restraints excluded: chain V residue 76 ILE Chi-restraints excluded: chain V residue 88 VAL Chi-restraints excluded: chain V residue 91 THR Chi-restraints excluded: chain V residue 153 ASP Chi-restraints excluded: chain V residue 163 ILE Chi-restraints excluded: chain V residue 200 VAL Chi-restraints excluded: chain W residue 281 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 561 random chunks: chunk 457 optimal weight: 0.7980 chunk 128 optimal weight: 20.0000 chunk 239 optimal weight: 0.9990 chunk 264 optimal weight: 8.9990 chunk 359 optimal weight: 0.6980 chunk 511 optimal weight: 8.9990 chunk 194 optimal weight: 0.9980 chunk 248 optimal weight: 3.9990 chunk 263 optimal weight: 2.9990 chunk 274 optimal weight: 5.9990 chunk 351 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 108 GLN R 109 ASN U 194 ASN ** V 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 194 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.127364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.105099 restraints weight = 67466.894| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 3.03 r_work: 0.3262 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6808 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 45452 Z= 0.124 Angle : 0.527 9.787 61435 Z= 0.268 Chirality : 0.041 0.151 7161 Planarity : 0.003 0.039 8030 Dihedral : 4.136 37.094 6260 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.40 % Allowed : 35.20 % Favored : 61.40 % 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: 0.50 (0.12), residues: 5676 helix: 1.59 (0.10), residues: 2860 sheet: -0.66 (0.17), residues: 968 loop : -1.04 (0.15), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 159 TYR 0.031 0.001 TYR H 139 PHE 0.007 0.001 PHE V 198 TRP 0.008 0.001 TRP D 92 HIS 0.003 0.000 HIS J 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (45452) covalent geometry : angle 0.52664 / 0.27 (61435) hydrogen bonds : bond 0.04627 / 3.15 ( 2660) hydrogen bonds : angle 4.58848 / 3.31 ( 7800) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11352 Ramachandran restraints generated. 5676 Oldfield, 0 Emsley, 5676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11352 Ramachandran restraints generated. 5676 Oldfield, 0 Emsley, 5676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 770 residues out of total 4730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 609 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 199 ILE cc_start: 0.6953 (OUTLIER) cc_final: 0.6709 (tp) REVERT: C 87 MET cc_start: 0.7772 (ptt) cc_final: 0.7237 (ttm) REVERT: C 113 ASP cc_start: 0.7197 (p0) cc_final: 0.6989 (p0) REVERT: C 134 TYR cc_start: 0.7583 (m-80) cc_final: 0.7304 (m-10) REVERT: C 162 ASN cc_start: 0.8090 (m-40) cc_final: 0.7665 (t0) REVERT: C 217 GLU cc_start: 0.8118 (tp30) cc_final: 0.7848 (tp30) REVERT: D 119 MET cc_start: 0.7678 (ttp) cc_final: 0.7400 (tmm) REVERT: D 269 LEU cc_start: 0.6657 (OUTLIER) cc_final: 0.6349 (tt) REVERT: E 70 LYS cc_start: 0.7917 (mtpt) cc_final: 0.7521 (mtpp) REVERT: E 102 ARG cc_start: 0.8096 (OUTLIER) cc_final: 0.7815 (ptp-170) REVERT: E 119 MET cc_start: 0.7828 (OUTLIER) cc_final: 0.7219 (tmm) REVERT: E 137 GLN cc_start: 0.7346 (tm-30) cc_final: 0.6900 (tm-30) REVERT: E 148 GLU cc_start: 0.8392 (mm-30) cc_final: 0.7903 (tt0) REVERT: F 134 TYR cc_start: 0.7529 (m-80) cc_final: 0.7062 (m-10) REVERT: G 199 ILE cc_start: 0.6793 (OUTLIER) cc_final: 0.6551 (tp) REVERT: G 217 GLU cc_start: 0.8032 (tp30) cc_final: 0.7579 (tp30) REVERT: G 219 GLU cc_start: 0.6995 (tp30) cc_final: 0.6604 (tp30) REVERT: H 70 LYS cc_start: 0.7683 (mtpt) cc_final: 0.7456 (mtpp) REVERT: H 137 GLN cc_start: 0.7345 (tm-30) cc_final: 0.6819 (tm-30) REVERT: H 186 LEU cc_start: 0.7316 (OUTLIER) cc_final: 0.6871 (tt) REVERT: H 231 ILE cc_start: 0.6379 (OUTLIER) cc_final: 0.6002 (tp) REVERT: I 74 ILE cc_start: 0.8997 (mm) cc_final: 0.8788 (mt) REVERT: I 80 ASP cc_start: 0.7580 (p0) cc_final: 0.7204 (p0) REVERT: I 92 TRP cc_start: 0.7845 (t60) cc_final: 0.6838 (t60) REVERT: I 119 MET cc_start: 0.7928 (ttp) cc_final: 0.7423 (tmm) REVERT: I 137 GLN cc_start: 0.7058 (tm-30) cc_final: 0.6589 (tm-30) REVERT: J 113 ASP cc_start: 0.7458 (p0) cc_final: 0.7214 (p0) REVERT: J 199 ILE cc_start: 0.7031 (OUTLIER) cc_final: 0.6769 (tp) REVERT: K 173 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7656 (tt) REVERT: K 199 ILE cc_start: 0.6900 (OUTLIER) cc_final: 0.6651 (tp) REVERT: L 70 LYS cc_start: 0.7509 (mtpt) cc_final: 0.7106 (mtpt) REVERT: L 118 GLN cc_start: 0.7448 (OUTLIER) cc_final: 0.7098 (mt0) REVERT: L 119 MET cc_start: 0.7601 (OUTLIER) cc_final: 0.6958 (tmm) REVERT: M 137 GLN cc_start: 0.7299 (tm-30) cc_final: 0.6796 (tm-30) REVERT: M 148 GLU cc_start: 0.8665 (mm-30) cc_final: 0.8321 (mm-30) REVERT: M 154 ILE cc_start: 0.7693 (tt) cc_final: 0.7331 (tt) REVERT: N 162 ASN cc_start: 0.7302 (OUTLIER) cc_final: 0.6837 (t0) REVERT: N 199 ILE cc_start: 0.6582 (OUTLIER) cc_final: 0.6359 (tp) REVERT: O 113 ASP cc_start: 0.7340 (p0) cc_final: 0.7083 (p0) REVERT: O 125 GLU cc_start: 0.8179 (tm-30) cc_final: 0.7792 (tm-30) REVERT: O 199 ILE cc_start: 0.6419 (OUTLIER) cc_final: 0.6192 (tp) REVERT: P 46 MET cc_start: 0.2751 (mmt) cc_final: 0.2523 (mmm) REVERT: P 137 GLN cc_start: 0.7561 (tp-100) cc_final: 0.7094 (tm-30) REVERT: P 163 VAL cc_start: 0.6902 (OUTLIER) cc_final: 0.6666 (p) REVERT: P 269 LEU cc_start: 0.7202 (OUTLIER) cc_final: 0.6956 (tt) REVERT: Q 46 MET cc_start: 0.4377 (mmm) cc_final: 0.4009 (mmp) REVERT: Q 163 VAL cc_start: 0.7037 (OUTLIER) cc_final: 0.6822 (p) REVERT: Q 218 LYS cc_start: 0.5754 (OUTLIER) cc_final: 0.5494 (ttmt) REVERT: Q 269 LEU cc_start: 0.6952 (OUTLIER) cc_final: 0.6738 (tt) REVERT: R 24 GLN cc_start: 0.6500 (mm110) cc_final: 0.6071 (mt0) REVERT: R 67 PHE cc_start: 0.5996 (OUTLIER) cc_final: 0.5561 (m-10) REVERT: R 199 ILE cc_start: 0.6742 (OUTLIER) cc_final: 0.6517 (tp) REVERT: S 70 ARG cc_start: 0.7975 (mtt180) cc_final: 0.7670 (ptp-170) REVERT: S 125 GLU cc_start: 0.7677 (tm-30) cc_final: 0.7047 (tm-30) REVERT: S 217 GLU cc_start: 0.8127 (tp30) cc_final: 0.7770 (tp30) REVERT: T 79 LYS cc_start: 0.8691 (mmtt) cc_final: 0.8335 (mtmt) REVERT: T 186 LEU cc_start: 0.7223 (OUTLIER) cc_final: 0.6787 (tt) REVERT: T 273 GLU cc_start: 0.7410 (tm-30) cc_final: 0.7182 (tm-30) REVERT: T 276 ARG cc_start: 0.7210 (mtp180) cc_final: 0.6899 (mtp180) REVERT: T 288 ASN cc_start: 0.8055 (m-40) cc_final: 0.7694 (m-40) REVERT: U 119 MET cc_start: 0.7776 (ttp) cc_final: 0.6944 (tmm) REVERT: V 113 ASP cc_start: 0.7863 (p0) cc_final: 0.7514 (p0) REVERT: V 206 GLU cc_start: 0.7834 (tt0) cc_final: 0.7554 (tt0) REVERT: V 217 GLU cc_start: 0.8136 (tp30) cc_final: 0.7843 (tp30) REVERT: W 119 MET cc_start: 0.8035 (ttp) cc_final: 0.7594 (tmm) outliers start: 161 outliers final: 128 residues processed: 753 average time/residue: 0.1525 time to fit residues: 196.6613 Evaluate side-chains 748 residues out of total 4730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 597 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain E residue 102 ARG Chi-restraints excluded: chain E residue 118 GLN Chi-restraints excluded: chain E residue 119 MET Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 250 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 76 ILE Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 242 GLU Chi-restraints excluded: chain H residue 118 GLN Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 208 SER Chi-restraints excluded: chain H residue 231 ILE Chi-restraints excluded: chain H residue 281 LEU Chi-restraints excluded: chain I residue 118 GLN Chi-restraints excluded: chain I residue 135 LEU Chi-restraints excluded: chain I residue 153 SER Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain I residue 208 SER Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 269 LEU Chi-restraints excluded: chain I residue 281 LEU Chi-restraints excluded: chain J residue 23 LEU Chi-restraints excluded: chain J residue 87 MET Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 106 ILE Chi-restraints excluded: chain J residue 199 ILE Chi-restraints excluded: chain J residue 200 VAL Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 126 VAL Chi-restraints excluded: chain K residue 163 ILE Chi-restraints excluded: chain K residue 165 LEU Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain K residue 199 ILE Chi-restraints excluded: chain K residue 200 VAL Chi-restraints excluded: chain K residue 242 GLU Chi-restraints excluded: chain K residue 250 THR Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 118 GLN Chi-restraints excluded: chain L residue 119 MET Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 153 SER Chi-restraints excluded: chain L residue 208 SER Chi-restraints excluded: chain L residue 281 LEU Chi-restraints excluded: chain M residue 135 LEU Chi-restraints excluded: chain M residue 153 SER Chi-restraints excluded: chain M residue 208 SER Chi-restraints excluded: chain M residue 269 LEU Chi-restraints excluded: chain M residue 281 LEU Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 88 VAL Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 154 LEU Chi-restraints excluded: chain N residue 162 ASN Chi-restraints excluded: chain N residue 163 ILE Chi-restraints excluded: chain N residue 199 ILE Chi-restraints excluded: chain O residue 23 LEU Chi-restraints excluded: chain O residue 88 VAL Chi-restraints excluded: chain O residue 91 THR Chi-restraints excluded: chain O residue 153 ASP Chi-restraints excluded: chain O residue 163 ILE Chi-restraints excluded: chain O residue 199 ILE Chi-restraints excluded: chain O residue 200 VAL Chi-restraints excluded: chain O residue 242 GLU Chi-restraints excluded: chain P residue 118 GLN Chi-restraints excluded: chain P residue 135 LEU Chi-restraints excluded: chain P residue 153 SER Chi-restraints excluded: chain P residue 163 VAL Chi-restraints excluded: chain P residue 208 SER Chi-restraints excluded: chain P residue 231 ILE Chi-restraints excluded: chain P residue 269 LEU Chi-restraints excluded: chain P residue 281 LEU Chi-restraints excluded: chain Q residue 108 VAL Chi-restraints excluded: chain Q residue 135 LEU Chi-restraints excluded: chain Q residue 153 SER Chi-restraints excluded: chain Q residue 163 VAL Chi-restraints excluded: chain Q residue 208 SER Chi-restraints excluded: chain Q residue 218 LYS Chi-restraints excluded: chain Q residue 269 LEU Chi-restraints excluded: chain Q residue 281 LEU Chi-restraints excluded: chain R residue 23 LEU Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 67 PHE Chi-restraints excluded: chain R residue 91 THR Chi-restraints excluded: chain R residue 109 ASN Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 199 ILE Chi-restraints excluded: chain S residue 22 LEU Chi-restraints excluded: chain S residue 88 VAL Chi-restraints excluded: chain S residue 200 VAL Chi-restraints excluded: chain S residue 251 LEU Chi-restraints excluded: chain T residue 135 LEU Chi-restraints excluded: chain T residue 153 SER Chi-restraints excluded: chain T residue 186 LEU Chi-restraints excluded: chain T residue 208 SER Chi-restraints excluded: chain T residue 269 LEU Chi-restraints excluded: chain U residue 118 GLN Chi-restraints excluded: chain U residue 135 LEU Chi-restraints excluded: chain U residue 153 SER Chi-restraints excluded: chain U residue 186 LEU Chi-restraints excluded: chain U residue 208 SER Chi-restraints excluded: chain U residue 269 LEU Chi-restraints excluded: chain U residue 281 LEU Chi-restraints excluded: chain V residue 76 ILE Chi-restraints excluded: chain V residue 88 VAL Chi-restraints excluded: chain V residue 91 THR Chi-restraints excluded: chain V residue 153 ASP Chi-restraints excluded: chain V residue 163 ILE Chi-restraints excluded: chain V residue 200 VAL Chi-restraints excluded: chain W residue 118 GLN Chi-restraints excluded: chain W residue 281 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 561 random chunks: chunk 477 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 329 optimal weight: 5.9990 chunk 507 optimal weight: 3.9990 chunk 179 optimal weight: 5.9990 chunk 229 optimal weight: 40.0000 chunk 15 optimal weight: 6.9990 chunk 532 optimal weight: 7.9990 chunk 461 optimal weight: 5.9990 chunk 467 optimal weight: 2.9990 chunk 256 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 137 GLN ** N 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 109 ASN R 162 ASN U 194 ASN ** V 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 194 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.115342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.091057 restraints weight = 65421.691| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 3.62 r_work: 0.2922 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6425 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 45452 Z= 0.206 Angle : 0.591 9.116 61435 Z= 0.302 Chirality : 0.043 0.159 7161 Planarity : 0.003 0.030 8030 Dihedral : 4.305 37.940 6260 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.83 % Allowed : 34.95 % Favored : 61.23 % 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: 0.34 (0.11), residues: 5676 helix: 1.38 (0.10), residues: 2926 sheet: -0.68 (0.17), residues: 968 loop : -1.10 (0.15), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 159 TYR 0.028 0.002 TYR H 139 PHE 0.015 0.001 PHE K 198 TRP 0.006 0.001 TRP L 92 HIS 0.003 0.001 HIS J 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.21 (45452) covalent geometry : angle 0.59129 / 0.30 (61435) hydrogen bonds : bond 0.05103 / 3.47 ( 2660) hydrogen bonds : angle 4.74772 / 3.42 ( 7800) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8704.03 seconds wall clock time: 149 minutes 53.06 seconds (8993.06 seconds total)